HDGF heparin binding growth factor [Homo sapiens (human)] - Gene

Summary

Official Symbol: HDGFprovided by HGNC
Official Full Name: heparin binding growth factorprovided by HGNC
Primary source: HGNC:HGNC:4856
See related: Ensembl:ENSG00000143321 MIM:600339; AllianceGenome:HGNC:4856
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: HMG1L2
Summary: This gene encodes a member of the hepatoma-derived growth factor family. The encoded protein has mitogenic and DNA-binding activity and may play a role in cellular proliferation and differentiation. High levels of expression of this gene enhance the growth of many tumors. This gene was thought initially to be located on chromosome X; however, that location has been determined to correspond to a related pseudogene. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Jan 2016]
Expression: Ubiquitous expression in bone marrow (RPKM 90.4), liver (RPKM 48.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1q23.1

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (156742107..156767366, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (155878940..155904217, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (156711899..156722240, complement)

Chromosome 1 - NC_000001.11 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: 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?

The m6A reader IGF2BP2 promotes ESCC progression by stabilizing HDGF mRNA.
Title: The m6A reader IGF2BP2 promotes ESCC progression by stabilizing HDGF mRNA.
Binding Behavior of Human Hepatoma-Derived Growth Factor on SMYD1.
Title: Binding Behavior of Human Hepatoma-Derived Growth Factor on SMYD1.
[miR-29a-3p Targets Hepatoma-Derived Growth Factor to Inhibit the Proliferation and Promote the Apoptosis of E6-1 Cells].
Title: [miR-29a-3p Targets Hepatoma-Derived Growth Factor to Inhibit the Proliferation and Promote the Apoptosis of E6-1 Cells].
Extracellular vesicle proteomic analysis leads to the discovery of HDGF as a new factor in multiple myeloma biology.
Title: Extracellular vesicle proteomic analysis leads to the discovery of HDGF as a new factor in multiple myeloma biology.
Specificity protein 1-induced serine peptidase inhibitor, Kunitz Type 1 antisense RNA1 regulates colorectal cancer cell proliferation, migration, invasion and apoptosis through targeting heparin binding growth factor via sponging microRNA-214.
Title: Specificity protein 1-induced serine peptidase inhibitor, Kunitz Type 1 antisense RNA1 regulates colorectal cancer cell proliferation, migration, invasion and apoptosis through targeting heparin binding growth factor via sponging microRNA-214.
miR-4323 targets hepatoma-derived growth factor (HDGF) to suppress colorectal cancer cell proliferation.
Title: miR-4323 targets hepatoma-derived growth factor (HDGF) to suppress colorectal cancer cell proliferation.
Recurrent co-alteration of HDGF and SETDB1 on chromosome 1q drives cutaneous melanoma progression and poor prognosis.
Title: Recurrent co-alteration of HDGF and SETDB1 on chromosome 1q drives cutaneous melanoma progression and poor prognosis.
Exosomal lncRNA HEIH promotes cisplatin resistance in tongue squamous cell carcinoma via targeting miR-3619-5p/HDGF axis.
Title: Exosomal lncRNA HEIH promotes cisplatin resistance in tongue squamous cell carcinoma via targeting miR-3619-5p/HDGF axis.
A novel HDGF-ALCAM axis promotes the metastasis of Ewing sarcoma via regulating the GTPases signaling pathway.
Title: A novel HDGF-ALCAM axis promotes the metastasis of Ewing sarcoma via regulating the GTPases signaling pathway.
Long intergenic noncoding RNA LINC01232 contributes to esophageal squamous cell carcinoma progression by sequestering microRNA6543p and consequently promoting hepatomaderived growth factor expression.
Title: Long intergenic non‑coding RNA LINC01232 contributes to esophageal squamous cell carcinoma progression by sequestering microRNA‑654‑3p and consequently promoting hepatoma‑derived growth factor expression.

