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HLTF Gene(Protein Coding)

Helicase Like Transcription Factor

GCID:
GC03M149030
GIFtS:
55
Genes Participants
UDN Logo

Aliases for HLTF Gene

Aliases for HLTF Gene

  • Helicase Like Transcription Factor 2 3 5
  • SWI/SNF Related, Matrix Associated, Actin Dependent Regulator Of Chromatin, Subfamily A, Member 3 2 3
  • SWI/SNF-Related Matrix-Associated Actin-Dependent Regulator Of Chromatin Subfamily A Member 3 3 4
  • RING-Type E3 Ubiquitin Transferase HLTF 3 4
  • Sucrose Nonfermenting Protein 2-Like 3 3 4
  • RING Finger Protein 80 3 4
  • SMARCA3 3 4
  • HIP116A 3 4
  • SNF2L3 3 4
  • HIP116 3 4
  • RNF80 3 4
  • ZBU1 3 4
  • DNA-Binding Protein/Plasminogen Activator Inhibitor-1 Regulator 3
  • DNA-Binding Protein/Plasminogen Activator Inhibitor 1 Regulator 4
  • Helicase-Like Transcription Factor 3
  • Sucrose Nonfermenting-Like 3 3
  • SNF2-Like 3 3
  • EC 2.3.2.27 4
  • EC 3.6.4.- 4
  • EC 3.6.1 61
  • HLTF1 3

External Ids for HLTF Gene

Previous HGNC Symbols for HLTF Gene

  • SNF2L3
  • SMARCA3

Previous GeneCards Identifiers for HLTF Gene

  • GC03M150231
  • GC03M148747
  • GC03M146119

Summaries for HLTF Gene

Entrez Gene Summary for HLTF Gene

  • This gene encodes a member of the SWI/SNF family. Members of this family have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin structure around those genes. The encoded protein contains a RING finger DNA binding motif. Two transcript variants encoding the same protein have been found for this gene. However, use of an alternative translation start site produces an isoform that is truncated at the N-terminus compared to the full-length protein. [provided by RefSeq, Jul 2008]

GeneCards Summary for HLTF Gene

HLTF (Helicase Like Transcription Factor) is a Protein Coding gene. Diseases associated with HLTF include Colorectal Cancer. Among its related pathways are PEDF Induced Signaling and AMPK Enzyme Complex Pathway. GO annotations related to this gene include nucleic acid binding and ligase activity. An important paralog of this gene is TTF2.

UniProtKB/Swiss-Prot for HLTF Gene

  • Has both helicase and E3 ubiquitin ligase activities. Possesses intrinsic ATP-dependent nucleosome-remodeling activity; This activity may be required for transcriptional activation or repression of specific target promoters (By similarity). These may include the SERPINE1 and HIV-1 promoters and the SV40 enhancer, to which this protein can bind directly. Plays a role in error-free postreplication repair (PRR) of damaged DNA and maintains genomic stability through acting as a ubiquitin ligase for Lys-63-linked polyubiquitination of chromatin-bound PCNA.

Gene Wiki entry for HLTF Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for HLTF Gene

Genomics for HLTF Gene

Products:

  1. Regulatory Element

Regulatory Elements for HLTF Gene

Enhancers for HLTF Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH03G149042 0.9 Ensembl ENCODE 28.7 +42.9 42872 2.5 HLF JUNB ZNF384 TBX21 ARID3A JUND FOS PRDM1 HLTF HLTF-AS1 GYG1 UBQLN4P1
GH03G149144 1.3 FANTOM5 Ensembl ENCODE dbSUPER 18.7 -59.9 -59871 3.5 GATA3 KLF1 KLF9 ETV6 SPI1 NR2F2 HLTF HLTF-AS1 GYG1 HPS3 GC03M149173
GH03G148990 1.3 ENCODE dbSUPER 15 +94.7 94705 3.1 FOXA2 CREB3L1 ARID4B SIN3A DMAP1 ZBTB7B YY1 ZNF207 FOS ZNF263 HLTF GYG1 HLTF-AS1
GH03G149085 1.1 ENCODE 17.6 +0.5 456 2.2 PKNOX1 CREB3L1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 ZNF766 HLTF HLTF-AS1 GYG1
GH03G149008 1.1 ENCODE dbSUPER 16.6 +75.9 75881 3.5 PKNOX1 FOXA2 ARID4B ZNF48 RAD21 RARA YY1 ELK1 FOS CREM HLTF GYG1 HLTF-AS1
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around HLTF on UCSC Golden Path with GeneCards custom track

