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KLF13 KLF transcription factor 13 [ Homo sapiens (human) ]

Gene ID: 51621, updated on 2-Nov-2024

Summary

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Official Symbol
KLF13provided by HGNC
Official Full Name
KLF transcription factor 13provided by HGNC
Primary source
HGNC:HGNC:13672
See related
Ensembl:ENSG00000169926 MIM:605328; AllianceGenome:HGNC:13672
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
BTEB3; FKLF2; NSLP1; RFLAT1; RFLAT-1
Summary
KLF13 belongs to a family of transcription factors that contain 3 classical zinc finger DNA-binding domains consisting of a zinc atom tetrahedrally coordinated by 2 cysteines and 2 histidines (C2H2 motif). These transcription factors bind to GC-rich sequences and related GT and CACCC boxes (Scohy et al., 2000 [PubMed 11087666]).[supplied by OMIM, Mar 2008]
Expression
Ubiquitous expression in bone marrow (RPKM 34.5), lung (RPKM 27.2) and 24 other tissues See more
Orthologs
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Genomic context

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See KLF13 in Genome Data Viewer
Location:
15q13.3
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (31326835..31435665)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (29120947..29230012)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (31619038..31727868)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903454 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:31517937-31518509 Neighboring gene Sharpr-MPRA regulatory region 5138 Neighboring gene long intergenic non-protein coding RNA 2352 Neighboring gene long intergenic non-protein coding RNA 3034 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:31548124-31548696 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:31570698-31571198 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:31571199-31571699 Neighboring gene KLF13-II enhancer Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:31594474-31595156 Neighboring gene KLF13-III enhancer Neighboring gene VISTA enhancer hs2231 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:31604403-31605163 Neighboring gene KLF13 promoter region Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:31621870-31622434 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:31628359-31628859 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:31627858-31628358 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:31634092-31634903 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:31634904-31635714 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:31649687-31650186 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:31666033-31667020 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6267 Neighboring gene uncharacterized LOC105370939 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:31727051-31727570 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:31732825-31733325 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:31756624-31757124 Neighboring gene ubiquitin conjugating enzyme E2 C pseudogene 4 Neighboring gene REX4 homolog, 3'-5' exonuclease pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:31782018-31782667 Neighboring gene uncharacterized LOC105370753 Neighboring gene OTU deubiquitinase 7A

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues 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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Related articles in PubMed

  1. RFLAT-1: a new zinc finger transcription factor that activates RANTES gene expression in T lymphocytes. Song A, et al. Immunity, 1999 Jan. PMID 10023774
  2. Kruppel-like Factors 3 Regulates Migration and Invasion of Gastric Cancer Cells Through NF-κB Pathway. Liang X, et al. Altern Ther Health Med, 2023 Mar. PMID 36580668
  3. Sp1 and its likes: biochemical and functional predictions for a growing family of zinc finger transcription factors. Cook T, et al. Ann N Y Acad Sci, 1999 Jun 30. PMID 10415854
  4. Functional domains and DNA-binding sequences of RFLAT-1/KLF13, a Krüppel-like transcription factor of activated T lymphocytes. Song A, et al. J Biol Chem, 2002 Aug 16. PMID 12050170
  5. KLF13 Loss-of-Function Mutations Underlying Familial Dilated Cardiomyopathy. Guo YH, et al. J Am Heart Assoc, 2022 Nov 15. PMID 36346048, Free PMC Article

