Description

Usher syndrome 1C (autosomal recessive, severe) [Source:HGNC Symbol;Acc:HGNC:12597]

Synonyms

AIE-75, DFNB18, harmonin, NY-CO-37, NY-CO-38, PDZ-73, PDZ73, PDZD7C

Location
About this transcript

This transcript has 27 exons, is annotated with 29 domains and features, is associated with 505 variations and maps to 46 oligo probes.

Gene
NameTranscript IDbpProteinTranslation IDBiotypeCCDSUniProtRefSeqFlags
USH1C-006ENST000000052262700899aaENSP00000005226
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
CCDS7825Q9Y6N9 NM_153676
NP_710142
TSL:5

Transcript Support Level 5, for transcripts that are not supported at all by either an mRNA or an EST.

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.

USH1C-001ENST000003180242237552aaENSP00000317018
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
CCDS31438Q9Y6N9 NM_005709
NP_005700
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.

USH1C-003ENST000005270202159533aaENSP00000436934
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
CCDS73265Q9Y6N9 NM_001297764
NP_001284693
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).
USH1C-005ENST000005277202278521aaENSP00000432944
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
-Q9Y6N9 -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).
USH1C-008ENST000005261811040318aaENSP00000437128
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
-E9PNW1 -CDS 3' incomplete3' truncation in transcript evidence prevents annotation of the end of the CDS.TSL:5

Transcript Support Level 5, for transcripts that are not supported at all by either an mRNA or an EST.

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.

USH1C-002ENST000005263132149403aaENSP00000432236
 
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.
-Q9Y6N9 -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.

USH1C-009ENST00000529563942No protein-
 
Processed transcriptTranscripts that don't contain an open reading frame (ORF) and cannot be placed in one of the other categories.
---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.

USH1C-011ENST00000530700403No 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.

USH1C-010ENST00000527551371No 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.

USH1C-012ENST00000534556244No protein-
 
Retained intronAlternatively spliced transcript that is believed to contain intronic sequence relative to other coding transcripts in a given locus.
---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.

USH1C-007ENST000006248111194No protein-
 
TEC
---TSL:NA

Transcript Support Level Not Analysed. Pseudogenes, single exon transcripts, HLA, T-cell receptor and Ig transcripts are not analysed and therefore not given any of the TSL categories.

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.

Statistics

Exons: 27 Coding exons: 27 Transcript length: 2,700 bps Translation length: 899 residues

CCDS

This transcript is a member of the Human CCDS set: CCDS7825

Uniprot

This transcript corresponds to the following Uniprot identifiers: Q9Y6N9

Transcript Support Level (TSL)

TSL:5

Ensembl version

ENST00000005226.10

Type

Known protein coding

Annotation Method

Transcript where the Ensembl genebuild transcript and the Vega manual annotation have the same sequence, for every base pair. See article.

Alternative transcripts

This transcript corresponds to the following database identifiers:

Havana transcript:
Annotation Attributes

dotter confirmed [Definitions]

GENCODE basic gene

This transcript is a member of the Gencode basic gene set.

Transcript-based displays