Description

LIM homeobox 6 [Source:HGNC Symbol;Acc:HGNC:21735]

Synonyms

LHX6.1

About this transcript

This transcript has 9 exons, is annotated with 14 domains and features, is associated with 123 variations and maps to 25 oligo probes.

Gene
NameTranscript IDbpProteinTranslation IDBiotypeCCDSUniProtRefSeqFlags
LHX6-008ENST000005598953587176aaENSP00000475927
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
CCDS59144Q9UPM6 NM_001242335
NP_001229264
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.

GENCODE basicThe GENCODE set is the gene set for human and mouse. GENCODE Basic is a subset of representative transcripts (splice variants).
LHX6-001ENST000003943193465392aaENSP00000377854
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
CCDS6838Q9UPM6 NM_014368
NP_055183
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 P1

PRINCIPAL1 - APPRIS candidate principal isoform.

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

LHX6-006ENST000003405873457377aaENSP00000340137
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
CCDS6837Q9UPM6 NM_199160
NP_954629
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).
LHX6-002ENST000003737553384363aaENSP00000362860
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
CCDS56583A0A024R852 Q9UPM6 NM_001242334
NP_001229263
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).
LHX6-009ENST000005413972942366aaENSP00000441464
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
CCDS56584Q9UPM6 NM_001242333
NP_001229262
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.

GENCODE basicThe GENCODE set is the gene set for human and mouse. GENCODE Basic is a subset of representative transcripts (splice variants).
LHX6-003ENST000003737543278348aaENSP00000362859
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
-Q9UPM6 -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).
LHX6-004ENST0000048206291850aaENSP00000453798
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
-H0YMY8 -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.

GENCODE basicThe GENCODE set is the gene set for human and mouse. GENCODE Basic is a subset of representative transcripts (splice variants).
LHX6-011ENST0000056048573634aaENSP00000453606
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
-H0YMH3 -CDS 3' incomplete3' truncation in transcript evidence prevents annotation of the end of the CDS.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.

LHX6-005ENST0000046448466635aaENSP00000452811
 
Protein codingGenes and/or transcript that contains an open reading frame (ORF).
-H0YKH7 -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.

GENCODE basicThe GENCODE set is the gene set for human and mouse. GENCODE Basic is a subset of representative transcripts (splice variants).
LHX6-010ENST00000559529550No protein-
 
Processed transcriptTranscripts that don't contain an open reading frame (ORF) and cannot be placed in one of the other categories.
---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.

LHX6-007ENST00000558672592No protein-
 
Retained intronAlternatively spliced transcript that is believed to contain intronic sequence relative to other coding transcripts in a given locus.
---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.

LHX6-012ENST00000560152582No 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.

Statistics

Exons: 9 Coding exons: 9 Transcript length: 2,942 bps Translation length: 366 residues

CCDS

This transcript is a member of the Human CCDS set: CCDS56584

Uniprot

This transcript corresponds to the following Uniprot identifiers: Q9UPM6

Transcript Support Level (TSL)

TSL:2

Ensembl version

ENST00000541397.2

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:
GENCODE basic gene

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

Transcript-based displays