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Transcript: ENST00000684293.1ITGA6-212

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Description

integrin subunit alpha 6 [Source:HGNC Symbol;Acc:HGNC:6142]

Gene Synonyms

CD49F, ITGA6A, ITGA6B, VLA-6

About this transcript

This transcript has26 exons, is annotated with40 domains and features, is associated with33162 variant alleles and maps to933 oligo probes.

Gene
Transcript IDNamebpProteinTranslation IDBiotypeCCDSUniProt MatchRefSeq MatchFlags
ENST00000684293.1ITGA6-21258161073aaENSP00000508249.1
 
Gene/transcipt that contains an open reading frame (ORF).Protein coding
CCDS2249P23229-2NM_000210.4The Matched Annotation from NCBI and EMBL-EBI is a collaboration between Ensembl/GENCODE and RefSeq. The MANE Select is a default transcript per human gene that is representative of biology, well-supported, expressed and highly-conserved. This transcript set matches GRCh38 and is 100% identical between RefSeq and Ensembl/GENCODE for 5' UTR, CDS, splicing and 3'UTR.MANE SelectA single transcript chosen for a gene which is the most conserved, most highly expressed, has the longest coding sequence and is represented in other key resources, such as NCBI and UniProt. This is defined in detail on http://www.ensembl.org/info/genome/genebuild/canonical.htmlEnsembl CanonicalGENCODE Primary represents a minimal set that contains MANE Select, MANE Plus Clinical and Ensembl Canonical transcripts and transcripts containing any conserved exons and common alternative splicing events (including exons skips) that are absent from the MANE and Ensembl Canonical transcripts for protein-coding genes. Other biotypes will have the GENCODE Primary flag added to the Ensembl Canonical transcript and for lncRNA genes only this will be the transcripts with the longest genomic span.GENCODE PrimaryA subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic

APPRIS P3: Where the APPRIS core modules are unable to choose a clear principal variant and there more than one of the variants have distinct CCDS identifiers, APPRIS selects the variant with lowest CCDS identifier as the principal variant. The lower the CCDS identifier, the earlier it was annotated.

APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods to identify the most functionally important transcript(s) of a gene.

APPRIS P3
ENST00000442250.6ITGA6-20658031130aaENSP00000406694.1
 
Gene/transcipt that contains an open reading frame (ORF).Protein coding
CCDS92897P23229-1NM_001394928.1Transcripts in the MANE Plus Clinical set are additional transcripts per locus necessary to support clinical variant reporting, for example transcripts containing known Pathogenic or Likely Pathogenic clinical variants not reportable using the MANE Select set. Note there may be additional clinically relevant transcripts in the wider RefSeq and Ensembl/GENCODE sets but not yet in MANE.MANE Plus ClinicalGENCODE Primary represents a minimal set that contains MANE Select, MANE Plus Clinical and Ensembl Canonical transcripts and transcripts containing any conserved exons and common alternative splicing events (including exons skips) that are absent from the MANE and Ensembl Canonical transcripts for protein-coding genes. Other biotypes will have the GENCODE Primary flag added to the Ensembl Canonical transcript and for lncRNA genes only this will be the transcripts with the longest genomic span.GENCODE PrimaryA subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic

TSL 5: A transcript where no single transcript supports the model structure.

The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users, based on the type and quality of the alignments used to annotate the transcript.

TSL:5
ENST00000409080.6ITGA6-20256861091aaENSP00000386896.1
 
Gene/transcipt that contains an open reading frame (ORF).Protein coding
CCDS46451P23229-3-A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic

APPRIS ALT1: For genes in which the APPRIS core modules are unable to choose a clear principal isoform, the ALT1 is the candidate transcript(s) models that is conserved in at least three tested species.

APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods to identify the most functionally important transcript(s) of a gene.

APPRIS ALT1

TSL 2: A transcript where the best supporting mRNA is flagged as suspect or the support is from multiple ESTs

The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users, based on the type and quality of the alignments used to annotate the transcript.

