Chd5 chromodomain helicase DNA binding protein 5 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Chd5provided by RGD
Official Full Name: chromodomain helicase DNA binding protein 5provided by RGD
Primary source: RGD:1582725
See related: EnsemblRapid:ENSRNOG00000011268 AllianceGenome:RGD:1582725
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: CHD-5
Summary: Enables chromatin binding activity. Involved in transcription by RNA polymerase II. Located in chromatin and nucleus. Orthologous to human CHD5 (chromodomain helicase DNA binding protein 5). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Brain (RPKM 123.5) and Testes (RPKM 57.0) See more
Orthologs: human mouse all
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Genomic context

Location:: 5q36

Exon count:: 43

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	5	NC_086023.1 (168130851..168181705)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	5	NC_051340.1 (162848273..162898997)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	5	NC_005104.4 (169519212..169572059)

Chromosome 5 - NC_086023.1 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?

CHD5 regulates expression of neuronal genes, cell cycle genes and remodeling genes, and is linked to regulation of genes implicated in aging and Alzheimer's disease.
Title: CHD5, a brain-specific paralog of Mi2 chromatin remodeling enzymes, regulates expression of neuronal genes.

Submit: New GeneRIF Correction

General gene information

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Markers

AU046936 (e-PCR)
- UniSTS:111001

D5S619 (e-PCR), detects polymorphism
- UniSTS:12022

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IBA Inferred from Biological aspect of Ancestor more info
enables ATP-dependent H2AZ histone chaperone activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent H3-H4 histone complex chaperone activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent chromatin remodeler activity	IBA Inferred from Biological aspect of Ancestor more info
enables DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA clamp loader activity	IEA Inferred from Electronic Annotation 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 chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
enables chromatin binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin extrusion motor activity	IEA Inferred from Electronic Annotation more info
enables cohesin loader activity	IEA Inferred from Electronic Annotation more info
enables double-stranded DNA helicase activity	IEA Inferred from Electronic Annotation more info
enables forked DNA-dependent helicase activity	IEA Inferred from Electronic Annotation more info
enables four-way junction helicase activity	IEA Inferred from Electronic Annotation more info
enables helicase activity	IEA Inferred from Electronic Annotation more info
enables histone binding	IBA Inferred from Biological aspect of Ancestor more info
enables histone binding	ISO Inferred from Sequence Orthology more info
enables histone deacetylase binding	ISO Inferred from Sequence Orthology more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables single-stranded 3'-5' DNA helicase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in DNA duplex unwinding	IEA Inferred from Electronic Annotation more info
involved_in biological_process	ND No biological Data available more info
involved_in cerebral cortex neuron differentiation	ISO Inferred from Sequence Orthology more info
involved_in cerebral cortex neuron differentiation	ISS Inferred from Sequence or Structural Similarity more info
involved_in chromatin looping	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	ISO Inferred from Sequence Orthology more info
involved_in chromatin remodeling	ISS Inferred from Sequence or Structural Similarity more info
involved_in negative regulation of cell population proliferation	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of signal transduction by p53 class mediator	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of signal transduction by p53 class mediator	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of cell differentiation	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in sperm DNA condensation	ISO Inferred from Sequence Orthology more info
involved_in sperm DNA condensation	ISS Inferred from Sequence or Structural Similarity more info
involved_in transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of NuRD complex	IBA Inferred from Biological aspect of Ancestor more info
part_of NuRD complex	ISO Inferred from Sequence Orthology more info
part_of NuRD complex	ISS Inferred from Sequence or Structural Similarity more info
located_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in chromatin	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in heterochromatin	ISO Inferred from Sequence Orthology more info
located_in heterochromatin	ISS Inferred from Sequence or Structural Similarity more info
located_in nuclear speck	IEA Inferred from Electronic Annotation more info
located_in nuclear speck	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology 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

General protein information

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Preferred Names: chromodomain-helicase-DNA-binding protein 5

Names: ATP-dependent helicase CHD5

NP_001258155.1

EC 3.6.4.12

XP_017449128.1

EC 3.6.4.12

XP_017449129.1

EC 3.6.4.12

XP_017449130.1

EC 3.6.4.12

XP_017449131.1

EC 3.6.4.12

XP_017449132.1

EC 3.6.4.12

XP_017449133.1

EC 3.6.4.12

XP_017449134.1

EC 3.6.4.12

XP_017449135.1

EC 3.6.4.12

XP_017449136.1

EC 3.6.4.12

XP_017449137.1

EC 3.6.4.12

XP_017449138.1

EC 3.6.4.12

XP_038966741.1

EC 3.6.4.12

XP_038966743.1

EC 3.6.4.12

XP_063144525.1

EC 3.6.4.12

XP_063144527.1

EC 3.6.4.12

XP_063144528.1

EC 3.6.4.12

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_001271226.2 → NP_001258155.1 chromodomain-helicase-DNA-binding protein 5

Status: VALIDATED

Source sequence(s)

JAXUCZ010000005

UniProtKB/Swiss-Prot

D3ZD32

Related

ENSRNOP00000087017.1, ENSRNOT00000112715.2

Conserved Domains (11) summary

smart00298
Location:590 → 623

CHROMO; Chromatin organization modifier domain

cd00046
Location:718 → 876

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.

