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The Human-transcriptome DataBase for Alternative Splicing (H-DBAS) is a database of alternatively spliced human transcripts based on H-Invitational. Alternative
Human-transcriptome DataBase for Alternative Splicing
Human-transcriptome_DataBase_for_Alternative_Splicing
Process by which a gene can code for multiple proteins
Alternative splicing, alternative RNA splicing, or differential splicing is an alternative splicing process during gene expression that allows a single
Alternative_splicing
Set of all RNA molecules in one cell or a population of cells
render the content of the transcriptome difficult to establish. These include alternative splicing, RNA editing and alternative transcription among others
Transcriptome
Human-transcriptome database for alternative splicing (H-DBAS) UniGene Full-parasites Exome sequencing Wettersrand, KA. "The Cost of Sequencing a Human Genome"
De novo transcriptome assembly
De_novo_transcriptome_assembly
Lab technique in cellular biology
occurring in >90% of human genes. There are multiple alternative splicing modes: exon skipping (most common splicing mode in humans and higher eukaryotes)
RNA-Seq
Virus of the herpes family
after transplantation. All EBV nuclear proteins are produced by alternative splicing of a transcript starting at either the Cp or Wp promoters at the
Epstein–Barr_virus
Aspect of genetics
and trypanosomes make extensive use of trans-splicing to generate chimeric RNAs. In these organisms, splicing reactions between a protein coding RNA and
Chimeric_RNA
Study of RNA transcripts
Blencowe BJ (December 2008). "Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing". Nature Genetics
Transcriptomics_technologies
existing alternative splicing events by focusing on intron excisions. LEMONS A Tool for the Identification of Splice Junctions in Transcriptomes of Organisms
List of RNA-Seq bioinformatics tools
List_of_RNA-Seq_bioinformatics_tools
Type of RNA found in cells
examples of alternative splicing is in the Drosophila DSCAM gene, which can give rise to approximately 30 thousand distinct alternatively spliced isoforms
Circular_RNA
Method used in molecular biology
many positions close to alternative exons, several of which were found to require Nova1/2 for their brains-specific splicing patterns. In 2008, CLIP was
Cross-linking immunoprecipitation
Cross-linking_immunoprecipitation
DNA sequencing
Benjamin J. (2008-12-01). "Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing". Nature Genetics
Third-generation_sequencing
Biological analysis approach
the genome, epigenome, transcriptome, proteome, metabolome, exposome, and microbiome (i.e., a meta-genome and/or meta-transcriptome, depending upon how it
Multiomics
RNA processing within a biological cell
that encode different protein sequences. This process is known as alternative splicing, and allows production of a large variety of proteins from a limited
Post-transcriptional modification
Post-transcriptional_modification
Non-protein coding transcripts longer than 200 nucleotides
expression including pre-mRNA processing and splicing, transport, translation, and degradation. The splicing of mRNA can induce its translation and functionally
Long_non-coding_RNA
Subspecies of insect
ago, and this established the latest date for the adoption of clothing by humans. However, recent transcriptome analyses casts doubt on whether lice provide
Body_louse
Biochemical changes to RNA
results in increased alternative splicing. Evidence supporting this claim identified that decreased m6A levels in the transcriptome lead to significantly
Epitranscriptome
Sequence of DNA that determines traits in an organism
single large mRNAs, alternative splicing enables a single genomic region to encode multiple distinct products and trans-splicing concatenates mRNAs from
Gene
Artificial intelligence program by DeepMind
(15 December 2022). "Structure-guided isoform identification for the human transcriptome". eLife. 11 e82556. doi:10.7554/eLife.82556. PMC 9812405. PMID 36519529
AlphaFold
Set of proteins that can be expressed by a genome, cell, tissue, or organism
