Smarcad1 SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Smarcad1provided by MGI
Official Full Name: SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1provided by MGI
Primary source: MGI:MGI:95453
See related: Ensembl:ENSMUSG00000029920 AllianceGenome:MGI:95453
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: Etl1; etl-1; D6Pas1; mKIAA1122
Summary: Predicted to enable DNA binding activity; chromatin binding activity; and nucleosome array spacer activity. Predicted to be involved in several processes, including DNA double-strand break processing; chromosome separation; and regulation of gene expression. Located in heterochromatin and nucleus. Is expressed in several structures, including alimentary system; central nervous system; eye; genitourinary system; and integumental system. Used to study asphyxiating thoracic dystrophy. Human ortholog(s) of this gene implicated in BASAN syndrome and adermatoglyphia. Orthologous to human SMARCAD1 (SWI/SNF-related, matrix-associated actin-dependent regulator of chromatin, subfamily a, containing DEAD/H box 1). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Broad expression in CNS E11.5 (RPKM 9.6), CNS E14 (RPKM 8.1) and 22 other tissues See more
Orthologs: human all
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Genomic context

Location:: 6 C1; 6 30.11 cM

Exon count:: 31

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	6	NC_000072.7 (65019577..65093045)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	6	NC_000072.6 (65042591..65116061)

Chromosome 6 - NC_000072.7 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: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The Conserved Chromatin Remodeler SMARCAD1 Interacts with TFIIIC and Architectural Proteins in Human and Mouse.
Title: The Conserved Chromatin Remodeler SMARCAD1 Interacts with TFIIIC and Architectural Proteins in Human and Mouse.
Smarcad1 mediates microbiota-induced inflammation in mouse and coordinates gene expression in the intestinal epithelium.
Title: Smarcad1 mediates microbiota-induced inflammation in mouse and coordinates gene expression in the intestinal epithelium.
Role of the ATP-dependent chromatin remodeling enzyme Fun30/Smarcad1 in the regulation of mRNA splicing.
Title: Role of the ATP-dependent chromatin remodeling enzyme Fun30/Smarcad1 in the regulation of mRNA splicing.
These findings uncover a role for the enzymatic activity of SMARCAD1 in cooperating with KAP1 to silence Endogenous retroviruses.
Title: SMARCAD1 ATPase activity is required to silence endogenous retroviruses in embryonic stem cells.
These data suggest a model in which SMARCAD1 regulates naive pluripotency by interacting with H3 arginine 26 citrullination and suppressing heterochromatin formation.
Title: SMARCAD1 Contributes to the Regulation of Naive Pluripotency by Interacting with Histone Citrullination.
Results suggest a novel model for gene regulation via the SMARCAD1/KIAA1122 protein complex.
Title: The novel protein complex with SMARCAD1/KIAA1122 binds to the vicinity of TSS.

Submit: New GeneRIF Correction

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (3)
Gene trapped (1) 1 citation
Targeted (4) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D6Rck333 (e-PCR), detects polymorphism
- UniSTS:142613

42.MMHAP62FLF6.seq (e-PCR)
- UniSTS:124470

AW226546 (e-PCR)
- UniSTS:179383

NoName (e-PCR)
- UniSTS:235460

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation 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	ISS Inferred from Sequence or Structural Similarity 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 binding	ISO Inferred from Sequence Orthology 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 nucleosome array spacer activity	IBA Inferred from Biological aspect of Ancestor more info
enables single-stranded 3'-5' DNA helicase activity	IEA Inferred from Electronic Annotation more info
enables ubiquitin binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in DNA double-strand break processing	IBA Inferred from Biological aspect of Ancestor more info
involved_in DNA double-strand break processing	ISO Inferred from Sequence Orthology more info
involved_in DNA double-strand break processing	ISS Inferred from Sequence or Structural Similarity more info
involved_in DNA duplex unwinding	IEA Inferred from Electronic Annotation more info
involved_in chromatin looping	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
involved_in chromosome separation	ISO Inferred from Sequence Orthology more info
involved_in chromosome separation	ISS Inferred from Sequence or Structural Similarity more info
involved_in heterochromatin formation	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of DNA recombination	ISS Inferred from Sequence or Structural Similarity more info	PubMed

Component	Evidence Code	Pubs
located_in chromatin	IBA Inferred from Biological aspect of Ancestor more info
located_in heterochromatin	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear replication fork	IEA Inferred from Electronic Annotation more info
located_in nuclear replication fork	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	IEA Inferred from Electronic Annotation 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 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 containing DEAD/H box 1

Names: ATP-dependent helicase SMARCAD1; enhancer trap locus 1; enhancer trap locus homolog 1

NP_001240321.1

EC 3.6.4.12

NP_001342177.1

EC 3.6.4.12

NP_001342178.1

EC 3.6.4.12

NP_001342179.1

EC 3.6.4.12

NP_001396719.1

EC 3.6.4.12

NP_001396720.1

EC 3.6.4.12

NP_031984.1

EC 3.6.4.12

XP_006505573.1

EC 3.6.4.12

XP_006505575.1

EC 3.6.4.12

XP_006505576.1

EC 3.6.4.12

XP_036021704.1

EC 3.6.4.12

XP_036021705.1

EC 3.6.4.12

XP_036021706.1

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_001253392.1 → NP_001240321.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform 2

See identical proteins and their annotated locations for NP_001240321.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate exon which results in the use of a downstream start codon, compared to variant 1. The resulting protein (isoform 2) is shorter when it is compared to isoform 1. Variants 2 and 6 both encode the same isoform (2).

