Smarcal1 SNF2 related chromatin remodeling annealing helicase 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Smarcal1provided by RGD
Official Full Name: SNF2 related chromatin remodeling annealing helicase 1provided by RGD
Primary source: RGD:1306134
See related: EnsemblRapid:ENSRNOG00000016503 AllianceGenome:RGD:1306134
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
Summary: Predicted to enable ATP-dependent DNA/DNA annealing activity and ATP-dependent activity, acting on DNA. Predicted to be involved in double-strand break repair via nonhomologous end joining; regulation of transcription by RNA polymerase II; and replication fork processing. Predicted to be located in nucleoplasm and site of double-strand break. Predicted to be part of DNA replication factor A complex. Predicted to be active in nuclear replication fork. Human ortholog(s) of this gene implicated in Schimke immuno-osseous dysplasia. Orthologous to human SMARCAL1 (SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a like 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Thymus (RPKM 78.9), Spleen (RPKM 63.6) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 9q33

Exon count:: 20

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	9	NC_086027.1 (81689446..81735406)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	9	NC_051344.1 (74239718..74286156)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	9	NC_005108.4 (79943775..79990230)

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 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

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP-dependent DNA/DNA annealing activity	ISO Inferred from Sequence Orthology more info
enables ATP-dependent DNA/DNA annealing activity	ISS Inferred from Sequence or Structural Similarity more info
enables ATP-dependent activity, acting on DNA	ISO Inferred from Sequence Orthology more info
enables ATP-dependent chromatin remodeler activity	IEA Inferred from Electronic Annotation more info
enables helicase activity	IEA Inferred from Electronic Annotation more info
enables hydrolase activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in DNA damage response	ISO Inferred from Sequence Orthology more info
involved_in DNA damage response	ISS Inferred from Sequence or Structural Similarity more info
involved_in DNA repair	IBA Inferred from Biological aspect of Ancestor more info
involved_in biological_process	ND No biological Data available more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in double-strand break repair via nonhomologous end joining	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in regulation of transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info
involved_in replication fork processing	IBA Inferred from Biological aspect of Ancestor more info
involved_in replication fork processing	ISO Inferred from Sequence Orthology more info
involved_in replication fork processing	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
part_of DNA replication factor A complex	ISO Inferred from Sequence Orthology more info
part_of DNA replication factor A complex	ISS Inferred from Sequence or Structural Similarity more info
is_active_in nuclear replication fork	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 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
located_in site of double-strand break	ISO Inferred from Sequence Orthology more info
located_in site of double-strand break	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1

Names: Swi/SNF related matrix associated, actin dependent regulator of chromatin, subfamily a-like 1; hepA-related protein; sucrose nonfermenting protein 2-like 1

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_001108222.1 → NP_001101692.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1

See identical proteins and their annotated locations for NP_001101692.1

Status: PROVISIONAL

Source sequence(s)

CH474004

UniProtKB/Swiss-Prot

B4F769

UniProtKB/TrEMBL

A0A8L2QV60

Related

ENSRNOP00000022459.4, ENSRNOT00000022459.7

Conserved Domains (5) summary

COG0553
Location:392 → 836

HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]

cd00046
Location:411 → 539

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.

pfam00271
Location:668 → 778

Helicase_C; Helicase conserved C-terminal domain

pfam07443
Location:300 → 353

HARP; HepA-related protein (HARP)

pfam15265
Location:33 → 172

FAM196; FAM196 family

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

81689446..81735406

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_039083662.2 → XP_038939590.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 isoform X5

Conserved Domains (3) summary

cd18793
Location:419 → 544

SF2_C_SNF; C-terminal helicase domain of the SNF family helicases

cd18010
Location:148 → 357

DEXHc_HARP_SMARCAL1; DEXH-box helicase domain of SMARCAL1

pfam07443
Location:55 → 109

HARP; HepA-related protein (HARP)
XM_039083659.2 → XP_038939587.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 isoform X3

Conserved Domains (3) summary

cd18793
Location:506 → 631

SF2_C_SNF; C-terminal helicase domain of the SNF family helicases

cd18010
Location:235 → 444

DEXHc_HARP_SMARCAL1; DEXH-box helicase domain of SMARCAL1

pfam07443
Location:142 → 196

HARP; HepA-related protein (HARP)
XM_008767235.3 → XP_008765457.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 isoform X1

See identical proteins and their annotated locations for XP_008765457.1

UniProtKB/Swiss-Prot

B4F769

UniProtKB/TrEMBL

A0A8L2QV60

Conserved Domains (5) summary

COG0553
Location:392 → 836

HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]

cd00046
Location:411 → 539

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.

pfam00271
Location:668 → 778

Helicase_C; Helicase conserved C-terminal domain

pfam07443
Location:300 → 353

HARP; HepA-related protein (HARP)

pfam15265
Location:33 → 172

FAM196; FAM196 family
XM_063267226.1 → XP_063123296.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 isoform X2

Related

ENSRNOP00000102121.1, ENSRNOT00000156253.1
XM_039083661.2 → XP_038939589.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 isoform X4

Conserved Domains (3) summary

cd18793
Location:458 → 583

SF2_C_SNF; C-terminal helicase domain of the SNF family helicases

cd18010
Location:187 → 396

DEXHc_HARP_SMARCAL1; DEXH-box helicase domain of SMARCAL1

pfam07443
Location:94 → 148

HARP; HepA-related protein (HARP)
XM_017596474.3 → XP_017451963.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A-like protein 1 isoform X1

UniProtKB/Swiss-Prot

B4F769

UniProtKB/TrEMBL

A0A8L2QV60

Conserved Domains (5) summary

COG0553
Location:392 → 836

HepA; Superfamily II DNA or RNA helicase, SNF2 family [Transcription, Replication, recombination and repair]

cd00046
Location:411 → 539

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.

pfam00271
Location:668 → 778

Helicase_C; Helicase conserved C-terminal domain

pfam07443
Location:300 → 353

HARP; HepA-related protein (HARP)

pfam15265
Location:33 → 172

FAM196; FAM196 family