HLTF helicase like transcription factor [Homo sapiens (human)] - Gene

Summary

Official Symbol: HLTFprovided by HGNC
Official Full Name: helicase like transcription factorprovided by HGNC
Primary source: HGNC:HGNC:11099
See related: Ensembl:ENSG00000071794 MIM:603257; AllianceGenome:HGNC:11099
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: ZBU1; HLTF1; RNF80; HIP116; SNF2L3; HIP116A; SMARCA3
Summary: 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]
Expression: Broad expression in testis (RPKM 29.4), adrenal (RPKM 14.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 3q24

Exon count:: 26

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (149030063..149086533, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (151780777..151837250, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (148747850..148804320, complement)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HLTF resolves G4s and promotes G4-induced replication fork slowing to maintain genome stability.
Title: HLTF resolves G4s and promotes G4-induced replication fork slowing to maintain genome stability.
The helicase-like transcription factor redirects the autophagic flux and restricts human T cell leukemia virus type 1 infection.
Title: The helicase-like transcription factor redirects the autophagic flux and restricts human T cell leukemia virus type 1 infection.
Helicase-like transcription factor-deletion from the tumor microenvironment in a cell line-derived xenograft model of colorectal cancer reprogrammed the human transcriptome-S-nitroso-proteome to promote inflammation and redirect metastasis.
Title: Helicase-like transcription factor-deletion from the tumor microenvironment in a cell line-derived xenograft model of colorectal cancer reprogrammed the human transcriptome-S-nitroso-proteome to promote inflammation and redirect metastasis.
Time for remodeling: SNF2-family DNA translocases in replication fork metabolism and human disease.
Title: Time for remodeling: SNF2-family DNA translocases in replication fork metabolism and human disease.
The Human RAD5 Homologs, HLTF and SHPRH, Have Separate Functions in DNA Damage Tolerance Dependent on The DNA Lesion Type.
Title: The Human RAD5 Homologs, HLTF and SHPRH, Have Separate Functions in DNA Damage Tolerance Dependent on The DNA Lesion Type.
Helicase-Like Transcription Factor HLTF and E3 Ubiquitin Ligase SHPRH Confer DNA Damage Tolerance through Direct Interactions with Proliferating Cell Nuclear Antigen (PCNA).
Title: Helicase-Like Transcription Factor HLTF and E3 Ubiquitin Ligase SHPRH Confer DNA Damage Tolerance through Direct Interactions with Proliferating Cell Nuclear Antigen (PCNA).
HLTF Promotes Fork Reversal, Limiting Replication Stress Resistance and Preventing Multiple Mechanisms of Unrestrained DNA Synthesis.
Title: HLTF Promotes Fork Reversal, Limiting Replication Stress Resistance and Preventing Multiple Mechanisms of Unrestrained DNA Synthesis.
HIV-1 Vpr counteracts HLTF-mediated restriction of HIV-1 infection in T cells.
Title: HIV-1 Vpr counteracts HLTF-mediated restriction of HIV-1 infection in T cells.
Molecular details of Rad5/HLTF recruitment and function at replication forks have emerged. [review]
Title: Post-replication repair: Rad5/HLTF regulation, activity on undamaged templates, and relationship to cancer.
HLTF depletion suppresses fork degradation in FANCJ-deficient cells. Combined loss of HLTF and FANCJ causes severe replication stress.
Title: Opposing Roles of FANCJ and HLTF Protect Forks and Restrain Replication during Stress.

Submit: New GeneRIF Correction See all GeneRIFs (48)

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Nef	nef	HIV-1 Nef upregulates the expression of helicase-like transcription factor (HLTF-1) in HeLa cells	PubMed
Vpr	vpr	HIV-1 Vpr downregulates HLTF in a DCAF1-dependent manner in HeLa, Jurkat T and primary T cells and primary macrophages as shown through DCAF1 siRNA knockdown	PubMed
	vpr	HIV-1 Vpr specifically binds HLTF and recruits it to the DCAF1-DDB1 module of the CRL4-DCAF1 E3 complex, thereby directing HLTF for degradation by proteasome	PubMed
	vpr	HIV-1 Vpr recruits HLTF for proteasome-dependent degradation via CRL4-DCAF1 E3	PubMed
	vpr	HIV-1 Vpr downregulates HLTF (CEM.SS-iH1.Vpr and U2OS-iH1.Vpr cells), a post-replication DNA helicase, independently of cell cycle position and of MUS81 depletion and independent of UNG2, yet all three require DCAF1	PubMed
	vpr	HIV-1 Vpr downregulates HLTF in infected HeLa, T cells and primary macrophages in a proteasome-dependent manner (in HeLa cells) and independent of Vpr-mediated G2 arrest in HeLa cells	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D3S3493 (e-PCR)
- UniSTS:154134

