Smarcd1 MGI Mouse Gene Detail - MGI:1933623 - SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1

Symbol

Smarcd1
Name

SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1
Synonyms

Baf60a, D15Kz1

Feature Type

protein coding gene
IDs

MGI:1933623
NCBI Gene: 83797
Gene Overview

MyGene.info: SMARCD1
Alliance

gene page
Transcription Start Sites

10 TSS

Sequence Map

Chr15:99702287-99713995 bp, + strand
From NCBI annotation of GRCm38

View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 15, 56.13 cM
Mapping Data

3 experiments

SNPs within 2kb

70 from dbSNP Build 142
Strain Annotations

18
RFLP

1

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1933623	protein coding gene	Chr15:99702129-99713995 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0022340	protein coding gene	Chr15:101573639-101590834 (+)
A/J	MGP_AJ_G0022298	protein coding gene	Chr15:97517260-97529917 (+)
AKR/J	MGP_AKRJ_G0022274	protein coding gene	Chr15:100519070-100532875 (+)
BALB/cJ	MGP_BALBcJ_G0022304	protein coding gene	Chr15:97704172-97715158 (+)
C3H/HeJ	MGP_C3HHeJ_G0022072	protein coding gene	Chr15:100587029-100600960 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0022749	protein coding gene	Chr15:105358513-105371040 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0020275	protein coding gene	Chr15:93411717-93422635 (+)
CAST/EiJ	MGP_CASTEiJ_G0021596	protein coding gene	Chr15:101457324-101469396 (+)
CBA/J	MGP_CBAJ_G0022041	protein coding gene	Chr15:108954081-108965067 (+)
DBA/2J	MGP_DBA2J_G0022168	protein coding gene	Chr15:96955105-96968475 (+)
FVB/NJ	MGP_FVBNJ_G0022148	protein coding gene	Chr15:95946348-95958552 (+)
LP/J	MGP_LPJ_G0022239	protein coding gene	Chr15:101721169-101735153 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0022168	protein coding gene	Chr15:112835792-112848231 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0022764	protein coding gene	Chr15:100638185-100650549 (+)
PWK/PhJ	MGP_PWKPhJ_G0021335	protein coding gene	Chr15:97098757-97110894 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0021170	protein coding gene	Chr15:100480246-100491113 (+)
WSB/EiJ	MGP_WSBEiJ_G0021647	protein coding gene	Chr15:101153184-101164731 (+)

Human Ortholog

SMARCD1, SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1

Vertebrate Orthologs

10

Human Ortholog

SMARCD1, SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 1
Orthology source: HomoloGene, HGNC
Synonyms

BAF60A, CRACD1, CSS11, Rsc6p
Links

HGNC:11106

NCBI Gene ID: 6602

neXtProt AC: NX_Q96GM5

UniProt: Q96GM5
Chr Location

12q13.12; chr12:50085200-50100711 (+) GRCh38.p7

HomoloGene

Vertebrate Homology Class 20670
1 human;1 mouse;1 rat;1 chimpanzee;1 cattle;1 dog;1 chicken;1 zebrafish;1 frog, western clawed;1 macaque, rhesus
HCOP

human homology predictions: SMARCD1
Protein SuperFamily

SWI/SNF-related matrix-associated actin-dependent regulator
Gene Tree

Smarcd1

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References

1 with disease annotations

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Phenotype Summary

11 phenotypes from 1 allele in 1 genetic background
3 phenotypes from multigenic genotypes
25 phenotype references

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	immune system	integument	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	neoplasm	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	vision/eye

Click cells to view annotations.

All Mutations and Alleles

20
Chemically induced (other)

1
Gene trapped

16
Radiation induced

2
Targeted

1
Genomic Mutations

3 involving Smarcd1
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

29 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

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All GO Annotations

27
GO References

13

External Resources

FuncBase

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell death	cell differentiation	cell population proliferation	cellular component organization	establishment of localization	homeostatic process	immune system process	lipid metabolic process	nucleic acid-templated transcription	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	non-membrane-bounded organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	synapse	vacuole

Click cells to view annotations.

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Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

763
Tissues

83
cDNA Data

107
Literature Summary

13

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase smarcd1

ZFIN smarcd1

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Smarcd1 interacts with 244 markers (Mir7-1, Mir7-2, Mir7b, ...) View All

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All Sequences

68
RefSeq

4
UniProt

6
CCDS

CCDS37204.1
UniGene

273756

Ensembl

ENSMUSG00000023018 (Evidence)
NCBI Gene

83797

			Length	Strain/Species	Flank
genomic	83797	NCBI Gene Model \| MGI Sequence Detail	11709	C57BL/6J	± kb
transcript	NM_031842	RefSeq \| MGI Sequence Detail	3153	C57BL/6
polypeptide	Q61466	UniProt \| EBI \| MGI Sequence Detail	515	Not Applicable

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UniProt

6 Sequences
Protein Ontology

PR:000015265 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1

(term hierarchy)
PDB

1UHR
InterPro Domains

IPR019835 SWIB domain

IPR003121 SWIB/MDM2 domain

IPR036885 SWIB/MDM2 domain superfamily

IPR038041 SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily D member 1

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All nucleic 112

Genomic 3

cDNA 108

Primer pair 1

Microarray probesets 3

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MGD-MRK-4023, MGI:2145894, MGI:90224

Summaries

All 75

Developmental Gene Expression 13

Diseases 1

Gene Ontology 13

Phenotypes 25
Earliest

J:7688 Lane PW, et al., Association of megacolon with a new dominant spotting gene (Dom) in the mouse. J Hered. 1984 Nov-Dec;75(6):435-9
Latest

J:292815 Liu T, et al., BAF60a deficiency uncouples chromatin accessibility and cold sensitivity from white fat browning. Nat Commun. 2020 May 13;11(1):2379

TSS for Smarcd1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr133047	Chr15:99702097-99702119 (+)	-179 bp
Tssr133048	Chr15:99702137-99702205 (+)	-116 bp
Tssr133049	Chr15:99702278-99702312 (+)	8 bp
Tssr133050	Chr15:99702630-99702656 (+)	356 bp
Tssr133051	Chr15:99704105-99704124 (+)	1,828 bp
Tssr133052	Chr15:99704136-99704148 (+)	1,855 bp
Tssr133053	Chr15:99704171-99704187 (+)	1,892 bp
Tssr133054	Chr15:99704308-99704322 (+)	2,028 bp
Tssr133057	Chr15:99712667-99712690 (+)	10,392 bp
Tssr133058	Chr15:99712804-99712821 (+)	10,526 bp

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB), Gene Ontology (GO)
Citing These Resources Funding Information Warranty Disclaimer & Copyright Notice Send questions and comments to User Support.	last database update 02/23/2021 MGI 6.16