more than one protein can be produced from most genes due to alternative splicing (e.g. human genome encodes about 20,000 proteins, but some estimates predicted
Proteome
Complete set of nucleic acid sequences for humans
rearrangements and alternative pre-mRNA splicing) can lead to the production of many more unique proteins than the number of protein-coding genes. The human reference
Human_genome
Type of protein
exclusion during splicing. These sites are referred to as exonic splicing enhancers (ESEs), exonic splicing silencers (ESSs), intronic splicing enhancers (ISEs)
RNA-binding_protein
Molecular process
Büttner A, Eisenmenger W, et al. (January 2010). "Alternative splicing and extensive RNA editing of human TPH2 transcripts". PLOS ONE. 5 (1) e8956. Bibcode:2010PLoSO
RNA_editing
Sub-field of genomics
C. (2003). "Discovery of novel splice forms and functional analysis of cancer-specific alternative splicing in human expressed sequences". Nucleic Acids
Oncogenomics
RNA that is read by the ribosome to produce a protein
serve as regulatory sequences in the pre-mRNA as exonic splicing enhancers or exonic splicing silencers. Untranslated regions (UTRs) are sections of the
Messenger_RNA
Protein found in humans
produces four different mRNAs: three alternatively spliced variants and one unspliced form. The three alternatively spliced mRNAs give rise to three known protein
CCDC121
Protein found in humans
O'Keeffe S, et al. (September 2014). "An RNA-sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex"
ASH1L
Elimination of mRNA with premature stop codons in eukaryotes
Brenner SE. 2003. Evidence for the widespread coupling of alternative splicing and nonsense-mediated mRNA decay in humans. Proceedings of the National
Nonsense-mediated_decay
Species of snake
expressed genes. Out of these genes, 12,346 belonged to the venom gland transcriptome, which included 139 genes from 33 toxin gene families. Additionally
Indian_cobra
DNA section marked with start and stop codon of different length
format. orfipy is particularly faster for data containing multiple smaller FASTA sequences, such as de-novo transcriptome assemblies. Coding region Putative
Open_reading_frame
Genome research project
importance of identifying alternative splicing in vertebrate genome annotation". Database. 2012 bas014. doi:10.1093/database/bas014. PMC 3308168. PMID 22434846
GENCODE
Collection of microscopic DNA spots attached to a solid surface
whole transcriptome shotgun approach to characterize and quantify gene expression. Unlike microarrays, which need a reference genome and transcriptome to
DNA_microarray
Part of the study of the genome
mammalian brains. There is also notable enrichment for more alternative splicing events in the human brain. Gene expression profiles also vary within specific
Neurogenomics
Pan-genome Graph Construction Methodology
Jordan M.; Novak, Adam M. (2023-02-01). "Pangenome-aware transcriptome analyses using spliced pangenome graphs". Nature Methods. 20 (2): 239–247. doi:10
Pan-genome_graph_construction
UniGene was a NCBI database of the transcriptome and thus, despite the name, not primarily a database for genes. Each entry is a set of transcripts that
UniGene
metabolism. A change in splicing can be caused by modifying any of the components of the splicing machinery such as splice sites or splice enhancers or silencers
SNP_annotation
Gene formed by the combination of two independent genes
by trans-splicing or read-through events. Since chromosomal translocations play such a significant role in neoplasia, a specialized database of chromosomal
Fusion_gene
Biological cell regulation mechanisms
by separating the two fractions by gentle lysis. Alternative splicing can be analysed with a splicing array or with a tiling array (see DNA microarray)
Regulation_of_gene_expression
The following is a list of Intelligent Systems for Molecular Biology (ISMB) keynote speakers. ISMB is an academic conference on the subjects of bioinformatics
List of Intelligent Systems for Molecular Biology keynote speakers
List_of_Intelligent_Systems_for_Molecular_Biology_keynote_speakers
Protein-coding gene in the species Homo sapiens
Verjovski-Almeida S, et al. (2000). "Shotgun sequencing of the human transcriptome with ORF expressed sequence tags". Proc. Natl. Acad. Sci. U.S.A.
