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TCF19 transcription factor 19 [ Homo sapiens (human) ]

Gene ID: 6941, updated on 21-Dec-2019

Summary

Official Symbol
TCF19provided by HGNC
Official Full Name
transcription factor 19provided by HGNC
Primary source
HGNC:HGNC:11629
See related
Ensembl:ENSG00000137310 MIM:600912
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SC1; TCF-19
Summary
This gene encodes a protein that contains a PHD-type zinc finger domain and likely functions as a transcription factor. The encoded protein plays a role proliferation and apoptosis of pancreatic beta cells. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
Expression
Ubiquitous expression in lymph node (RPKM 8.0), appendix (RPKM 5.7) and 25 other tissues See more
Orthologs

Genomic context

See TCF19 in Genome Data Viewer
Location:
6p21.33
Exon count:
5
Annotation release Status Assembly Chr Location
109.20191205 current GRCh38.p13 (GCF_000001405.39) 6 NC_000006.12 (31158589..31164215)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (31126303..31134183)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene RNA polymerase II subunit L pseudogene 1 Neighboring gene coiled-coil alpha-helical rod protein 1 Neighboring gene POU class 5 homeobox 1 Neighboring gene POU5F1 5' regulatory region Neighboring gene psoriasis susceptibility 1 candidate 3

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

Description
A genome-wide association study identified new variants associated with the risk of chronic hepatitis B.
NHGRI GWA Catalog
A whole-genome association study of major determinants for allopurinol-related Stevens-Johnson syndrome and toxic epidermal necrolysis in Japanese patients.
NHGRI GWA Catalog
Common variation at 3q26.2, 6p21.33, 17p11.2 and 22q13.1 influences multiple myeloma risk.
NHGRI GWA Catalog
Genome-wide association study of Stevens-Johnson Syndrome and Toxic Epidermal Necrolysis in Europe.
NHGRI GWA Catalog
Genome-wide trans-ancestry meta-analysis provides insight into the genetic architecture of type 2 diabetes susceptibility.
NHGRI GWA Catalog
Risk HLA-DQA1 and PLA(2)R1 alleles in idiopathic membranous nephropathy.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA-binding transcription factor activity IEA
Inferred from Electronic Annotation
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
regulation of gene expression IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of transcription, DNA-templated IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
transcription factor 19
Names
transcription factor SC1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

  1. NM_001077511.2NP_001070979.1  transcription factor 19

    See identical proteins and their annotated locations for NP_001070979.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) uses an alternate splice site in the 5' UTR compared to variant 1. Variants 1, 2, and 3 encode the same protein.
    Source sequence(s)
    AL662844, BC033086, BP365938, DA116232
    Consensus CDS
    CCDS43446.1
    UniProtKB/Swiss-Prot
    Q9Y242
    UniProtKB/TrEMBL
    A0A1U9X8M7
    Related
    ENSP00000365431.4, ENST00000376255.4
    Conserved Domains (3) summary
    cd00060
    Location:5122
    FHA; Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins ...
    cd15609
    Location:291339
    PHD_TCF19; PHD finger found in Transcription factor 19 (TCF-19) and similar proteins
    cl26464
    Location:106295
    Atrophin-1; Atrophin-1 family
  2. NM_001318908.2NP_001305837.1  transcription factor 19

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) lacks an alternate segment in the 5' UTR compared to variant 1. Variants 1, 2, and 3 encode the same protein.
    Source sequence(s)
    AL662844, BC044632, BP365938, DA930848
    Consensus CDS
    CCDS43446.1
    UniProtKB/Swiss-Prot
    Q9Y242
    UniProtKB/TrEMBL
    A0A1U9X8M7
    Conserved Domains (3) summary
    cd00060
    Location:5122
    FHA; Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins ...
    cd15609
    Location:291339
    PHD_TCF19; PHD finger found in Transcription factor 19 (TCF-19) and similar proteins
    cl26464
    Location:106295
    Atrophin-1; Atrophin-1 family
  3. NM_007109.3NP_009040.2  transcription factor 19

    See identical proteins and their annotated locations for NP_009040.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longest transcript. Variants 1, 2, and 3 encode the same protein.
    Source sequence(s)
    AL662844, BC033086, BP365938, DA115077, DA485961, DB260358
    Consensus CDS
    CCDS43446.1
    UniProtKB/Swiss-Prot
    Q9Y242
    UniProtKB/TrEMBL
    A0A1U9X8M7
    Related
    ENSP00000365433.3, ENST00000376257.8
    Conserved Domains (3) summary
    cd00060
    Location:5122
    FHA; Forkhead associated domain (FHA); found in eukaryotic and prokaryotic proteins. Putative nuclear signalling domain. FHA domains may bind phosphothreonine, phosphoserine and sometimes phosphotyrosine. In eukaryotes, many FHA domain-containing proteins ...
    cd15609
    Location:291339
    PHD_TCF19; PHD finger found in Transcription factor 19 (TCF-19) and similar proteins
    cl26464
    Location:106295
    Atrophin-1; Atrophin-1 family

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20191205

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000006.12 Reference GRCh38.p13 Primary Assembly

    Range
    31158589..31164215
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_2

Genomic

  1. NT_113891.3 Reference GRCh38.p13 ALT_REF_LOCI_2

    Range
    2641017..2646639
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_3

Genomic

  1. NT_167245.2 Reference GRCh38.p13 ALT_REF_LOCI_3

    Range
    2417909..2423531
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_4

Genomic

  1. NT_167246.2 Reference GRCh38.p13 ALT_REF_LOCI_4

    Range
    2469124..2474716
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_5

Genomic

  1. NT_167247.2 Reference GRCh38.p13 ALT_REF_LOCI_5

    Range
    2502738..2508330
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_6

Genomic

  1. NT_167248.2 Reference GRCh38.p13 ALT_REF_LOCI_6

    Range
    2416621..2422248
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p13 ALT_REF_LOCI_7

Genomic

  1. NT_167249.2 Reference GRCh38.p13 ALT_REF_LOCI_7

    Range
    2462004..2467631
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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