Source sequence(s)

AK122454, AK147884, X69942

UniProtKB/Swiss-Prot

Q04692

Conserved Domains (2) summary

PLN03142
Location:286 → 808

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd17998
Location:307 → 489

DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1
NM_001355248.2 → NP_001342177.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform 3

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks several exons and includes an alternate 3' terminal exon, compared to variant 1. The encoded protein (isoform 3) is shorter and has a distinct C-terminus, compared to isoform 1. Variants 3, 4, and 7 all encode the same protein (isoform 3).

Source sequence(s)

AC138622

Consensus CDS

CCDS90055.1

UniProtKB/TrEMBL

A0A0N4SUQ5, A0A0N4SVS7

Related

ENSMUSP00000144776.2, ENSMUST00000204696.3
NM_001355249.2 → NP_001342178.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform 3

Status: VALIDATED

Description

Transcript Variant: This variant (4) differs in the 5' UTR, lacks several exons and includes an alternate 3' terminal exon, compared to variant 1. The encoded protein (isoform 3) is shorter and has a distinct C-terminus, compared to isoform 1. Variants 3, 4, and 7 all encode the same protein (isoform 3).

Source sequence(s)

AC138622

Consensus CDS

CCDS90055.1

UniProtKB/TrEMBL

A0A0N4SUQ5, A0A0N4SVS7

Related

ENSMUSP00000145340.2, ENSMUST00000205118.3
NM_001355250.2 → NP_001342179.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform 1

Status: VALIDATED

Description

Transcript Variant: This variant (5) differs in the 5' UTR, compared to variant 1, and encodes isoform 1. Variants 1 and 5 encode the same protein (isoform 1).

Source sequence(s)

AC138622, AC143330

Consensus CDS

CCDS20204.1

UniProtKB/Swiss-Prot

Q04692, Q3UGK6, Q3UYR6

Conserved Domains (2) summary

PLN03142
Location:471 → 993

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd17998
Location:492 → 674

DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1
NM_001409790.1 → NP_001396719.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform 2

Status: VALIDATED

Source sequence(s)

AC138622, AC143330
NM_001409791.1 → NP_001396720.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform 3

Status: VALIDATED

Source sequence(s)

AC138622

UniProtKB/TrEMBL

A0A0N4SUQ5
NM_007958.3 → NP_031984.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform 1

See identical proteins and their annotated locations for NP_031984.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longest protein (isoform 1). Variants 1 and 5 encode the same protein (isoform 1).

Source sequence(s)

AC138622, AC143330

Consensus CDS

CCDS20204.1

UniProtKB/Swiss-Prot

Q04692, Q3UGK6, Q3UYR6

Related

ENSMUSP00000031984.7, ENSMUST00000031984.9

Conserved Domains (2) summary

PLN03142
Location:471 → 993

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd17998
Location:492 → 674

DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000072.7 Reference GRCm39 C57BL/6J

Range

65019577..65093045

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_036165811.1 → XP_036021704.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform X2

Conserved Domains (2) summary

PLN03142
Location:471 → 964

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd17998
Location:492 → 674

DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1
XM_036165812.1 → XP_036021705.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform X2

Conserved Domains (2) summary

PLN03142
Location:471 → 964

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd17998
Location:492 → 674

DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1
XM_036165813.1 → XP_036021706.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform X3

Conserved Domains (2) summary

PLN03142
Location:286 → 808

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd17998
Location:307 → 489

DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1
XM_006505510.4 → XP_006505573.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform X1

See identical proteins and their annotated locations for XP_006505573.1

UniProtKB/Swiss-Prot

Q04692, Q3UGK6, Q3UYR6

Conserved Domains (2) summary

PLN03142
Location:471 → 993

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd17998
Location:492 → 674

DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1
XM_006505512.5 → XP_006505575.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform X3

See identical proteins and their annotated locations for XP_006505575.1

UniProtKB/Swiss-Prot

Q04692

Conserved Domains (2) summary

PLN03142
Location:286 → 808

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd17998
Location:307 → 489

DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1
XM_006505513.5 → XP_006505576.1 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily A containing DEAD/H box 1 isoform X4

Conserved Domains (2) summary

PLN03142
Location:46 → 568

PLN03142; Probable chromatin-remodeling complex ATPase chain; Provisional

cd17998
Location:67 → 249

DEXHc_SMARCAD1; DEXH-box helicase domain of SMARCAD1