HNRNPL
Process in computational biology
likely that these databases are both incomplete and contain small but significant amounts of erroneous data. New high-throughput transcriptome sequencing technologies
Gene_prediction
Protein-coding gene in the species Homo sapiens
coordinates/positions are for GRCh38.p7. SLC46A3 has multiple transcript variants produced by different promoter regions and alternative splicing. A total of 4 transcript
SLC46A3
Modification in mRNA, DNA
individual m6A sites in many mRNAs is highly similar between human and mouse, and transcriptome-wide analysis reveals that m6A is found in regions of high
N6-Methyladenosine
Protein found in humans
cytoplasm. Transcript variants derived from alternative splicing exist; they encode the same protein. As is typical for genes encoding ribosomal proteins, there
60S_ribosomal_protein_L36
Protein-coding gene in the species Homo sapiens
predicted were NRF1 with scores of 0.204 and 0.199. In a GEO large-scale human transcriptome, FAM98A was ubiquitously expressed, though not uniformly expressed
FAM98A
Inherited retrovirus encoded in an organism's genome
the rebirth of the human immunity related GTPase gene (IRGM). ERV insertions have also been shown to generate alternative splice sites either by direct
Endogenous_retrovirus
Skin cancer originating in melanocytes
nonsense, or splice site mutations. The transcriptomes of over 100 melanomas has also been sequenced and analyzed. Almost 70% of all human protein-coding
Melanoma
Laboratory technique
Analyze the Electrophysiology, Morphology and Transcriptome of Whole Single Neurons Derived From Human Pluripotent Stem Cells". Frontiers in Molecular
Patch-sequencing
Protein-coding gene in the species Homo sapiens
large-scale identification and characterization of putative alternative promoters of human genes". Genome Res. 16 (1): 55–65. doi:10.1101/gr.4039406. PMC 1356129
RNF38
Protein encoding gene in mammals
and SNORA70B. C2orf74 has 6 validated mRNA products created via alternative splicing that give rise to two different isoforms. An extended version of
C2orf74
Study of biochemical processes in an individual cell
transcriptome of single cells, and to quantify their proteome and metabolome. Mass spectrometry techniques have become important analytical tools for
Single-cell_analysis
Species of beetle
beetle is known as Td-dsx which stands for T. dichotomus dsx homologue. During development, alternative splicing of Td-dsx results in the formation of
Japanese_rhinoceros_beetle
Species of yeast
Systematic Open Reading Frame (ORF) and Other Genetic Designations". Alternative Pre-mRNA Splicing: Theory and Protocols. Wiley-Blackwell. pp. 605–7. doi:10.1002/9783527636778
Saccharomyces_cerevisiae
Protein found in most eukaryotes
is on the positive strand. In humans, there are 20 alternative splicings of FAM86B1, and 19 mRNA transcripts. In humans, FAM86B1 is expressed ubiquitously
FAM86B1
Protein-coding gene in humans
Emi M, Nakamura Y (1994). "Human metalloprotease/disintegrin-like (MDC) gene: exon-intron organization and alternative splicing". Cytogenet. Cell Genet.
ADAM11
and long ncRNA. In 2012, the first two methods for m6A sequencing came out that enabled transcriptome-wide profile of m6A in mammalian cells. These two
Epitranscriptomic_sequencing
Cytoplasmic biomolecular condensates of proteins and RNA occurring in cells under stress
enriched. These data imply that the stress granule transcriptome is influenced by the valency of RNA (for proteins or other RNA) and by the rates of RNA run-off
Stress_granule
Protein
There are four validated transcript variants for TMEM39B produced by different promoters and alternative splicing. Transcript variant 1 is translated into
TMEM39B
Molecular biology technique
Although SAGE was originally conceived for use in cancer studies, it has been successfully used to describe the transcriptome of other diseases and in a wide
Serial analysis of gene expression
Serial_analysis_of_gene_expression
expression, miRNA expression, 3D genome organization, and identify alternative splicing events in addition to sequence data. The first report of cancer genome
Cancer_genome_sequencing
Protein-coding gene in the species Homo sapiens
ribosome and incorporation of ROS-damaged amino acid into proteins. Alternative splicing results in multiple transcript variants. ATP + L-phenylalanine +