TSL:2
ENST00000715295.1ITGA6-2135669977aaENSP00000520448.1
 
Gene/transcipt that contains an open reading frame (ORF).Protein coding
--A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic
ENST00000264107.12ITGA6-20154881058aaENSP00000264107.8
 
Gene/transcipt that contains an open reading frame (ORF).Protein coding
CCDS92898A0A8C8KBL6-GENCODE Primary represents a minimal set that contains MANE Select, MANE Plus Clinical and Ensembl Canonical transcripts and transcripts containing any conserved exons and common alternative splicing events (including exons skips) that are absent from the MANE and Ensembl Canonical transcripts for protein-coding genes. Other biotypes will have the GENCODE Primary flag added to the Ensembl Canonical transcript and for lncRNA genes only this will be the transcripts with the longest genomic span.GENCODE PrimaryA subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic

TSL 1: A transcript where all splice junctions are supported by at least one non-suspect mRNA.

The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users, based on the type and quality of the alignments used to annotate the transcript.

TSL:1
ENST00000409532.5ITGA6-2033544954aaENSP00000386614.1
 
Gene/transcipt that contains an open reading frame (ORF).Protein coding
CCDS82534P23229-7-A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic

TSL 2: A transcript where the best supporting mRNA is flagged as suspect or the support is from multiple ESTs

The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users, based on the type and quality of the alignments used to annotate the transcript.

TSL:2
ENST00000458358.5ITGA6-20732611086aaENSP00000394169.1
 
Gene/transcipt that contains an open reading frame (ORF).Protein coding
P23229-5-A subset of the GENCODE transcript set, containing only 5' and 3' complete transcripts at protein-coding genes.GENCODE Basic

TSL 5: A transcript where no single transcript supports the model structure.

The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users, based on the type and quality of the alignments used to annotate the transcript.

TSL:5
ENST00000412899.5ITGA6-204970231aaENSP00000413470.1
 
Gene/transcipt that contains an open reading frame (ORF).Protein coding
C9JXX7-

TSL 1: A transcript where all splice junctions are supported by at least one non-suspect mRNA.

The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users, based on the type and quality of the alignments used to annotate the transcript.

TSL:13' truncation in transcript evidence prevents annotation of the end of the CDS.CDS 3' incomplete
ENST00000416789.1ITGA6-205853258aaENSP00000388435.1
 
Gene/transcipt that contains an open reading frame (ORF).Protein coding
H7BZ97-

TSL 3: A transcript where the only support is from a single EST

The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users, based on the type and quality of the alignments used to annotate the transcript.

TSL:35' truncation in transcript evidence prevents annotation of the start of the CDS.CDS 5' incomplete
ENST00000469534.1ITGA6-208581No protein-
 
An alternatively spliced transcript believed to contain intronic sequence relative to other, coding, transcripts of the same gene.Retained intron
--

TSL 2: A transcript where the best supporting mRNA is flagged as suspect or the support is from multiple ESTs

The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users, based on the type and quality of the alignments used to annotate the transcript.

TSL:2
ENST00000475302.1ITGA6-210577No protein-
 
An alternatively spliced transcript believed to contain intronic sequence relative to other, coding, transcripts of the same gene.Retained intron
--

TSL 3: A transcript where the only support is from a single EST

The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users, based on the type and quality of the alignments used to annotate the transcript.

TSL:3
ENST00000497107.1ITGA6-211573No protein-
 
An alternatively spliced transcript believed to contain intronic sequence relative to other, coding, transcripts of the same gene.Retained intron
--

TSL 2: A transcript where the best supporting mRNA is flagged as suspect or the support is from multiple ESTs

The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users, based on the type and quality of the alignments used to annotate the transcript.

TSL:2
ENST00000470259.1ITGA6-209365No protein-
 
An alternatively spliced transcript believed to contain intronic sequence relative to other, coding, transcripts of the same gene.Retained intron
--

TSL 3: A transcript where the only support is from a single EST

The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users, based on the type and quality of the alignments used to annotate the transcript.

TSL:3

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Statistics

Exons: 26,Coding exons: 25,Transcript length: 5,816 bps,Translation length: 1,073 residues

MANE

This MANE Select transcript containsENSP00000508249 and matches toNM_000210.4 andNP_000201.2

Uniprot

This transcript corresponds to the following Uniprot identifiers:P23229

CCDS

This transcript is a member of the Human CCDS set:CCDS2249

Version

ENST00000684293.1

Type

Protein coding

Annotation Method

Transcript where the Ensembl genebuild transcript and the Havana manual annotation have the same sequence, for every base pair. Seearticle.

Annotation Attributes

CAGE supported TSS [Definitions]

GENCODE basic gene

This transcript is a member of theGencode basic gene set.

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Ensembl release 113 - October 2024 ©EMBL-EBIEMBL-EBI
http://asia.ensembl.org

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