Description

lymphocyte antigen 9 [Source:HGNC Symbol;Acc:HGNC:6730]

Synonyms

CD229, hly9, mLY9, SLAMF3

INSDC coordinates

chromosome:GRCh38:CM000663.2:160796074:160828261:1

About this gene

This gene has 11 transcripts (splice variants), 42 orthologues, 4 paralogues, is a member of 3 Ensembl protein families and is associated with 159 phenotypes.

NameTranscript IDbpProteinTranslation IDBiotypeCCDSUniProtRefSeqFlags
LY9-003ENST000003680372485641aaENSP00000357016
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
CCDS65695Q9HBG7 NM_001261456
NP_001248385
TSL:1

Transcript Support Level 1, when transcripts 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. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.

GENCODE basicThe GENCODE set is the gene set for human and mouse. GENCODE Basic is a subset of representative transcripts (splice variants).APPRIS ALT2

ALTERNATIVE2 - APPRIS candidate principal isoform that appears to be conserved in fewer than three tested non-primate species.

APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods.

LY9-001ENST000002632852443655aaENSP00000263285
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
CCDS30916Q9HBG7 NM_002348
NP_002339
TSL:1

Transcript Support Level 1, when transcripts 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. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.

GENCODE basicThe GENCODE set is the gene set for human and mouse. GENCODE Basic is a subset of representative transcripts (splice variants).APPRIS P3

PRINCIPAL3 - APPRIS candidate principal isoform (earliest CCDS).

APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods.

LY9-002ENST000003922032213565aaENSP00000376039
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
CCDS65696Q5VYH9 NM_001261457
NP_001248386
TSL:1

Transcript Support Level 1, when transcripts 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. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.

GENCODE basicThe GENCODE set is the gene set for human and mouse. GENCODE Basic is a subset of representative transcripts (splice variants).APPRIS ALT2

ALTERNATIVE2 - APPRIS candidate principal isoform that appears to be conserved in fewer than three tested non-primate species.

APPRIS is a system to annotate alternatively spliced transcripts based on a range of computational methods.

LY9-005ENST000003680391364193aaENSP00000357018
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
CCDS30917-NM_001033667
NP_001028839
TSL:1

Transcript Support Level 1, when transcripts 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. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.

GENCODE basicThe GENCODE set is the gene set for human and mouse. GENCODE Basic is a subset of representative transcripts (splice variants).
LY9-004ENST000003680351463341aaENSP00000357014
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
-Q5VYI1 -CDS 5' incomplete5' truncation in transcript evidence prevents annotation of the start of the CDS.TSL:1

Transcript Support Level 1, when transcripts 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. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.

LY9-008ENST0000047499884761aaENSP00000476321
 
Nonsense mediated decayTranscript is thought to undergo nonsense mediated decay, a process which detects nonsense mutations and prevents the expression of truncated or erroneous proteins.
-V9GY30 -TSL:4

Transcript Support Level 4, for transcripts supported by an EST flagged as suspect.

The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.

LY9-011ENST0000049090280171aaENSP00000473643
 
Nonsense mediated decayTranscript is thought to undergo nonsense mediated decay, a process which detects nonsense mutations and prevents the expression of truncated or erroneous proteins.
-R4GNG7 -CDS 5' incomplete5' truncation in transcript evidence prevents annotation of the start of the CDS.TSL:3

Transcript Support Level 3, when transcripts are supported by a single EST only.

The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.

LY9-009ENST000004718161056No protein-
 
Processed transcriptTranscripts that don't contain an open reading frame (ORF) and cannot be placed in one of the other categories.
---TSL:3

Transcript Support Level 3, when transcripts are supported by a single EST only.

The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.

LY9-012ENST00000485624940No protein-
 
Processed transcriptTranscripts that don't contain an open reading frame (ORF) and cannot be placed in one of the other categories.
---TSL:3

Transcript Support Level 3, when transcripts are supported by a single EST only.

The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.

LY9-010ENST00000480837705No protein-
 
Processed transcriptTranscripts that don't contain an open reading frame (ORF) and cannot be placed in one of the other categories.
---TSL:3

Transcript Support Level 3, when transcripts are supported by a single EST only.

The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.

LY9-006ENST000004796635083No protein-
 
Retained intronAlternatively spliced transcript that is believed to contain intronic sequence relative to other coding transcripts in a given locus.
---TSL:2

Transcript Support Level 2, when transcripts are supported by multiple ESTs or by an mRNA flagged as suspect.

The Transcript Support Level (TSL) is a method to highlight the well-supported and poorly-supported transcript models for users. The method relies on the primary data that can support full-length transcript structure: mRNA and EST alignments supplied by UCSC and Ensembl.

Gene-based displays