SHGC-77432 (e-PCR)
- UniSTS:69400

SHGC-12604 (e-PCR)
- UniSTS:36124

STS-L34673 (e-PCR)
- UniSTS:47492

D3S2876E (e-PCR)
- UniSTS:14492

G19843 (e-PCR)
- UniSTS:60863

A002A11 (e-PCR)
- UniSTS:60864

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP-dependent activity, acting on DNA	IBA Inferred from Biological aspect of Ancestor more info
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables RNA binding	HDA more info	PubMed
enables helicase activity	IEA Inferred from Electronic Annotation more info
enables hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ubiquitin protein ligase activity	EXP Inferred from Experiment more info	PubMed
enables ubiquitin protein ligase binding	IDA Inferred from Direct Assay more info	PubMed
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in DNA repair	IBA Inferred from Biological aspect of Ancestor more info
involved_in chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in mRNA transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in protein ubiquitination	IEA Inferred from Electronic Annotation more info
involved_in protein ubiquitination	TAS Traceable Author Statement more info
involved_in regulation of neurogenesis	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
part_of RNA polymerase II transcription regulator complex	EXP Inferred from Experiment more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in membrane	HDA more info	PubMed
located_in nuclear matrix	NAS Non-traceable Author Statement more info	PubMed
located_in nucleolus	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in plasma membrane	NAS Non-traceable Author Statement more info	PubMed

General protein information

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Preferred Names: helicase-like transcription factor

Names: DNA-binding protein/plasminogen activator inhibitor-1 regulator; RING finger protein 80; RING-type E3 ubiquitin transferase HLTF; SNF2-like 3; SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 3; SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A member 3; sucrose nonfermenting protein 2-like 3; sucrose nonfermenting-like 3

NP_001305863.1

EC 2.3.2.27

NP_001305864.1

EC 2.3.2.27

NP_003062.2

EC 2.3.2.27

NP_620636.1

EC 2.3.2.27

XP_011511393.1

EC 2.3.2.27

XP_011511394.1

EC 2.3.2.27

XP_011511395.1

EC 2.3.2.27

XP_016862567.1

EC 2.3.2.27

XP_016862568.1

EC 2.3.2.27

XP_054203600.1

EC 2.3.2.27

XP_054203601.1

EC 2.3.2.27

XP_054203602.1

EC 2.3.2.27

XP_054203603.1

EC 2.3.2.27

XP_054203604.1

EC 2.3.2.27

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)

NM_001318934.2 → NP_001305863.1 helicase-like transcription factor isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate splice site in the central coding region compared to variant 1. The encoded isoform (2) is shorter than isoform 1.

Source sequence(s)

AC021059, BC044659

Consensus CDS

CCDS82856.1

UniProtKB/TrEMBL

A0A0C4DGA6, A8K5B6

Related

ENSP00000420745.1, ENST00000465259.5

Conserved Domains (6) summary

smart00487
Location:238 → 320

DEXDc; DEAD-like helicases superfamily

cd00046
Location:477 → 587

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

cd00162
Location:758 → 803

RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

pfam00176
Location:471 → 721

SNF2_N; SNF2 family N-terminal domain

pfam00271
Location:831 → 949

Helicase_C; Helicase conserved C-terminal domain

pfam08797
Location:60 → 155

HIRAN; HIRAN domain
NM_001318935.2 → NP_001305864.1 helicase-like transcription factor isoform 1

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 3' UTR compared to variant 1. Variants 1, 2 and 3 encode the same isoform (1).

Source sequence(s)

AC021059, AK291231

Consensus CDS

CCDS33875.1

UniProtKB/Swiss-Prot

D3DNH3, Q14527, Q14536, Q16051, Q7KYJ6, Q86YA5, Q92652, Q96KM9

UniProtKB/TrEMBL

A8K5B6

Related

ENSP00000420429.1, ENST00000494055.5

Conserved Domains (6) summary

smart00487
Location:238 → 320

DEXDc; DEAD-like helicases superfamily

cd00046
Location:478 → 588

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

cd00162
Location:759 → 804

RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

pfam00176
Location:472 → 722

SNF2_N; SNF2 family N-terminal domain

pfam00271
Location:832 → 950

Helicase_C; Helicase conserved C-terminal domain

pfam08797
Location:60 → 155

HIRAN; HIRAN domain
NM_003071.4 → NP_003062.2 helicase-like transcription factor isoform 1

See identical proteins and their annotated locations for NP_003062.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript. Variants 1, 2 and 3 encode the same isoform (1).

Source sequence(s)

AC021059, AI971472, BC030976, BC044659, L34673

Consensus CDS

CCDS33875.1

UniProtKB/Swiss-Prot

D3DNH3, Q14527, Q14536, Q16051, Q7KYJ6, Q86YA5, Q92652, Q96KM9

UniProtKB/TrEMBL

A8K5B6

Related

ENSP00000308944.5, ENST00000310053.10

Conserved Domains (6) summary

smart00487
Location:238 → 320

DEXDc; DEAD-like helicases superfamily

cd00046
Location:478 → 588

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

cd00162
Location:759 → 804

RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

pfam00176
Location:472 → 722

SNF2_N; SNF2 family N-terminal domain

pfam00271
Location:832 → 950

Helicase_C; Helicase conserved C-terminal domain

pfam08797
Location:60 → 155

HIRAN; HIRAN domain
NM_139048.3 → NP_620636.1 helicase-like transcription factor isoform 1

See identical proteins and their annotated locations for NP_620636.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 3' UTR compared to variant 1. Variants 1, 2 and 3 encode the same isoform (1).