Promoters for HLTF Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000159913 254 1401 PKNOX1 CREB3L1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 ZNF766

Transcription factor binding sites by QIAGEN in the HLTF gene promoter:

Genomic Location for HLTF Gene

Chromosome:
3
Start:
149,030,117 bp from pter
End:
149,086,554 bp from pter
Size:
56,438 bases
Orientation:
Minus strand

Genomic View for HLTF Gene

Genes around HLTF on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
HLTF Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for HLTF Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for HLTF Gene

Proteins for HLTF Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for HLTF Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q14527-HLTF_HUMAN
    Recommended name:
    Helicase-like transcription factor
    Protein Accession:
    Q14527
    Secondary Accessions:
    • D3DNH3
    • Q14536
    • Q16051
    • Q7KYJ6
    • Q86YA5
    • Q92652
    • Q96KM9

    Protein attributes for HLTF Gene

    Size:
    1009 amino acids
    Molecular mass:
    113929 Da
    Quaternary structure:
    • Interacts with SP1 and SP3 independently of DNA; the interaction with these transcriptional factors may be required for basal transcription of target genes. Interacts with EGR1; the interaction requires prior binding to DNA and represses c-Rel via a DNA looping mechanism (By similarity). Interacts with GATA4 (By similarity). Interacts with PCNA; the interaction promotes polyubiquitination of PCNA through association with the UBE2B-RAD18 and UBE2V2-UBE2N ubiquitin ligase complexes. Interacts with RAD18, SHPRH, UBE2V2 and UBE2N.
    Miscellaneous:
    • Subject to frequent epigenetic inactivation by promoter methylation in colon cancer.

    Three dimensional structures from OCA and Proteopedia for HLTF Gene

    Alternative splice isoforms for HLTF Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for HLTF Gene

Protein Expression for HLTF Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Selected DME Specific Peptides for HLTF Gene

Q14527:
  • LADDMGLGKT
  • GGVGLNL
  • MGLGKTL
  • LRQICCH
  • HQKQALAW
  • LLLRLRQ

Post-translational modifications for HLTF Gene

  • Ubiquitination at posLast=1212, isoforms=95, posLast=158158, isoforms=2176, isoforms=2216, posLast=258258, posLast=340340, isoforms=2349, isoforms=2355, isoforms=2433, posLast=523523, isoforms=2571, posLast=638638, isoforms=2662, isoforms=2682, isoforms=2952, and posLast=959959
  • Modification sites at PhosphoSitePlus

Other Protein References for HLTF Gene

ENSEMBL proteins:
REFSEQ proteins:

Antibody Products

Domains & Families for HLTF Gene

Gene Families for HLTF Gene

HGNC:

Protein Domains for HLTF Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for HLTF Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q14527

UniProtKB/Swiss-Prot:

HLTF_HUMAN :
  • Belongs to the SNF2/RAD54 helicase family. RAD16 subfamily.
Family:
  • Belongs to the SNF2/RAD54 helicase family. RAD16 subfamily.
genes like me logo Genes that share domains with HLTF: view

Function for HLTF Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line
  7. Flow Cytometry

Molecular function for HLTF Gene

UniProtKB/Swiss-Prot CatalyticActivity:
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine.
UniProtKB/Swiss-Prot Function:
Has both helicase and E3 ubiquitin ligase activities. Possesses intrinsic ATP-dependent nucleosome-remodeling activity; This activity may be required for transcriptional activation or repression of specific target promoters (By similarity). These may include the SERPINE1 and HIV-1 promoters and the SV40 enhancer, to which this protein can bind directly. Plays a role in error-free postreplication repair (PRR) of damaged DNA and maintains genomic stability through acting as a ubiquitin ligase for Lys-63-linked polyubiquitination of chromatin-bound PCNA.

