Chd6 chromodomain helicase DNA binding protein 6 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Chd6provided by RGD
Official Full Name: chromodomain helicase DNA binding protein 6provided by RGD
Primary source: RGD:1310465
See related: EnsemblRapid:ENSRNOG00000016744 AllianceGenome:RGD:1310465
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-6
Summary: Predicted to enable several functions, including ATP hydrolysis activity; ATP-dependent chromatin remodeler activity; and transcription coregulator binding activity. Predicted to be involved in cell redox homeostasis; chromatin remodeling; and positive regulation of transcription by RNA polymerase II. Predicted to be located in chromatin and nucleoplasm. Predicted to be active in nucleus. Orthologous to human CHD6 (chromodomain helicase DNA binding protein 6). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Biased expression in Thymus (RPKM 176.4), Kidney (RPKM 121.6) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 3q42

Exon count:: 43

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	3	NC_086021.1 (170016204..170177480, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	3	NC_051338.1 (149596509..149757765, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	3	NC_005102.4 (156937746..157099328, complement)

Chromosome 3 - NC_086021.1 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?

Submit: New GeneRIF Correction

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D3Mco22 (e-PCR)
- UniSTS:239916

RH143820 (e-PCR)
- UniSTS:233066

RH144348 (e-PCR)
- UniSTS:233593

AW522475 (e-PCR)
- UniSTS:243446

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 activity, acting on DNA	IEA Inferred from Electronic Annotation more info
enables ATP-dependent activity, acting on DNA	ISO Inferred from Sequence Orthology more info
enables ATP-dependent activity, acting on DNA	ISS Inferred from Sequence or Structural Similarity 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 clamp loader activity	IEA Inferred from Electronic Annotation more info
enables chromatin binding	IBA Inferred from Biological aspect of Ancestor more info
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 hydrolase activity	IEA Inferred from Electronic Annotation more info
enables single-stranded 3'-5' DNA helicase activity	IEA Inferred from Electronic Annotation more info
enables transcription coregulator binding	IEA Inferred from Electronic Annotation more info
enables transcription coregulator binding	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in DNA duplex unwinding	IEA Inferred from Electronic Annotation more info
involved_in cell redox homeostasis	IEA Inferred from Electronic Annotation more info
involved_in cell redox homeostasis	ISO Inferred from Sequence Orthology more info
involved_in chromatin looping	IEA Inferred from Electronic Annotation more info
involved_in chromatin organization	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of gene expression	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISS Inferred from Sequence or Structural Similarity more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: chromodomain-helicase-DNA-binding protein 6

Names: ATP-dependent helicase CHD6

NP_001101267.1

EC 3.6.4.12

XP_006235546.2

EC 3.6.4.12

XP_008760567.1

EC 3.6.4.12

XP_008760568.1

EC 3.6.4.12

XP_017447279.2

EC 3.6.4.12

XP_038961032.1

EC 3.6.4.12

XP_038961033.1

EC 3.6.4.12

XP_038961034.1

EC 3.6.4.12

XP_038961035.1

EC 3.6.4.12

XP_038961036.1

EC 3.6.4.12

XP_038961037.1

EC 3.6.4.12

XP_038961039.1

EC 3.6.4.12

XP_038961040.1

EC 3.6.4.12

XP_038961041.1

EC 3.6.4.12

XP_038961042.1

EC 3.6.4.12

XP_038961043.1

EC 3.6.4.12

XP_038961044.1

EC 3.6.4.12

XP_063139932.1

EC 3.6.4.12

XP_063139933.1

EC 3.6.4.12

XP_063139934.1

EC 3.6.4.12

XP_063139935.1

EC 3.6.4.12

XP_063139936.1

EC 3.6.4.12

XP_063139937.1

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_001107797.2 → NP_001101267.1 chromodomain-helicase-DNA-binding protein 6 isoform 2

See identical proteins and their annotated locations for NP_001101267.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000003

UniProtKB/Swiss-Prot

D3ZA12

UniProtKB/TrEMBL

A0A8I5Y6Q9

Conserved Domains (5) summary

cd00046
Location:479 → 628

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.

