KLF6 KLF transcription factor 6 [Homo sapiens (human)] - Gene

Summary

Official Symbol: KLF6provided by HGNC
Official Full Name: KLF transcription factor 6provided by HGNC
Primary source: HGNC:HGNC:2235
See related: Ensembl:ENSG00000067082 MIM:602053; AllianceGenome:HGNC:2235
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: GBF; ZF9; BCD1; CBA1; CPBP; PAC1; ST12; COPEB
Summary: This gene encodes a member of the Kruppel-like family of transcription factors. The zinc finger protein is a transcriptional activator, and functions as a tumor suppressor. Multiple transcript variants encoding different isoforms have been found for this gene, some of which are implicated in carcinogenesis. [provided by RefSeq, May 2009]
Expression: Ubiquitous expression in bone marrow (RPKM 165.8), gall bladder (RPKM 117.9) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 10p15.2

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (3775996..3785209, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	10	NC_060934.1 (3779895..3789103, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (3818188..3827401, complement)

Chromosome 10 - NC_000010.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

GSE1 promotes the proliferation and migration of lung adenocarcinoma cells by downregulating KLF6 expression.
Title: GSE1 promotes the proliferation and migration of lung adenocarcinoma cells by downregulating KLF6 expression.
WTAP-MEDIATED M6A MODIFICATION OF KLF6 AGGRAVATES HYPOXIA/REOXYGENATION-INDUCED HUMAN CARDIOMYOCYTE INJURY.
Title: WTAP-MEDIATED M6A MODIFICATION OF KLF6 AGGRAVATES HYPOXIA/REOXYGENATION-INDUCED HUMAN CARDIOMYOCYTE INJURY.
Decreased expression of KLF6 in ectopic endometrial stromal cells contributes to endometriosis progression by targeting CTNNB1.
Title: Decreased expression of KLF6 in ectopic endometrial stromal cells contributes to endometriosis progression by targeting CTNNB1.
miRNA-21 promotes the progression of acute liver failure via the KLF6/autophagy/IL-23 signaling pathway.
Title: miRNA‑21 promotes the progression of acute liver failure via the KLF6/autophagy/IL‑23 signaling pathway.
KLF6 activates Sp1-mediated prolidase transcription during TGF-beta1 signaling.
Title: KLF6 activates Sp1-mediated prolidase transcription during TGF-β(1) signaling.
Machine learning-based classification of deubiquitinase USP26 and its cell proliferation inhibition through stabilizing KLF6 in cervical cancer.
Title: Machine learning-based classification of deubiquitinase USP26 and its cell proliferation inhibition through stabilizing KLF6 in cervical cancer.
Roles of Kruppel-Like Transcription Factors KLF6 and KLF15 in Proximal Tubular Metabolism.
Title: Roles of Krüppel-Like Transcription Factors KLF6 and KLF15 in Proximal Tubular Metabolism.
MiR-191-5p inhibits KLF6 to promote epithelial-mesenchymal transition in breast cancer.
Title: MiR-191-5p inhibits KLF6 to promote epithelial-mesenchymal transition in breast cancer.
TNF-alpha stimulated exosome derived from fibroblast-like synoviocytes isolated from rheumatoid arthritis patients promotes HUVEC migration, invasion and angiogenesis by targeting the miR-200a-3p/KLF6/VEGFA axis.
Title: TNF-α stimulated exosome derived from fibroblast-like synoviocytes isolated from rheumatoid arthritis patients promotes HUVEC migration, invasion and angiogenesis by targeting the miR-200a-3p/KLF6/VEGFA axis.
The Kruppel-like factor 6 represses proliferation and invasion of cutaneous malignant melanoma.
Title: The Krüppel-like factor 6 represses proliferation and invasion of cutaneous malignant melanoma.

