Hdgfl2 HDGF like 2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Hdgfl2provided by RGD
Official Full Name: HDGF like 2provided by RGD
Primary source: RGD:621013
See related: Ensembl:ENSRNOG00000049142 AllianceGenome:RGD:621013
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: Hdgf2; Hdgfrp2
Summary: Predicted to enable chromatin binding activity; double-stranded DNA binding activity; and transcription coregulator activity. Predicted to be involved in positive regulation of cell growth and regulation of transcription by RNA polymerase II. Predicted to be active in nucleus. Orthologous to human HDGFL2 (HDGF like 2). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Thymus (RPKM 144.0), Brain (RPKM 133.0) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 9q11

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	9	NC_086027.1 (996687..1016352)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	9	NC_051344.1 (909581..929195)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	9	NC_005108.4 (10972342..10991938, complement)

Chromosome 9 - NC_086027.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HDGF-2 expression was significantly upregulated in the embryonic spinal cord and injured spinal cord.
Title: Hepatoma-derived growth factor-2 is highly expressed during development and in spinal cord injury.
HRP-2 was strongly expressed in neurons, astrocytes and oligodendrocytes in the thalamus, prefrontal and parietal cortex, neurohypophysis, and the cerebellum.
Title: Expression of hepatoma-derived growth factor family members in the adult central nervous system.

Submit: New GeneRIF Correction

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables H3K27me3 modified histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables H3K27me3 modified histone binding	IEA Inferred from Electronic Annotation more info
enables H3K27me3 modified histone binding	ISO Inferred from Sequence Orthology more info
enables H3K27me3 modified histone binding	ISS Inferred from Sequence or Structural Similarity more info
enables H3K9me3 modified histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables H3K9me3 modified histone binding	IEA Inferred from Electronic Annotation more info
enables H3K9me3 modified histone binding	ISO Inferred from Sequence Orthology more info
enables H3K9me3 modified histone binding	ISS Inferred from Sequence or Structural Similarity more info
NOT enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables chromatin binding	ISO Inferred from Sequence Orthology more info
enables histone reader activity	IEA Inferred from Electronic Annotation more info
enables histone reader activity	ISO Inferred from Sequence Orthology more info
enables methylated histone binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in DNA recombination	IEA Inferred from Electronic Annotation more info
involved_in DNA repair	IEA Inferred from Electronic Annotation more info
involved_in DNA repair-dependent chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in DNA repair-dependent chromatin remodeling	ISO Inferred from Sequence Orthology more info
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in muscle cell differentiation	IEA Inferred from Electronic Annotation more info
involved_in muscle cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in muscle organ development	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of cell growth	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of cell growth	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cell growth	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of double-strand break repair via homologous recombination	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of double-strand break repair via homologous recombination	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of double-strand break repair via homologous recombination	ISS Inferred from Sequence or Structural Similarity more info
involved_in skeletal muscle tissue regeneration	IEA Inferred from Electronic Annotation more info
involved_in skeletal muscle tissue regeneration	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IEA Inferred from Electronic Annotation 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
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: hepatoma-derived growth factor-related protein 2

Names: HDGF-3; HRP-2; hepatoma-derived growth factor 3

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_133548.1 → NP_598232.1 hepatoma-derived growth factor-related protein 2

See identical proteins and their annotated locations for NP_598232.1

Status: PROVISIONAL

Source sequence(s)

AF355102

UniProtKB/Swiss-Prot

Q5PPH2, Q68G63, Q925G1

UniProtKB/TrEMBL

A6KR02

Conserved Domains (2) summary

cd05834
Location:3 → 87

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, ...

pfam11467
Location:468 → 552

LEDGF; Lens epithelium-derived growth factor (LEDGF)

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086027.1 Reference GRCr8

Range

996687..1016352

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006244289.5 → XP_006244351.1 hepatoma-derived growth factor-related protein 2 isoform X1

UniProtKB/Swiss-Prot

Q5PPH2, Q68G63, Q925G1

UniProtKB/TrEMBL

A0A8L2QVL5, A6KR02

Related

ENSRNOP00000064555.2

Conserved Domains (2) summary

cd05834
Location:3 → 87

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, ...

pfam11467
Location:477 → 561

LEDGF; Lens epithelium-derived growth factor (LEDGF)
XM_006244290.5 → XP_006244352.1 hepatoma-derived growth factor-related protein 2 isoform X2

UniProtKB/Swiss-Prot

Q5PPH2, Q68G63, Q925G1

UniProtKB/TrEMBL

A6KR02

Conserved Domains (2) summary

cd05834
Location:3 → 87

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, ...

pfam11467
Location:477 → 561

LEDGF; Lens epithelium-derived growth factor (LEDGF)
XM_006244291.5 → XP_006244353.1 hepatoma-derived growth factor-related protein 2 isoform X3

See identical proteins and their annotated locations for XP_006244353.1

UniProtKB/Swiss-Prot

Q5PPH2, Q68G63, Q925G1

UniProtKB/TrEMBL

A6KR02

Related

ENSRNOP00000070603.2

Conserved Domains (2) summary

cd05834
Location:3 → 87

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, ...

pfam11467
Location:468 → 552

LEDGF; Lens epithelium-derived growth factor (LEDGF)
XM_039082995.2 → XP_038938923.1 hepatoma-derived growth factor-related protein 2 isoform X7

UniProtKB/TrEMBL

A6KR05

Conserved Domains (1) summary

cd05834
Location:3 → 87

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, ...
XM_063266617.1 → XP_063122687.1 hepatoma-derived growth factor-related protein 2 isoform X4
XM_063266619.1 → XP_063122689.1 hepatoma-derived growth factor-related protein 2 isoform X6
XM_063266618.1 → XP_063122688.1 hepatoma-derived growth factor-related protein 2 isoform X5

UniProtKB/TrEMBL

A6KR04