Sec24d MGI Mouse Gene Detail - MGI:1916858 - SEC24 homolog D, COPII coat complex component

Symbol

Sec24d
Name

SEC24 homolog D, COPII coat complex component
Synonyms

2310020L09Rik, LOC383951

Feature Type

protein coding gene
IDs

MGI:1916858
NCBI Gene: 69608
Alliance

gene page
Transcription Start Sites

7 TSS

Sequence Map

Chr3:123061104-123159290 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 3, 53.82 cM, cytoband G3
Mapping Data

4 experiments

SNPs within 2kb

3580 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1916858	protein coding gene	Chr3:123058451-123159290 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0027848	protein coding gene	Chr3:125579321-125678111 (+)
A/J	MGP_AJ_G0027807	protein coding gene	Chr3:121364958-121465445 (+)
AKR/J	MGP_AKRJ_G0027772	protein coding gene	Chr3:124466093-124566910 (+)
BALB/cJ	MGP_BALBcJ_G0027819	protein coding gene	Chr3:121179309-121277488 (+)
C3H/HeJ	MGP_C3HHeJ_G0027549	protein coding gene	Chr3:124863235-124963684 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0028264	protein coding gene	Chr3:130117383-130219437 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0025601	protein coding gene	Chr3:116786433-116888322 (+)
CAST/EiJ	MGP_CASTEiJ_G0027004	protein coding gene	Chr3:124274307-124377613 (+)
CBA/J	MGP_CBAJ_G0027524	protein coding gene	Chr3:134513041-134624279 (+)
DBA/2J	MGP_DBA2J_G0027665	protein coding gene	Chr3:120494287-120592440 (+)
FVB/NJ	MGP_FVBNJ_G0027633	protein coding gene	Chr3:118117389-118218453 (+)
LP/J	MGP_LPJ_G0027775	protein coding gene	Chr3:127100775-127201981 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0027663	protein coding gene	Chr3:142088439-142205175 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0028320	protein coding gene	Chr3:124023163-124133372 (+)
PWK/PhJ	MGP_PWKPhJ_G0026730	protein coding gene	Chr3:120241389-120342432 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0026554	protein coding gene	Chr3:122129130-122234080 (+)
WSB/EiJ	MGP_WSBEiJ_G0027084	protein coding gene	Chr3:124769415-124877650 (+)

Human Ortholog

SEC24D, SEC24 homolog D, COPII coat complex component

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

SEC24D, SEC24 homolog D, COPII coat complex component
Synonyms

CLCRP2
Links

HGNC:10706

NCBI Gene ID: 9871

neXtProt AC: NX_O94855

UniProt: O94855
Chr Location

4q26; chr4:118722823-118838683 (-) GRCh38

MGI Vertebrate Homology

Sec24d stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: SEC24D
Gene Tree

Sec24d

Diseases

1 with human SEC24D associations

				Human Disease	Mouse Models
				Cole-Carpenter syndrome IDs Cole-Carpenter syndrome DOID:0060438 MESH:C535963 NCI:C130985 OMIM:112240 OMIM:616294 ORDO:2050

Click on a disease name to see all genes associated with that disease.

References

1 with disease annotations

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Phenotype Summary

7 phenotypes from 4 alleles in 3 genetic backgrounds
1 phenotype from multigenic genotypes
16 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

12
Chemically induced (other)

1
Endonuclease-mediated

2
Gene trapped

4
Radiation induced

1
Targeted

4
Genomic Mutations

2 involving Sec24d
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

59 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a knock-out allele exhibit early embryonic lethality. A hypomorphic gene trap allele results in lethality during organogenesis.

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All GO Annotations

13
GO References

4

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

731
Tissues

7
cDNA Data

71
Literature Summary

6

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase sec24d

ZFIN sec24d

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All Sequences

60
RefSeq

10
UniProt

4
CCDS

CCDS38621.1

Ensembl

ENSMUSG00000039234 (Evidence)
NCBI Gene

69608

			Length	Strain/Species	Flank
genomic	ENSMUSG00000039234	Ensembl Gene Model \| MGI Sequence Detail	98187	C57BL/6J	± kb
transcript	ENSMUST00000047923	Ensembl \| MGI Sequence Detail	3903	Not Applicable
polypeptide	ENSMUSP00000035823	Ensembl \| MGI Sequence Detail	1032	Not Applicable

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UniProt

4 Sequences
InterPro Domains

IPR029006 ADF-H/Gelsolin-like domain superfamily

IPR007123 Gelsolin-like domain

IPR036180 Gelsolin-like domain superfamily

IPR012990 Sec23/Sec24 beta-sandwich

IPR050550 SEC23/SEC24 family, SEC24 subfamily

IPR006900 Sec23/Sec24, helical domain

IPR036175 Sec23/Sec24 helical domain superfamily

IPR006896 Sec23/Sec24, trunk domain

IPR041742 Sec24-like, trunk domain

IPR036465 von Willebrand factor A-like domain superfamily

IPR006895 Zinc finger, Sec23/Sec24-type
GlyGen

Q6NXL1 1 site, 1 O-linked glycan (1 site)

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All nucleic 72

cDNA 71

Other 1

Microarray probesets 3

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MGI:2686195

Summaries

All 43

Developmental Gene Expression 6

Diseases 1

Gene Ontology 4

Phenotypes 16
Earliest

J:65060 Kawai J, et al., Functional annotation of a full-length mouse cDNA collection. Nature. 2001 Feb 8;409(6821):685-90
Latest

J:345621 Adams DJ, et al., Genetic determinants of micronucleus formation in vivo. Nature. 2024 Mar;627(8002):130-136

TSS for Sec24d:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr31542	Chr3:123060830-123060851 (+)	-263 bp
Tssr31543	Chr3:123060857-123060870 (+)	-240 bp
Tssr31544	Chr3:123061094-123061149 (+)	18 bp
Tssr31545	Chr3:123063341-123063354 (+)	2,244 bp
Tssr31546	Chr3:123087332-123087358 (+)	26,241 bp
Tssr31547	Chr3:123087407-123087455 (+)	26,327 bp
Tssr31548	Chr3:123149202-123149235 (+)	88,115 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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