Submit: New GeneRIF Correction See all GeneRIFs (81)

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

EBI GWAS Catalog

Description
Discovery and refinement of loci associated with lipid levels. 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)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Vpr	vpr	A stable-isotope labeling by amino acids in cell culture coupled with mass spectrometry-based proteomics identifies downregulation of hepatoma-derived growth factor (HDGF) expression by HIV-1 Vpr in Vpr transduced macrophages	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

RH17641 (e-PCR)
- UniSTS:17480

SHGC-12542 (e-PCR)
- UniSTS:80764

SHGC-132090 (e-PCR)
- UniSTS:170639

RH11678 (e-PCR)
- UniSTS:33975

SHGC-132399 (e-PCR)
- UniSTS:181944

SHGC-2664 (e-PCR)
- UniSTS:14543

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables RNA binding	HDA more info	PubMed
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IEA Inferred from Electronic Annotation more info
enables actin binding	IDA Inferred from Direct Assay more info	PubMed
enables growth factor activity	IEA Inferred from Electronic Annotation more info
NOT enables heparin binding	IDA Inferred from Direct Assay more info	PubMed
enables heparin binding	IDA Inferred from Direct Assay more info	PubMed
enables heparin binding	IEA Inferred from Electronic Annotation more info
enables nucleotide binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transcription corepressor activity	IDA Inferred from Direct Assay more info	PubMed
enables transcription corepressor binding	IPI Inferred from Physical Interaction more info	PubMed
enables tubulin binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
NOT involved_in positive regulation of cell division	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of cell division	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in protein localization to nucleus	IEA Inferred from Electronic Annotation more info
involved_in signal transduction	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in collagen-containing extracellular matrix	HDA more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in extracellular region	HDA more info	PubMed
located_in extracellular space	HDA more info	PubMed
located_in extracellular space	IDA Inferred from Direct Assay more info	PubMed
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 nucleus	IDA Inferred from Direct Assay more info	PubMed
part_of transcription repressor complex	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: hepatoma-derived growth factor

Names: epididymis secretory sperm binding protein; hepatoma derived growth factor; high mobility group protein 1-like 2

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_001126050.2 → NP_001119522.1 hepatoma-derived growth factor isoform b

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs uses an alternate in-frame splice junction compared to variant 4. The resulting isoform (b) has the same N- and C-termini but is shorter compared to isoform d.

Source sequence(s)

AL590666

Consensus CDS

CCDS44247.1

UniProtKB/TrEMBL

B7Z958

Related

ENSP00000357189.5, ENST00000368206.5

Conserved Domains (1) summary

cl02554
Location:40 → 108

PWWP; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins ...
NM_001126051.1 → NP_001119523.1 hepatoma-derived growth factor isoform c

See identical proteins and their annotated locations for NP_001119523.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence and uses an alternate in-frame splice junction compared to variant 4. The resulting isoform (c) has a shorter and distinct N-terminus and lacks an alternate internal segment compared to isoform d.

Source sequence(s)

AL590666, D16431, DA207052, DA367806, F36780

Consensus CDS

CCDS44248.1

UniProtKB/TrEMBL

B7Z958

Related

ENSP00000357192.5, ENST00000368209.9

Conserved Domains (1) summary

cl02554
Location:21 → 85

PWWP; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins ...
NM_001319186.2 → NP_001306115.1 hepatoma-derived growth factor isoform d

Status: REVIEWED

Description

Transcript Variant: This variant (4) encodes the longest isoform (d).

Source sequence(s)

AL590666

UniProtKB/TrEMBL

B7Z958

Conserved Domains (1) summary

cl02554
Location:40 → 108

PWWP; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins ...
NM_001319187.2 → NP_001306116.1 hepatoma-derived growth factor isoform e

Status: REVIEWED

Description

Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence and uses an alternate in-frame splice junction compared to variant 4. The resulting isoform (e) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform d. Variants 5 and 6 both encode the same isoform (e).

Source sequence(s)

AL590666

UniProtKB/TrEMBL

A8K8G0, B7Z958

Conserved Domains (1) summary

cl02554
Location:7 → 60

PWWP; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins ...
NM_001319188.2 → NP_001306117.1 hepatoma-derived growth factor isoform e

Status: REVIEWED

Description

Transcript Variant: This variant (6) differs in the 5' UTR and coding sequence and uses an alternate in-frame splice junction compared to variant 4. The resulting isoform (e) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform d. Variants 5 and 6 both encode the same isoform (e).