Source sequence(s)

AC021059, AI971472, BC030976, L34673

Consensus CDS

CCDS33875.1

UniProtKB/Swiss-Prot

D3DNH3, Q14527, Q14536, Q16051, Q7KYJ6, Q86YA5, Q92652, Q96KM9

UniProtKB/TrEMBL

A8K5B6

Related

ENSP00000376644.2, ENST00000392912.6

Conserved Domains (6) summary

smart00487
Location:238 → 320

DEXDc; DEAD-like helicases superfamily

cd00046
Location:478 → 588

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

cd00162
Location:759 → 804

RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

pfam00176
Location:472 → 722

SNF2_N; SNF2 family N-terminal domain

pfam00271
Location:832 → 950

Helicase_C; Helicase conserved C-terminal domain

pfam08797
Location:60 → 155

HIRAN; HIRAN domain

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_000003.12 Reference GRCh38.p14 Primary Assembly

Range

149030063..149086533 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017007079.3 → XP_016862568.1 helicase-like transcription factor isoform X3

UniProtKB/TrEMBL

A0A0C4DGA6, A8K5B6

Conserved Domains (6) summary

smart00487
Location:238 → 320

DEXDc; DEAD-like helicases superfamily

cd00046
Location:477 → 587

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

cd00162
Location:758 → 803

RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

pfam00176
Location:471 → 721

SNF2_N; SNF2 family N-terminal domain

pfam00271
Location:831 → 949

Helicase_C; Helicase conserved C-terminal domain

pfam08797
Location:60 → 155

HIRAN; HIRAN domain
XM_017007078.2 → XP_016862567.1 helicase-like transcription factor isoform X2

UniProtKB/TrEMBL

A8K5B6

Conserved Domains (6) summary

smart00487
Location:238 → 320

DEXDc; DEAD-like helicases superfamily

cd00046
Location:477 → 587

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

cd00162
Location:762 → 807

RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

pfam00176
Location:471 → 721

SNF2_N; SNF2 family N-terminal domain

pfam00271
Location:835 → 953

Helicase_C; Helicase conserved C-terminal domain

pfam08797
Location:60 → 155

HIRAN; HIRAN domain
XM_011513093.3 → XP_011511395.1 helicase-like transcription factor isoform X2

UniProtKB/TrEMBL

A8K5B6

Conserved Domains (6) summary

smart00487
Location:238 → 320

DEXDc; DEAD-like helicases superfamily

cd00046
Location:477 → 587

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

cd00162
Location:762 → 807

RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

pfam00176
Location:471 → 721

SNF2_N; SNF2 family N-terminal domain

pfam00271
Location:835 → 953

Helicase_C; Helicase conserved C-terminal domain

pfam08797
Location:60 → 155

HIRAN; HIRAN domain
XM_011513092.3 → XP_011511394.1 helicase-like transcription factor isoform X1

See identical proteins and their annotated locations for XP_011511394.1

UniProtKB/TrEMBL

A8K5B6

Conserved Domains (6) summary

smart00487
Location:238 → 320

DEXDc; DEAD-like helicases superfamily

cd00046
Location:478 → 588

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

cd00162
Location:763 → 808

RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

pfam00176
Location:472 → 722

SNF2_N; SNF2 family N-terminal domain

pfam00271
Location:836 → 954

Helicase_C; Helicase conserved C-terminal domain

pfam08797
Location:60 → 155

HIRAN; HIRAN domain
XM_011513091.3 → XP_011511393.1 helicase-like transcription factor isoform X1

See identical proteins and their annotated locations for XP_011511393.1

UniProtKB/TrEMBL

A8K5B6

Conserved Domains (6) summary

smart00487
Location:238 → 320

DEXDc; DEAD-like helicases superfamily

cd00046
Location:478 → 588

DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

cd00162
Location:763 → 808

RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...

pfam00176
Location:472 → 722

SNF2_N; SNF2 family N-terminal domain

pfam00271
Location:836 → 954

Helicase_C; Helicase conserved C-terminal domain

pfam08797
Location:60 → 155

HIRAN; HIRAN domain

Alternate T2T-CHM13v2.0

Genomic

NC_060927.1 Alternate T2T-CHM13v2.0

Range

151780777..151837250 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054347629.1 → XP_054203604.1 helicase-like transcription factor isoform X3

UniProtKB/TrEMBL

A0A0C4DGA6, A8K5B6
XM_054347628.1 → XP_054203603.1 helicase-like transcription factor isoform X2

UniProtKB/TrEMBL

A8K5B6
XM_054347627.1 → XP_054203602.1 helicase-like transcription factor isoform X2

UniProtKB/TrEMBL

A8K5B6
XM_054347626.1 → XP_054203601.1 helicase-like transcription factor isoform X1

UniProtKB/TrEMBL

A8K5B6
XM_054347625.1 → XP_054203600.1 helicase-like transcription factor isoform X1

UniProtKB/TrEMBL

A8K5B6