FARS2
Protein-coding gene in the species Homo sapiens
reading frame in humans (19q13.2). There are two isoform constructs known for MEGF8, which differ by a 67 amino acid indel. The isoform 2 splice version (analyzed
Multiple epidermal growth factor-like domains 8
Multiple_epidermal_growth_factor-like_domains_8
Protein found in humans
hormone type 2 receptors by multiple promoters and alternative splicing: identification of multiple splice variants". Molecular Endocrinology. 17 (3): 395–410
Corticotropin-releasing hormone receptor 2
Corticotropin-releasing_hormone_receptor_2
Subtype of serotonin receptor
that HTR2A undergoes a variety of different splicing events, including utilization of alternative splice acceptor sites, exon skipping, rare exon usage
5-HT2A_receptor
Functionless relative of a gene
insertions occasionally contribute exons to existing genes, usually via alternatively spliced transcripts. A further characteristic of processed pseudogenes is
Pseudogene
Computational analysis of large, complex sets of biological data
protein function prediction. For instance, if a protein is found in the nucleus it may be involved in gene regulation or splicing. By contrast, if a protein
Bioinformatics
Evolution of novel genes from non-genic DNA sequence
overprinting. These studies were conducted using the accessory gland transcriptomes of Drosophila yakuba and Drosophila erecta and they identified 20 putative
De_novo_gene_birth
Protein-coding gene in the species Homo sapiens
with the stoichiometry of 2:2:1, which accounts for 43% of all GABAA receptors. Alternative splicing of the GABRB2 gene leads at least to four isoforms
GABRB2
Protein-coding gene in the species Homo sapiens
Halgren RG, Lim B, Fernandez E, Cibelli JB (September 2006). "The transcriptome of human oocytes". Proceedings of the National Academy of Sciences of the
FAM76A
Species of yeast
opportunities for an increase of range of protein types produced from alternative splicing and genes that code for comparable genes in human. 81% of the
Schizosaccharomyces_pombe
Human protein-coding gene on chromosome 7
1 May 2015. "Q8WVR3 -CG043_HUMAN". UniProt. Retrieved 8 May 2015. "C7orf43-Large-scale analysis of the human transcriptome (HG-U133A)". NCBI GEO Profiles
TRAPPC14
Protein-coding gene in the species Homo sapiens
and antiretroviral nucleoside analogs in HIV-infected patients. Alternative splicing of this gene has been detected; however, the complete sequence and
ABCC5
Description of the structure and function of a genome
Grabherr MG, Guttman M, Trapnell C (June 2011). "Computational methods for transcriptome annotation and quantification using RNA-seq". Nature Methods. 8 (6):
DNA_annotation
Protein-coding gene in humans
expression is particularly high in brain and B lymphocytes. Alternative promoters and alternative splicing allow the protein to exist as several different transcript
BLCAP
Protein-coding gene in the species Homo sapiens
gene produces multiple alternatively spliced transcripts. The gene contains 14 distinct introns and produces 8 alternatively spliced mRNAs, with the longest
C6orf118
Protein-coding gene in the species Homo sapiens
PI".[permanent dead link] "Aceview". "Large-scale analysis of the human transcriptome (HG-U133A". Woodfield GW, Chen Y, Bair TB, Domann FE, Weigel RJ (October
Tetratricopeptide_repeat_39A
Precursor microRNA family
scrutinised for regulatory elements. Publicly available sequence databases were used to identify a gene cluster which encodes the homologue to the human miR15
Mir-16 microRNA precursor family
Mir-16_microRNA_precursor_family
Protein-coding gene
Yang Q, Zhang W, Zhang Y, et al. (September 2017). "Transcriptome-wide piRNA profiling in human brains of Alzheimer's disease". Neurobiology of Aging
Envoplakin-like
Project to catalogue genetic mutations responsible for cancer
Network; Rätsch, Gunnar (2018-08-13). "Comprehensive Analysis of Alternative Splicing Across Tumors from 8,705 Patients". Cancer Cell. 34 (2): 211–224
The_Cancer_Genome_Atlas
Protein-coding gene in the species Homo sapiens
Toyama S, Usami R, Ohtoko K, Kato S (August 2011). "Full-length transcriptome analysis of human retina-derived cell lines ARPE-19 and Y79 using the vector-capping
FAM208b