Submit: New GeneRIF Correction See all GeneRIFs (182)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Gastric cancer MedGen: C0024623 OMIM: 613659 GeneReviews: Not available	not available
Malignant tumor of prostate MedGen: C0376358 GeneReviews: Not available	not available

EBI GWAS Catalog

Description
A genome-wide association study of bronchodilator response in asthmatics. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetics of coronary artery calcification among African Americans, a meta-analysis. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

WI-12084 (e-PCR)
- UniSTS:33039

COPEB_2513 (e-PCR)
- UniSTS:462115

D10S1368E (e-PCR)
- UniSTS:49498

D10S2364 (e-PCR)
- UniSTS:52875

G62122 (e-PCR)
- UniSTS:139172

COPEB (e-PCR)
- UniSTS:278228

STS-AA018922 (e-PCR)
- UniSTS:55521

RH48829 (e-PCR)
- UniSTS:2022

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription factor activity, RNA polymerase II-specific	ISA Inferred from Sequence Alignment more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sequence-specific double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in B cell differentiation	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of DNA-templated transcription	TAS Traceable Author Statement more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in chromatin	ISA Inferred from Sequence Alignment more info
located_in cytosol	IDA Inferred from Direct Assay more info
located_in fibrillar center	IDA Inferred from Direct Assay more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in nucleolus	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleus	TAS Traceable Author Statement more info	PubMed

General protein information

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Preferred Names: Krueppel-like factor 6

Names: B-cell-derived protein 1; GC-rich binding factor; GC-rich sites-binding factor GBF; Kruppel like factor 6; Kruppel-like zinc finger protein Zf9; core promoter element binding protein; proto-oncogene BCD1; protooncogene B-cell derived 1; suppression of tumorigenicity 12 (prostate); suppressor of tumorigenicity 12 protein; transcription factor Zf9

NCBI Reference Sequences (RefSeq)

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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.

Genomic

NG_012277.1 RefSeqGene

Range

5073..14286

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001160124.2 → NP_001153596.1 Krueppel-like factor 6 isoform B

See identical proteins and their annotated locations for NP_001153596.1

Status: REVIEWED

Description

Transcript Variant: This variant (B), also known as sv2, uses an alternate splice site in the central coding region that results in a frameshift, compared to variant A. The resulting isoform (B) has a shorter and distinct C-terminus, compared to isoform A.

Source sequence(s)

AL450322, BC000311, BP357332, BQ017028

UniProtKB/TrEMBL

D3GC14

Conserved Domains (3) summary

sd00017
Location:190 → 212

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:218 → 240

zf-C2H2; Zinc finger, C2H2 type

pfam13465
Location:204 → 229

zf-H2C2_2; Zinc-finger double domain
NM_001160125.2 → NP_001153597.1 Krueppel-like factor 6 isoform C

See identical proteins and their annotated locations for NP_001153597.1

Status: REVIEWED

Description

Transcript Variant: This variant (C), also known as sv3, lacks an alternate exon in the 3' coding region that results in a frameshift, compared to variant A. The resulting isoform (C) has a shorter and distinct C-terminus, compared to isoform A.

Source sequence(s)

AL450322, BC000311, BM695496, BP357332, BQ017028

Consensus CDS

CCDS53490.1

UniProtKB/Swiss-Prot

Q99612

Related

ENSP00000445301.1, ENST00000542957.1

Conserved Domains (2) summary

sd00017
Location:202 → 224

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:200 → 224

zf-C2H2; Zinc finger, C2H2 type
NM_001300.6 → NP_001291.3 Krueppel-like factor 6 isoform A

See identical proteins and their annotated locations for NP_001291.3

Status: REVIEWED

Description

Transcript Variant: This variant (A) represents the longest transcript and encodes the longest isoform (A).

Source sequence(s)

AL450322, BC000311, BP357332, BQ017028

Consensus CDS

CCDS7060.1

UniProtKB/Swiss-Prot

B2RE86, B4DDN0, D3DRR1, F5H3M5, Q5VUT7, Q5VUT8, Q99612, Q9BT79

Related

ENSP00000419923.1, ENST00000497571.6

Conserved Domains (3) summary

COG5048
Location:177 → 265

COG5048; FOG: Zn-finger [General function prediction only]

sd00017
Location:205 → 224

ZF_C2H2; C2H2 Zn finger [structural motif]

pfam00096
Location:260 → 282

zf-C2H2; Zinc finger, C2H2 type

RNA

NR_027653.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (D), also known as sv1, uses an alternate splice site, compared to variant A. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant A, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AL450322, AL513303, BC000311, BP357332, BQ017028

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000010.11 Reference GRCh38.p14 Primary Assembly

Range

3775996..3785209 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060934.1 Alternate T2T-CHM13v2.0

Range

3779895..3789103 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001008490.1: Suppressed sequence

Description

NM_001008490.1: This RefSeq was suppressed because the 3'UTR structure is not strongly supported and it renders the transcript a candidate for nonsense-mediated decay (NMD).