Csde1 MGI Mouse Gene Detail - MGI:92356 - cold shock domain containing E1, RNA binding

Symbol

Csde1
Name

cold shock domain containing E1, RNA binding
Synonyms

D3Jfr1, mKIAA0885, unr

Feature Type

protein coding gene
IDs

MGI:92356
NCBI Gene: 229663
Alliance

genome feature page
Transcription Start Sites

7 TSS

Sequence Map

Chr3:102927742-102965502 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 3, 45.25 cM
Mapping Data

2 experiments

SNPs within 2kb

628 from dbSNP Build 142
Strain Annotations

19

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_92356	protein coding gene	Chr3:102927347-102965502 (+)
129S1/SvImJ	ENSMUSG00200040545	protein coding gene	Chr3:99536196-99573921 (+)
A/J	ENSMUSG00195043966	protein coding gene	Chr3:99938857-99976608 (+)
AKR/J	ENSMUSG00220036266	protein coding gene	Chr3:98309601-98347326 (+)
BALB/cJ	ENSMUSG00180031629	protein coding gene	Chr3:99873414-99911140 (+)
C3H/HeJ	ENSMUSG00175026884	protein coding gene	Chr3:99421254-99459005 (+)
C57BL/6NJ	ENSMUSG00215035464	protein coding gene	Chr3:100197440-100235199 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0025444	protein coding gene	Chr3:97093032-97129922 (+)
CAST/EiJ	ENSTCUG00005019388	protein coding gene	Chr3:100134217-100172006 (+)
CBA/J	ENSMUSG00210050380	protein coding gene	Chr3:100043282-100081033 (+)
DBA/2J	ENSMUSG00185044147	protein coding gene	Chr3:100533657-100571417 (+)
FVB/NJ	ENSMUSG00205015427	protein coding gene	Chr3:99114653-99152378 (+)
JF1/MsJ	ENSUMUG00000041678	protein coding gene	Chr3:99262267-99299877 (+)
LP/J	ENSMUSG00230016236	protein coding gene	Chr3:102464596-102502321 (+)
NOD/ShiLtJ	ENSMUSG00190026726	protein coding gene	Chr3:100725439-100763168 (+)
NZO/HlLtJ	ENSMUSG00225017759	protein coding gene	Chr3:104927297-104965022 (+)
PWK/PhJ	ENSLUMG00010028111	protein coding gene	Chr3:99328665-99366328 (+)
SPRET/EiJ	ENSMSPG00010037669	protein coding gene	Chr3:99564711-99601806 (+)
WSB/EiJ	ENSIUOG00005025672	protein coding gene	Chr3:100058918-100096650 (+)

Human Ortholog

CSDE1, cold shock domain containing E1

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

CSDE1, cold shock domain containing E1
Synonyms

D1S155E, UNR
Links

HGNC:29905

NCBI Gene ID: 7812

UniProt: O75534
Chr Location

1p13.2; chr1:114716913-114758704 (-) GRCh38

MGI Vertebrate Homology

Csde1 stringent orthology
1 human;1 mouse;2 rat;1 zebrafish
HCOP

vertebrate homology predictions: CSDE1
Gene Tree

Csde1

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References

1 with disease annotations

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Phenotype Summary

17 phenotypes from 1 allele in 1 genetic background
19 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	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

99
Chemically induced (other)

1
Endonuclease-mediated

6
Gene trapped

87
Radiation induced

1
Targeted

4
Genomic Mutations

2 involving Csde1
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

77 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a knock-out allele exhibit embryonic growth retardation, delayed heart development, absence of neural tube closure, and complete embryonic lethality during organogenesis associated with placental developmental defects.

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All GO Annotations

41
GO References

9

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 differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	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	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	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

639
Tissues

17
cDNA Data

33
Literature Summary

9

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase csde1

ZFIN csde1

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All Sequences

111
RefSeq

10
UniProt

14
CCDS

CCDS38569.1, CCDS79990.1, CCDS79991.1

Ensembl

ENSMUSG00000068823 (Evidence)
NCBI Gene

229663

			Length	Strain/Species	Flank
genomic	ENSMUSG00000068823	Ensembl Gene Model \| MGI Sequence Detail	37761	C57BL/6J	± kb
transcript	ENSMUST00000197827	Ensembl \| MGI Sequence Detail	2671	Not Applicable
polypeptide	ENSMUSP00000143503	Ensembl \| MGI Sequence Detail	798	Not Applicable

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UniProt

14 Sequences
Protein Ontology

PR:000005928 cold shock domain-containing protein E1

(term hierarchy)
InterPro Domains

IPR011129 Cold-shock domain

IPR019844 Cold-shock domain, conserved site

IPR056400 Cold shock domain-containing protein E1, CSD domain

IPR002059 Cold-shock domain, DNA-binding

IPR012340 Nucleic acid-binding, OB-fold

IPR024642 SUZ-C domain
GlyGen

Q91W50 3 sites, 2 N-linked glycans (2 sites), 1 O-linked glycan (1 site)

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All nucleic 38

cDNA 36

Primer pair 2

Microarray probesets 3

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MGD-MRK-6231, MGI:2139611, MGI:2385887

Summaries

All 60

Developmental Gene Expression 9

Diseases 1

Gene Ontology 9

Phenotypes 19
Earliest

J:10710 Jeffers M, et al., Characterization of unr; a gene closely linked to N-ras. Nucleic Acids Res. 1990 Aug 25;18(16):4891-9
Latest

J:364356 Chen P, et al., A Csde1-Strap complex regulates plasma cell differentiation by coupling mRNA translation and decay. Nat Commun. 2025 Mar 25;16(1):2906

TSS for Csde1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr30948	Chr3:102927910-102927951 (+)	189 bp
Tssr30949	Chr3:102936158-102936184 (+)	8,429 bp
Tssr30950	Chr3:102936299-102936384 (+)	8,600 bp
Tssr30951	Chr3:102936421-102936446 (+)	8,692 bp
Tssr30952	Chr3:102937448-102937493 (+)	9,729 bp
Tssr30953	Chr3:102950939-102950962 (+)	23,209 bp
Tssr30954	Chr3:102956971-102956983 (+)	29,235 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)
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