See all (57) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. KLF13 restrains Dll4-muscular Notch2 axis to improve the muscle atrophy.
    Title: KLF13 restrains Dll4-muscular Notch2 axis to improve the muscle atrophy.
  2. Kruppel-like factor 13 acts as a tumor suppressor in thyroid carcinoma by downregulating IFIT1.
    Title: Kruppel-like factor 13 acts as a tumor suppressor in thyroid carcinoma by downregulating IFIT1.
  3. Kruppel-like Factors 3 Regulates Migration and Invasion of Gastric Cancer Cells Through NF-kappaB Pathway.
    Title: Kruppel-like Factors 3 Regulates Migration and Invasion of Gastric Cancer Cells Through NF-κB Pathway.
  4. UC-BSCs Exosomes Regulate Th17/Treg Balance in Patients with Systemic Lupus Erythematosus via miR-19b/KLF13.
    Title: UC-BSCs Exosomes Regulate Th17/Treg Balance in Patients with Systemic Lupus Erythematosus via miR-19b/KLF13.
  5. KLF13 Loss-of-Function Mutations Underlying Familial Dilated Cardiomyopathy.
    Title: KLF13 Loss-of-Function Mutations Underlying Familial Dilated Cardiomyopathy.
  6. The inhibitory effect of LINC00261 upregulation on the pancreatic cancer EMT process is mediated by KLF13 via the mTOR signaling pathway.
    Title: The inhibitory effect of LINC00261 upregulation on the pancreatic cancer EMT process is mediated by KLF13 via the mTOR signaling pathway.
  7. KLF13 loss-of-function variation contributes to familial congenital heart defects.
    Title: KLF13 loss-of-function variation contributes to familial congenital heart defects.
  8. Molecular Mechanisms for Kruppel-Like Factor 13 Actions in Hippocampal Neurons.
    Title: Molecular Mechanisms for Krüppel-Like Factor 13 Actions in Hippocampal Neurons.
  9. Our results show that the S156N and P163S variants may affect the transcriptional function of KLF13 and physical interaction with TBX5. These results identified KLF13 as a potential genetic risk factor for congenital heart disease.
    Title: Identification and analysis of KLF13 variants in patients with congenital heart disease.
  10. Results show that cg07814318 methylation in blood was significantly associated with obesity and correlated with several obesity-related physical and biochemical traits. The exome sequencing of KLF13 gene in blood identified nine SNPs within its gene body, and two SNPs as cis-meQTL of cg07814318. The sequencing variations within KLF13 genes could drive dynamic modifications of obesity-related CpG methylation.
    Title: Obesity-related CpG Methylation (cg07814318) of Kruppel-like Factor-13 (KLF13) Gene with Childhood Obesity and its cis-Methylation Quantitative Loci.
Submit: New GeneRIF Correction See all GeneRIFs (27)

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
Chromosome 15q13.3 microdeletion syndrome
MedGen: C2677613 OMIM: 612001 GeneReviews: 15q13.3 Recurrent Deletion
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EBI GWAS Catalog

Description
Genome-wide association analysis of eosinophilic esophagitis provides insight into the tissue specificity of this allergic disease.
EBI GWAS Catalog

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ36439, FLJ45109

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables DNA-binding transcription activator activity, RNA polymerase II-specific IEA
Inferred from Electronic Annotation
more info
  
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 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 negative regulation of cell population proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in negative regulation of erythrocyte differentiation IEA
Inferred from Electronic Annotation
more info
  
involved_in positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
involved_in regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in transcription by RNA polymerase II TAS
Traceable Author Statement
more info
 PubMed 
Component Evidence Code Pubs
located_in chromatin ISA
Inferred from Sequence Alignment
more info
  
located_in nucleus IEA
Inferred from Electronic Annotation
more info
  

General protein information

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Preferred Names
Krueppel-like factor 13
Names
BTE-binding protein 3
Kruppel like factor 13
RANTES factor of late activated T lymphocytes-1
basic transcription element binding protein 3
novel Sp1-like zinc finger transcription factor 1
transcription factor BTEB3
transcription factor NSLP1

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.

mRNA and Protein(s)

  1. NM_001302461.2 → NP_001289390.1  Krueppel-like factor 13 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (2) has a distinct C-terminus and is shorter than isoform 1.
    Source sequence(s)
    AC012236, AF132599, AI084187, BX096457
    UniProtKB/Swiss-Prot
    Q9Y2Y9
    Conserved Domains (2) summary
    sd00017
    Location:169 → 191
    ZF_C2H2; C2H2 Zn finger [structural motif]
    pfam00096
    Location:167 → 191
    zf-C2H2; Zinc finger, C2H2 type

  2. NM_015995.4 → NP_057079.2  Krueppel-like factor 13 isoform 1

    See identical proteins and their annotated locations for NP_057079.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC012236, AF132599, AL390127, BC064552, BX474032
    Consensus CDS
    CCDS10025.1
    UniProtKB/Swiss-Prot
    Q9Y2Y9, Q9Y356
    UniProtKB/TrEMBL
    A0A087X1K6, X5DNR2
    Related
    ENSP00000302456.3, ENST00000307145.4
    Conserved Domains (3) summary
    COG5048
    Location:162 → 252
    COG5048; FOG: Zn-finger [General function prediction only]
    sd00017
    Location:169 → 191
    ZF_C2H2; C2H2 Zn finger [structural motif]
    cd21571
    Location:7 → 168
    KLF13_N; N-terminal domain of Kruppel-like factor 13

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

  1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    31326835..31435665
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_011332701.1 Reference GRCh38.p14 PATCHES

    Range
    3500207..3609057
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

  1. NT_187660.1 Reference GRCh38.p14 ALT_REF_LOCI_2

    Range
    3612659..3721509
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    29120947..29230012
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NR_033741.1: Suppressed sequence

    Description
    NR_033741.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9Y2Y9.1 GenPept UniProtKB/Swiss-Prot:Q9Y2Y9

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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