Protein-coding gene in the species Homo sapiens
de Souza SJ, Simpson AJ (March 2000). "Shotgun sequencing of the human transcriptome with ORF expressed sequence tags". Proceedings of the National Academy
FBXO7
Small non-coding ribonucleic acid molecule
human genome may encode over 1900 miRNAs, However, only about 500 human miRNAs represent bona fide miRNAs in the manually curated miRNA gene database
MicroRNA
Short length polypeptides
point in time. This collection of data, known as a transcriptome, can then be used as a resource for finding potential sORFs. Because of the strong likelihood
Micropeptide
Protein-coding gene in the species Homo sapiens
interactions. Subcellularly, the protein localizes to cytoplasmic bodies. Alternative splicing results in multiple transcript variants encoding different isoforms
BTBD1
Protein-coding gene in the species Homo sapiens
with Catch 22 syndrome as well as cardiac and craniofacial defects. Alternative splicing results in multiple transcript variants encoding different isoforms
UFD1L
Protein-coding gene in the species Homo sapiens
PMC 528930. PMID 15489336. Oh JH, Yang JO, Hahn Y, et al. (2006). "Transcriptome analysis of human gastric cancer". Mamm. Genome. 16 (12): 942–54. doi:10.1007/s00335-005-0075-2
RNF216
Family of RNA viruses including the influenza viruses
produced from an alternative reading frame in PB1. The M and NS genes produce two genes each (4 genes total) via alternative splicing. Typically, influenza
Orthomyxoviridae
Protein-coding gene in the species Homo sapiens
Sue; Wiltshire, T (April 20, 2004). "Large-scale analysis of the human transcriptome (HG-U133A)". "Gene TF Analysis". genomatix.de.[permanent dead link]
LOC100287387
Motor protein in humans
MA, da Silva W, et al. (March 2000). "Shotgun sequencing of the human transcriptome with ORF expressed sequence tags". Proceedings of the National Academy
KIF1A
B, et al. (October 2018). "Chromosome-level reference genome and alternative splicing atlas of moso bamboo (Phyllostachys edulis)". GigaScience. 7 (10)
List of sequenced plant genomes
List_of_sequenced_plant_genomes
Large secreted extracellular matrix glycoprotein involved in neuronal migration
approximately 450 kb. One exon, coding for only two amino acids near the protein's C-terminus, undergoes alternative splicing, but the exact functional impact
Reelin
instructions (mRNAs) for building different proteins – in the mouse and human cortex and release the transcriptomes on a public database. A tech company reveals
2021_in_science
DNA testing for endangerment assessment
be used to assembly the genome. The RNA extraction is essential for the transcriptome assembly and the extraction process start from stem, roots, fruits
Genome sequencing of endangered species
Genome_sequencing_of_endangered_species
Numerous human diseases are characterised by a widespread dysregulation of RNA-binding proteins (RBPs) and massively altered transcriptome patterns.
Cluster of Excellence Frankfurt Macromolecular Complexes
Cluster_of_Excellence_Frankfurt_Macromolecular_Complexes
HUMAN TRANSCRIPTOME-DATABASE-FOR-ALTERNATIVE-SPLICING
HUMAN TRANSCRIPTOME-DATABASE-FOR-ALTERNATIVE-SPLICING
Boy/Male
Hindu
Human
Male
Chamoru
, Jehovah's gift or grace.
Girl/Female
Hindu, Indian
Human
Female
Native American
Native American Hopi name SHUMAN means "rattlesnake handler."
Girl/Female
Tamil
Manveet | மாநà¯à®µà®¿à®¤Â
Human
Manveet | மாநà¯à®µà®¿à®¤Â
Boy/Male
Tamil
Human
Male
Hebrew
(הָמָן) Hebrew name of Persian origin, HAMAN means "magnificent." In the bible, this is the name of a wicked prime minister.
Boy/Male
Hindu, Indian
Himan was the Name of One of the Famous Slaves that had a Hand in Building the Tomb of Queen Venika
Surname or Lastname
English
English : partly from an unattested late Old English personal name, Hygemann, composed of the elements hyge ‘mind’ (cognate with the underlying Germanic element in Hugh) + mann ‘man’. In some cases this may also have been an occupational name for a servant (Middle English man) of a man called Hugh.Perhaps an altered spelling of German Homann.
Surname or Lastname
English
English : occupational name denoting the servant (Middle English man) of someone called Hudde (see Hutt).
Boy/Male
Indian, Punjabi, Sikh
Love for Human Being
Boy/Male
Hindu
Human
Male
Egyptian
, a lord or chief of Memphis.