Enzyme Numbers (IUBMB) for HLTF Gene

Gene Ontology (GO) - Molecular Function for HLTF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000978 RNA polymerase II core promoter proximal region sequence-specific DNA binding IEA --
GO:0001077 transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding IEA --
GO:0003676 nucleic acid binding IEA --
GO:0003677 DNA binding TAS 7876228
GO:0003723 RNA binding IDA 22658674
genes like me logo Genes that share ontologies with HLTF: view
genes like me logo Genes that share phenotypes with HLTF: view

Animal Models for HLTF Gene

MGI Knock Outs for HLTF:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Flow Cytometry Products

No data available for Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for HLTF Gene

Localization for HLTF Gene

Subcellular locations from UniProtKB/Swiss-Prot for HLTF Gene

Cytoplasm. Nucleus. Nucleus, nucleolus. Nucleus, nucleoplasm. Note=Nuclear localization is stimulated by progesterone. {ECO:0000250}.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for HLTF gene
Compartment Confidence
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for HLTF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA,TAS --
GO:0005654 nucleoplasm TAS,IDA --
GO:0005730 nucleolus IEA --
GO:0005737 cytoplasm IEA --
GO:0016020 membrane IDA 19946888
genes like me logo Genes that share ontologies with HLTF: view

Pathways & Interactions for HLTF Gene

genes like me logo Genes that share pathways with HLTF: view

Pathways by source for HLTF Gene

1 BioSystems pathway for HLTF Gene

UniProtKB/Swiss-Prot Q14527-HLTF_HUMAN

  • Pathway: Protein modification; protein ubiquitination.

Gene Ontology (GO) - Biological Process for HLTF Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000209 protein polyubiquitination IEA --
GO:0006301 postreplication repair IEA --
GO:0006351 transcription, DNA-templated IEA --
GO:0006355 regulation of transcription, DNA-templated TAS 7876228
GO:0006357 regulation of transcription from RNA polymerase II promoter IEA --
genes like me logo Genes that share ontologies with HLTF: view

No data available for SIGNOR curated interactions for HLTF Gene

Drugs & Compounds for HLTF Gene

Products:

  1. Drug

(1) Drugs for HLTF Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials
genes like me logo Genes that share compounds with HLTF: view

Transcripts for HLTF Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone
  5. Flow Cytometry

mRNA/cDNA for HLTF Gene

(9) REFSEQ mRNAs :
(9) Additional mRNA sequences :
(237) Selected AceView cDNA sequences:
(9) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for HLTF Gene

Helicase-like transcription factor:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for HLTF Gene

ExUns: 1a · 1b · 1c ^ 2 ^ 3 ^ 4 ^ 5 ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17a · 17b ^ 18 ^ 19a · 19b ^ 20a · 20b ^ 21a ·
SP1: - -
SP2: - -
SP3: - -
SP4: -
SP5: -
SP6:

ExUns: 21b ^ 22 ^ 23 ^ 24 ^ 25 ^ 26
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:

Relevant External Links for HLTF Gene

GeneLoc Exon Structure for
HLTF
ECgene alternative splicing isoforms for
HLTF

Expression for HLTF Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for HLTF Gene

mRNA expression in normal human tissues for HLTF Gene
mRNA expression by BioGPS for HLTF GenemRNA expression by GTEx for HLTF Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for HLTF Gene

This gene is overexpressed in Fetal testis (29.1), Testis (8.2), Fetal ovary (7.5), Tonsil (6.8), and Adrenal (6.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for HLTF Gene



Protein tissue co-expression partners for HLTF Gene

NURSA nuclear receptor signaling pathways regulating expression of HLTF Gene:

HLTF

SOURCE GeneReport for Unigene cluster for HLTF Gene:

Hs.3068

mRNA Expression by UniProt/SwissProt for HLTF Gene:

Q14527-HLTF_HUMAN
Tissue specificity: Expressed in brain, heart, kidney, liver, lung, pancreas, placenta and skeletal muscle.

Evidence on tissue expression from TISSUES for HLTF Gene

  • Nervous system(3.9)
genes like me logo Genes that share expression patterns with HLTF: view

Primer Products

No data available for mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for HLTF Gene