pfam00176
Location:463 → 750

SNF2_N; SNF2 family N-terminal domain

pfam00271
Location:782 → 896

Helicase_C; Helicase conserved C-terminal domain

pfam00385
Location:375 → 428

Chromo; Chromo (CHRromatin Organization MOdifier) domain

cl00146
Location:104 → 257

TFIIS_I; N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme
NM_001434092.1 → NP_001421021.1 chromodomain-helicase-DNA-binding protein 6 isoform 1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000003

UniProtKB/TrEMBL

A0A8I5Y6Q9

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_086021.1 Reference GRCr8

Range

170016204..170177480 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039105105.2 → XP_038961033.1 chromodomain-helicase-DNA-binding protein 6 isoform X3

Conserved Domains (5) summary

PTZ00449
Location:100 → 372

PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

PLN03142
Location:458 → 983

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd18663
Location:371 → 429

CD2_tandem_CHD5-9_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins

cd18668
Location:287 → 352

CD1_tandem_CHD5-9_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins

cl28899
Location:459 → 680

DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily
XM_017591790.3 → XP_017447279.2 chromodomain-helicase-DNA-binding protein 6 isoform X4

UniProtKB/TrEMBL

A0A8I6AKM1, A0A8I6ARM3

Conserved Domains (5) summary

PTZ00449
Location:100 → 372

PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

PLN03142
Location:459 → 984

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd18663
Location:371 → 429

CD2_tandem_CHD5-9_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins

cd18668
Location:287 → 352

CD1_tandem_CHD5-9_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins

cl28899
Location:460 → 681

DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily
XM_006235484.5 → XP_006235546.2 chromodomain-helicase-DNA-binding protein 6 isoform X6

UniProtKB/TrEMBL

A0A8I6AKM1

Related

ENSRNOP00000093958.2, ENSRNOT00000106235.2

Conserved Domains (5) summary

PTZ00449
Location:100 → 372

PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

PLN03142
Location:459 → 984

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd18663
Location:371 → 429

CD2_tandem_CHD5-9_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins

cd18668
Location:287 → 352

CD1_tandem_CHD5-9_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins

cl28899
Location:460 → 681

DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily
XM_039105107.2 → XP_038961035.1 chromodomain-helicase-DNA-binding protein 6 isoform X8

UniProtKB/TrEMBL

A0A8I5Y6Q9

Conserved Domains (5) summary

PTZ00449
Location:100 → 372

PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

PLN03142
Location:459 → 984

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd18663
Location:371 → 429

CD2_tandem_CHD5-9_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins

cd18668
Location:287 → 352

CD1_tandem_CHD5-9_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins

cl28899
Location:460 → 681

DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily
XM_039105106.2 → XP_038961034.1 chromodomain-helicase-DNA-binding protein 6 isoform X7

UniProtKB/TrEMBL

A0A8I5Y6Q9

Related

ENSRNOP00000071893.2, ENSRNOT00000089958.3

Conserved Domains (5) summary

PTZ00449
Location:100 → 372

PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

PLN03142
Location:459 → 984

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd18663
Location:371 → 429

CD2_tandem_CHD5-9_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins

cd18668
Location:287 → 352

CD1_tandem_CHD5-9_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins

cl28899
Location:460 → 681

DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily
XM_008762345.4 → XP_008760567.1 chromodomain-helicase-DNA-binding protein 6 isoform X1

UniProtKB/TrEMBL

A0A8I5Y6Q9, A0A8L2QC41

Related

ENSRNOP00000022861.7, ENSRNOT00000022861.8

Conserved Domains (5) summary

PTZ00449
Location:100 → 372

PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

PLN03142
Location:459 → 984

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd18663
Location:371 → 429

CD2_tandem_CHD5-9_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins

cd18668
Location:287 → 352

CD1_tandem_CHD5-9_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins

cl28899
Location:460 → 681

DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily
XM_063283862.1 → XP_063139932.1 chromodomain-helicase-DNA-binding protein 6 isoform X1

UniProtKB/TrEMBL

A0A8I5Y6Q9, A0A8L2QC41
XM_063283864.1 → XP_063139934.1 chromodomain-helicase-DNA-binding protein 6 isoform X2

UniProtKB/TrEMBL

A0A0G2K1L7, A0A8I5Y6Q9

Related

ENSRNOP00000094454.2, ENSRNOT00000107966.2
XM_008762346.4 → XP_008760568.1 chromodomain-helicase-DNA-binding protein 6 isoform X5