Surname or Lastname
Altered spelling of German Homann.English
Altered spelling of German Homann.English : variant of Holman. This surname has been in Ireland since the 17th century.Dutch : status name from Middle Dutch hovetman, hooftman ‘head man’, ‘leader’, ‘adviser’.Dutch : variant of Hoffman 2.Slovenian : unexplained.
Surname or Lastname
Jewish (American)
Jewish (American) : Americanized variant of Heiman.English : variant of Hayman.Americanized spelling of Heimann.
Boy/Male
Indian, Punjabi, Sikh
Human Form
Male
Yiddish
 Yiddish altered form of Hebrew Hyam, HYMAN means "life." Compare with another form of Hyman.
Boy/Male
Tamil
Human
Surname or Lastname
Altered spelling of German Luhmann or Lohmann.English
Altered spelling of German Luhmann or Lohmann.English : unexplained.
Girl/Female
Hindu
Human
HUMAN TRANSCRIPTOME-DATABASE-FOR-ALTERNATIVE-SPLICING
HUMAN TRANSCRIPTOME-DATABASE-FOR-ALTERNATIVE-SPLICING
Boy/Male
Indian
Mighty creator
Boy/Male
Indian
Blacksmith
Girl/Female
Indian
Sunflower
Girl/Female
Bengali, French, Hebrew, Indian
One who is Always First and Best
Surname or Lastname
English
English : probably a habitational name from a lost or unidentified place. This might be Pinglestone Farm in Hampshire.
Girl/Female
Indian, Telugu
Heavenly
Girl/Female
Indian
Name of Goddess Parvati
Girl/Female
Muslim Sanskrit
Starling. Heaven. Glass.
Male
Croatian
, of the sea.
Girl/Female
Arabic, Muslim
Dignity; Heavy and Precious Thing; Souvenir; Heavy and Precious
HUMAN TRANSCRIPTOME-DATABASE-FOR-ALTERNATIVE-SPLICING
HUMAN TRANSCRIPTOME-DATABASE-FOR-ALTERNATIVE-SPLICING
HUMAN TRANSCRIPTOME-DATABASE-FOR-ALTERNATIVE-SPLICING
HUMAN TRANSCRIPTOME-DATABASE-FOR-ALTERNATIVE-SPLICING
HUMAN TRANSCRIPTOME-DATABASE-FOR-ALTERNATIVE-SPLICING
n.
An argument which presents an antagonist with two or more alternatives, but is equally conclusive against him, whichever alternative he chooses.
a.
Alternate; reciprocal.
n.
A human being.
a.
Done as from a copy; having the style or appearance of a transcription.
a.
Designating the members in a series, which regularly intervene between the members of another series, as the odd or even numbers of the numerals; every other; every second; as, the alternate members 1, 3, 5, 7, etc. ; read every alternate line.
adv.
In the manner of alternatives, or that admits the choice of one out of two things.
a.
Resembling a human being in form or nature; human.
conj.
Because; by reason that; for that; indicating, in Old English, the reason of anything.
v. i.
To happen, succeed, or act by turns; to follow reciprocally in place or time; -- followed by with; as, the flood and ebb tides alternate with each other.
n.
The boundary line of a material object. In painting, more generally, the human body.
n.
Either of two things or propositions offered to one's choice. Thus when two things offer a choice of one only, the two things are called alternatives.
a.
Having the feelings and inclinations creditable to man; having a disposition to treat other human beings or animals with kindness; kind; benevolent.
a.
Pertaining to man; human.
n.
An alterative.
a.
Belonging to man or mankind; having the qualities or attributes of a man; of or pertaining to man or to the race of man; as, a human voice; human shape; human nature; human sacrifices.
a.
Disjunctive; as, an alternative conjunction.
n.
The reciprocal succession of things in time or place; the act of following and being followed by turns; alternate succession, performance, or occurrence; as, the alternation of day and night, cold and heat, summer and winter, hope and fear.
n.
A greenish chloritic mineral common in certain igneous rocks, as diabase, as a result of alternation.
n.
Alternate succession; alternation; a mingling.
p. pr. & vb. n.
of Alternate