Orthologs for HLTF Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for HLTF Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia HLTF 34 35
  • 99.74 (n)
dog
(Canis familiaris)
 Mammalia HLTF 34 35
  • 93.68 (n)
cow
(Bos Taurus)
 Mammalia HLTF 34 35
  • 92.04 (n)
rat
(Rattus norvegicus)
 Mammalia Hltf 34
  • 86.62 (n)
mouse
(Mus musculus)
 Mammalia Hltf 34 16 35
  • 85.71 (n)
oppossum
(Monodelphis domestica)
 Mammalia HLTF 35
  • 81 (a)
 OneToOne
platypus
(Ornithorhynchus anatinus)
 Mammalia HLTF 35
  • 81 (a)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia HLTF 35
  • 65 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia hltf 34
  • 66.56 (n)
African clawed frog
(Xenopus laevis)
 Amphibia Xl.12354 34
zebrafish
(Danio rerio)
 Actinopterygii hltf 34 35
  • 60.32 (n)
rainbow trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.10762 34
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes RAD5 35
  • 23 (a)
 OneToOne
RAD16 37
thale cress
(Arabidopsis thaliana)
 eudicotyledons AT5G05130 34
  • 50.21 (n)
rice
(Oryza sativa)
 Liliopsida Os07g0642400 34
  • 47.52 (n)
bread mold
(Neurospora crassa)
 Ascomycetes NCU07975 34
  • 46.65 (n)
Species where no ortholog for HLTF was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • chicken (Gallus gallus)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • fruit fly (Drosophila melanogaster)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for HLTF Gene

ENSEMBL:
Gene Tree for HLTF (if available)
TreeFam:
Gene Tree for HLTF (if available)

Paralogs for HLTF Gene

Paralogs for HLTF Gene

(2) SIMAP similar genes for HLTF Gene using alignment to 5 proteins:

genes like me logo Genes that share paralogs with HLTF: view

Variants for HLTF Gene

Sequence variations from dbSNP and Humsavar for HLTF Gene

SNP ID Clin Chr 03 pos Sequence Context AA Info Type
rs1000068981 -- 149,050,055(+) ATAAA(A/C)TGCAA intron-variant
rs1000128086 -- 149,057,545(+) GTATG(C/T)GCACA intron-variant
rs1000188918 -- 149,037,100(+) TAGTT(A/T)CAAAT intron-variant
rs1000231412 -- 149,035,815(+) GACAT(A/G)ATCAT intron-variant
rs1000279234 -- 149,082,286(+) ACCCC(A/G)TCTCT intron-variant

Structural Variations from Database of Genomic Variants (DGV) for HLTF Gene

Variant ID Type Subtype PubMed ID
esv1349617 CNV deletion 17803354
esv2726035 CNV deletion 23290073
esv3041777 CNV deletion 24192839
nsv1127997 CNV deletion 24896259
nsv1131735 CNV deletion 24896259
nsv528849 CNV gain 19592680
nsv829752 CNV loss 17160897
nsv829753 CNV gain 17160897

Variation tolerance for HLTF Gene

Residual Variation Intolerance Score: 52.2% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.81; 73.77% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for HLTF Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
HLTF

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for HLTF Gene

Disorders for HLTF Gene

MalaCards: The human disease database

(1) MalaCards diseases for HLTF Gene - From: DISEASES, Novoseek, and GeneCards

Disorder Aliases PubMed IDs
colorectal cancer
  • colorectal cancer, somatic
- elite association - COSMIC cancer census association via MalaCards
Search HLTF in MalaCards View complete list of genes associated with diseases

Relevant External Links for HLTF

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
HLTF
genes like me logo Genes that share disorders with HLTF: view

No data available for UniProtKB/Swiss-Prot and Genatlas for HLTF Gene

Publications for HLTF Gene

  1. Human HLTF functions as a ubiquitin ligase for proliferating cell nuclear antigen polyubiquitination. (PMID: 18316726) Unk I. … Haracska L. (Proc. Natl. Acad. Sci. U.S.A. 2008) 3 4 22 64
  2. Polyubiquitination of proliferating cell nuclear antigen by HLTF and SHPRH prevents genomic instability from stalled replication forks. (PMID: 18719106) Motegi A. … Myung K. (Proc. Natl. Acad. Sci. U.S.A. 2008) 3 4 22 64
  3. HLTF gene silencing in human colon cancer. (PMID: 11904375) Moinova H.R. … Markowitz S.D. (Proc. Natl. Acad. Sci. U.S.A. 2002) 3 4 22 64
  4. Functional interactions between Sp1 or Sp3 and the helicase-like transcription factor mediate basal expression from the human plasminogen activator inhibitor-1 gene. (PMID: 10391891) Ding H. … Belayew A. (J. Biol. Chem. 1999) 3 4 22 64
  5. Developmental regulation of Zbu1, a DNA-binding member of the SWI2/SNF2 family. (PMID: 9126292) Gong X. … Rosenthal N. (Dev. Biol. 1997) 3 4 22 64

Products for HLTF Gene

  • Addgene plasmids for HLTF

Sources for HLTF Gene

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