cd15531
Location:343 → 385

PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins

cd15532
Location:416 → 458

PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins

pfam00176
Location:701 → 997

SNF2_N; SNF2 family N-terminal domain

pfam00271
Location:1021 → 1136

Helicase_C; Helicase conserved C-terminal domain

pfam06375
Location:196 → 296

BLVR; Bovine leukaemia virus receptor (BLVR)

pfam06461
Location:1386 → 1527

DUF1086; Domain of Unknown Function (DUF1086)

pfam06465
Location:1296 → 1356

DUF1087; Domain of Unknown Function (DUF1087)

pfam08073
Location:149 → 198

CHDNT; CHDNT (NUC034) domain

pfam08074
Location:1726 → 1897

CHDCT2; CHDCT2 (NUC038) domain

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_086023.1 Reference GRCr8

Range

168130851..168181705

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017593639.3 → XP_017449128.1 chromodomain-helicase-DNA-binding protein 5 isoform X1

UniProtKB/Swiss-Prot

D3ZD32
XM_017593647.3 → XP_017449136.1 chromodomain-helicase-DNA-binding protein 5 isoform X8

UniProtKB/Swiss-Prot

D3ZD32

UniProtKB/TrEMBL

A0A8I6A737

Related

ENSRNOP00000086830.1, ENSRNOT00000101697.2
XM_017593648.3 → XP_017449137.1 chromodomain-helicase-DNA-binding protein 5 isoform X11

UniProtKB/Swiss-Prot

D3ZD32
XM_017593649.3 → XP_017449138.1 chromodomain-helicase-DNA-binding protein 5 isoform X12

UniProtKB/Swiss-Prot

D3ZD32

Related

ENSRNOP00000099286.1, ENSRNOT00000170038.1
XM_017593640.3 → XP_017449129.1 chromodomain-helicase-DNA-binding protein 5 isoform X2

UniProtKB/Swiss-Prot

D3ZD32
XM_063288457.1 → XP_063144527.1 chromodomain-helicase-DNA-binding protein 5 isoform X13

UniProtKB/Swiss-Prot

D3ZD32
XM_017593642.3 → XP_017449131.1 chromodomain-helicase-DNA-binding protein 5 isoform X4

UniProtKB/Swiss-Prot

D3ZD32
XM_063288455.1 → XP_063144525.1 chromodomain-helicase-DNA-binding protein 5 isoform X9

UniProtKB/Swiss-Prot

D3ZD32
XM_063288458.1 → XP_063144528.1 chromodomain-helicase-DNA-binding protein 5 isoform X14

UniProtKB/Swiss-Prot

D3ZD32
XM_017593643.3 → XP_017449132.1 chromodomain-helicase-DNA-binding protein 5 isoform X5

UniProtKB/Swiss-Prot

D3ZD32
XM_039110813.2 → XP_038966741.1 chromodomain-helicase-DNA-binding protein 5 isoform X10

UniProtKB/Swiss-Prot

D3ZD32

Conserved Domains (10) summary

PLN03142
Location:696 → 1214

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

PRK13108
Location:1530 → 1680

PRK13108; prolipoprotein diacylglyceryl transferase; Reviewed

cd15531
Location:343 → 385

PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins

cd15532
Location:416 → 458

PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins

cd18662
Location:587 → 640

CD2_tandem_CHD3-4_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and 4, and similar proteins

cd18667
Location:463 → 542

CD1_tandem_CHD3-4_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and 4, and similar proteins

pfam06461
Location:1386 → 1527

DUF1086; Domain of Unknown Function (DUF1086)

pfam06465
Location:1296 → 1349

DUF1087; Domain of Unknown Function (DUF1087)

pfam08073
Location:144 → 199

CHDNT; CHDNT (NUC034) domain

pfam08074
Location:1726 → 1852

CHDCT2; CHDCT2 (NUC038) domain
XM_017593641.3 → XP_017449130.1 chromodomain-helicase-DNA-binding protein 5 isoform X3

UniProtKB/Swiss-Prot

D3ZD32
XM_017593645.3 → XP_017449134.1 chromodomain-helicase-DNA-binding protein 5 isoform X6

UniProtKB/Swiss-Prot

D3ZD32
XM_017593646.3 → XP_017449135.1 chromodomain-helicase-DNA-binding protein 5 isoform X7

UniProtKB/Swiss-Prot

D3ZD32
XM_039110815.2 → XP_038966743.1 chromodomain-helicase-DNA-binding protein 5 isoform X16

Conserved Domains (8) summary

PLN03142
Location:696 → 1214

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd15531
Location:343 → 385

PHD1_CHD_II; PHD finger 1 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins

cd15532
Location:416 → 458

PHD2_CHD_II; PHD finger 2 found in class II Chromodomain-Helicase-DNA binding (CHD) proteins

cd18662
Location:587 → 640

CD2_tandem_CHD3-4_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and 4, and similar proteins

cd18667
Location:463 → 542

CD1_tandem_CHD3-4_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 3 and 4, and similar proteins

pfam06461
Location:1389 → 1515

DUF1086; Domain of Unknown Function (DUF1086)

pfam06465
Location:1296 → 1349

DUF1087; Domain of Unknown Function (DUF1087)

pfam08073
Location:144 → 199

CHDNT; CHDNT (NUC034) domain
XM_017593644.3 → XP_017449133.1 chromodomain-helicase-DNA-binding protein 5 isoform X15

UniProtKB/TrEMBL

A0A0H2UHP5

Related

ENSRNOP00000084279.2, ENSRNOT00000101172.2