Source sequence(s)

AL590666

UniProtKB/TrEMBL

A8K8G0, B7Z958

Conserved Domains (1) summary

cl02554
Location:7 → 60

PWWP; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins ...
NM_004494.3 → NP_004485.1 hepatoma-derived growth factor isoform a

See identical proteins and their annotated locations for NP_004485.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) differs in the 5' UTR and coding sequence and uses an alternate in-frame splice junction compared to variant 4. The resulting isoform (a) has a shorter and distinct N-terminus and lacks an alternate internal segment compared to isoform d.

Source sequence(s)

AL590666

Consensus CDS

CCDS1156.1

UniProtKB/Swiss-Prot

B3KU21, D3DVC9, P51858, Q5SZ07, Q5SZ08, Q5SZ09

UniProtKB/TrEMBL

A0A384NPW1, B2RDE8

Related

ENSP00000349878.5, ENST00000357325.10

Conserved Domains (1) summary

cd05834
Location:8 → 92

HDGF_related; The PWWP domain is an essential part of the Hepatoma Derived Growth Factor (HDGF) family of proteins, and is necessary for DNA binding by HDGF. This family of endogenous nuclear-targeted mitogens includes HRP (HDGF-related proteins 1, 2, 3, 4, or HPR1, ...

RNA

NR_135008.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (7) contains an alternate exon and uses an alternate splice junction compared to variant 4. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AL590666

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_000001.11 Reference GRCh38.p14 Primary Assembly

Range

156742107..156767366 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047418832.1 → XP_047274788.1 hepatoma-derived growth factor isoform X1

UniProtKB/TrEMBL

A8K8G0
XM_047418831.1 → XP_047274787.1 hepatoma-derived growth factor isoform X1

UniProtKB/TrEMBL

A8K8G0

Related

ENST00000465180.5
XM_047418833.1 → XP_047274789.1 hepatoma-derived growth factor isoform X1

UniProtKB/TrEMBL

A8K8G0
XM_011509455.3 → XP_011507757.1 hepatoma-derived growth factor isoform X1

See identical proteins and their annotated locations for XP_011507757.1

UniProtKB/TrEMBL

A8K8G0, B7Z958

Conserved Domains (1) summary

cl02554
Location:7 → 60

PWWP; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins ...
XM_011509454.3 → XP_011507756.1 hepatoma-derived growth factor isoform X1

See identical proteins and their annotated locations for XP_011507756.1

UniProtKB/TrEMBL

A8K8G0, B7Z958

Conserved Domains (1) summary

cl02554
Location:7 → 60

PWWP; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins ...
XM_011509453.3 → XP_011507755.2 hepatoma-derived growth factor isoform X1

UniProtKB/TrEMBL

A8K8G0, B7Z958

Conserved Domains (1) summary

cl02554
Location:7 → 60

PWWP; The PWWP domain, named for a conserved Pro-Trp-Trp-Pro motif, is a small domain consisting of 100-150 amino acids. The PWWP domain is found in numerous proteins that are involved in cell division, growth and differentiation. Most PWWP-domain proteins ...

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

155878940..155904217 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054336208.1 → XP_054192183.1 hepatoma-derived growth factor isoform X1

UniProtKB/TrEMBL

A8K8G0
XM_054336207.1 → XP_054192182.1 hepatoma-derived growth factor isoform X1

UniProtKB/TrEMBL

A8K8G0
XM_054336209.1 → XP_054192184.1 hepatoma-derived growth factor isoform X1

UniProtKB/TrEMBL

A8K8G0
XM_054336205.1 → XP_054192180.1 hepatoma-derived growth factor isoform X1

UniProtKB/TrEMBL

A8K8G0
XM_054336206.1 → XP_054192181.1 hepatoma-derived growth factor isoform X1

UniProtKB/TrEMBL

A8K8G0
XM_054336204.1 → XP_054192179.1 hepatoma-derived growth factor isoform X1

UniProtKB/TrEMBL

A8K8G0