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 21 exons, is annotated with 16 domains and features, is associated with 340 variations and maps to 11 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

TSL5: No single transcript (mRNA or EST) supports this transcript model's structure.

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 PI3APPRIS candidate principal isoform (earliest CCDS)
Glossary entry for APPRIS
APPRIS website
USH1C-001ENST000003180242237552aaENSP00000317018
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
CCDS31438Q9Y6N9 NM_005709
NP_005700
TSL:1

TSL1: All splice junctions of the transcript 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 ALT2APPRIS candidate principal isoform that appears to be conserved in fewer than three tested non-primate species
Glossary entry for APPRIS
APPRIS website
USH1C-003ENST000005270202159533aaENSP00000436934
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
CCDS73265Q9Y6N9 NM_001297764
NP_001284693
TSL:1

TSL1: All splice junctions of the transcript 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

TSL1: All splice junctions of the transcript 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

TSL5: No single transcript (mRNA or EST) supports this transcript model's structure.

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

TSL1: All splice junctions of the transcript 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

TSL2: 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. 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

TSL3:The only support for this transcript 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. 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

TSL2: 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. 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

TSL3:The only support for this transcript 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. 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

TSL:NA:The transcript was not analyzed for one of the following reasons:

  • Pseudogene annotation, including transcribed pseudogenes
  • Human leukocyte antigen (HLA) transcript
  • Immunoglobin gene transcript
  • T-cell receptor transcript
  • Single-exon transcript (will be included in a future version)

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.

Protein domains for ENSP00000317018.4

Transcript-based displays