UniProtKB/TrEMBL

A0A8I6AKM1

Related

ENSRNOP00000076519.1, ENSRNOT00000119650.2

Conserved Domains (5) summary

cd00046
Location:457 → 606

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.

pfam00176
Location:441 → 728

SNF2_N; SNF2 family N-terminal domain

pfam00271
Location:760 → 874

Helicase_C; Helicase conserved C-terminal domain

pfam00385
Location:353 → 406

Chromo; Chromo (CHRromatin Organization MOdifier) domain

cl00146
Location:82 → 235

TFIIS_I; N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme
XM_063283863.1 → XP_063139933.1 chromodomain-helicase-DNA-binding protein 6 isoform X1

UniProtKB/TrEMBL

A0A8I5Y6Q9, A0A8L2QC41
XM_039105104.2 → XP_038961032.1 chromodomain-helicase-DNA-binding protein 6 isoform X1

UniProtKB/TrEMBL

A0A8I5Y6Q9, A0A8L2QC41

Conserved Domains (5) summary

PTZ00449
Location:100 → 372

PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

PLN03142
Location:459 → 984

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd18663
Location:371 → 429

CD2_tandem_CHD5-9_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins

cd18668
Location:287 → 352

CD1_tandem_CHD5-9_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins

cl28899
Location:460 → 681

DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily
XM_063283865.1 → XP_063139935.1 chromodomain-helicase-DNA-binding protein 6 isoform X10

UniProtKB/TrEMBL

A0A8I6AKM1
XM_039105108.2 → XP_038961036.1 chromodomain-helicase-DNA-binding protein 6 isoform X9

UniProtKB/TrEMBL

A0A8I6A6R3, A0A8I6AKM1

Related

ENSRNOP00000086889.1, ENSRNOT00000114568.2

Conserved Domains (4) summary

PLN03142
Location:211 → 736

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd18663
Location:123 → 181

CD2_tandem_CHD5-9_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins

cd18668
Location:39 → 104

CD1_tandem_CHD5-9_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins

cl28899
Location:212 → 433

DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily
XM_039105111.2 → XP_038961039.1 chromodomain-helicase-DNA-binding protein 6 isoform X14
XM_039105112.2 → XP_038961040.1 chromodomain-helicase-DNA-binding protein 6 isoform X15
XM_039105113.2 → XP_038961041.1 chromodomain-helicase-DNA-binding protein 6 isoform X16
XM_039105116.2 → XP_038961044.1 chromodomain-helicase-DNA-binding protein 6 isoform X19
XM_039105109.2 → XP_038961037.1 chromodomain-helicase-DNA-binding protein 6 isoform X12

Conserved Domains (5) summary

PTZ00449
Location:81 → 372

PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

PLN03142
Location:459 → 984

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd18663
Location:371 → 429

CD2_tandem_CHD5-9_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins

cd18668
Location:287 → 352

CD1_tandem_CHD5-9_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins

cl28899
Location:460 → 681

DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily
XM_063283867.1 → XP_063139937.1 chromodomain-helicase-DNA-binding protein 6 isoform X13
XM_063283866.1 → XP_063139936.1 chromodomain-helicase-DNA-binding protein 6 isoform X11
XM_039105115.2 → XP_038961043.1 chromodomain-helicase-DNA-binding protein 6 isoform X17

Conserved Domains (5) summary

PTZ00449
Location:100 → 372

PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

PLN03142
Location:459 → 984

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd18663
Location:371 → 429

CD2_tandem_CHD5-9_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins

cd18668
Location:287 → 352

CD1_tandem_CHD5-9_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins

cl28899
Location:460 → 681

DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily
XM_039105114.2 → XP_038961042.1 chromodomain-helicase-DNA-binding protein 6 isoform X18

Conserved Domains (5) summary

PTZ00449
Location:100 → 372

PTZ00449; 104 kDa microneme/rhoptry antigen; Provisional

PLN03142
Location:459 → 984

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd18663
Location:371 → 429

CD2_tandem_CHD5-9_like; repeat 2 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins

cd18668
Location:287 → 352

CD1_tandem_CHD5-9_like; repeat 1 of the paired tandem chromodomains of chromodomain helicase DNA-binding protein 5-9, and similar proteins

cl28899
Location:460 → 681

DEAD-like_helicase_N; N-terminal helicase domain of the DEAD-box helicase superfamily