Sdf4 MGI Mouse Gene Detail - MGI:108079 - stromal cell derived factor 4

Symbol

Sdf4
Name

stromal cell derived factor 4
Synonyms

Cab45

Feature Type

protein coding gene
IDs

MGI:108079
NCBI Gene: 20318
Alliance

gene page
Transcription Start Sites

19 TSS

Sequence Map

Chr4:156077329-156098067 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 4, 87.66 cM, cytoband E2
Mapping Data

2 experiments

SNPs within 2kb

890 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_108079	protein coding gene	Chr4:156077300-156098067 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0029242	protein coding gene	Chr4:160358927-160383386 (+)
A/J	MGP_AJ_G0029207	protein coding gene	Chr4:153603014-153623467 (+)
AKR/J	MGP_AKRJ_G0029155	protein coding gene	Chr4:157781166-157804238 (+)
BALB/cJ	MGP_BALBcJ_G0029223	protein coding gene	Chr4:154078860-154099274 (+)
C3H/HeJ	MGP_C3HHeJ_G0028944	protein coding gene	Chr4:158344238-158367330 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0029672	protein coding gene	Chr4:166044445-166064826 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0026916	protein coding gene	Chr4:145880480-145901074 (+)
CAST/EiJ	MGP_CASTEiJ_G0028356	protein coding gene	Chr4:155784241-155805237 (+)
CBA/J	MGP_CBAJ_G0028906	protein coding gene	Chr4:171081370-171107368 (+)
DBA/2J	MGP_DBA2J_G0029055	protein coding gene	Chr4:153624653-153644797 (+)
FVB/NJ	MGP_FVBNJ_G0029018	protein coding gene	Chr4:152872032-152892774 (+)
LP/J	MGP_LPJ_G0029145	protein coding gene	Chr4:160299904-160319739 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0029045	protein coding gene	Chr4:173876898-173899039 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0029704	protein coding gene	Chr4:158423631-158449104 (+)
PWK/PhJ	MGP_PWKPhJ_G0028077	protein coding gene	Chr4:149763602-149784108 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0027911	protein coding gene	Chr4:152676476-152696427 (+)
WSB/EiJ	MGP_WSBEiJ_G0028436	protein coding gene	Chr4:158588136-158613307 (+)

Human Ortholog

SDF4, stromal cell derived factor 4

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

SDF4, stromal cell derived factor 4
Synonyms

Cab45, SDF-4
Links

HGNC:24188

NCBI Gene ID: 51150

neXtProt AC: NX_Q9BRK5

UniProt: Q9BRK5
Chr Location

1p36.33; chr1:1216931-1232031 (-) GRCh38

MGI Vertebrate Homology

Sdf4 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: SDF4
Gene Tree

Sdf4

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Phenotype Summary

7 phenotype references

All Mutations and Alleles

34
Endonuclease-mediated

2
Gene trapped

32
Incidental Mutations

APF , CvDC
Find Mice (IMSR)

38 strains or lines available

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All GO Annotations

20
GO References

6

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

752
Tissues

45
cDNA Data

262
Literature Summary

1

Images

Tissue x Stage Matrix

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase sdf4

ZFIN sdf4

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All Sequences

63
RefSeq

8
UniProt

1
CCDS

CCDS19054.1, CCDS80198.1

Ensembl

ENSMUSG00000029076 (Evidence)
NCBI Gene

20318

			Length	Strain/Species	Flank
genomic	ENSMUSG00000029076	Ensembl Gene Model \| MGI Sequence Detail	20739	C57BL/6J	± kb
transcript	ENSMUST00000050078	Ensembl \| MGI Sequence Detail	5177	Not Applicable
polypeptide	ENSMUSP00000053175	Ensembl \| MGI Sequence Detail	361	Not Applicable

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UniProt

1 Sequence
Protein Ontology

PR:000014562 45 kDa calcium-binding protein

(term hierarchy)
InterPro Domains

IPR027240 Calcium-binding protein CAB45, EF-hand

IPR018247 EF-Hand 1, calcium-binding site

IPR002048 EF-hand domain

IPR011992 EF-hand domain pair
GlyGen

Q61112 1 site

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All nucleic 263

cDNA 262

Primer pair 1

Microarray probesets 5

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MGD-MRK-35048, MGD-MRK-37116, MGI:106592

Summaries

All 34

Developmental Gene Expression 1

Gene Ontology 6

Phenotypes 7
Earliest

J:32511 Scherer PE, et al., Cab45, a novel (Ca2+)-binding protein localized to the Golgi lumen. J Cell Biol. 1996 Apr;133(2):257-68
Latest

J:153498 Diez-Roux G, et al., A high-resolution anatomical atlas of the transcriptome in the mouse embryo. PLoS Biol. 2011;9(1):e1000582

TSS for Sdf4:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr40748	Chr4:156076857-156076870 (+)	-465 bp
Tssr1404	Chr4:156077396-156077403 (+)	71 bp
Tssr40749	Chr4:156077600-156077644 (+)	293 bp
Tssr40750	Chr4:156077687-156077753 (+)	391 bp
Tssr40751	Chr4:156077762-156077773 (+)	439 bp
Tssr40752	Chr4:156077905-156077912 (+)	580 bp
Tssr40753	Chr4:156080796-156080813 (+)	3,476 bp
Tssr40754	Chr4:156086730-156086733 (+)	9,403 bp
Tssr40755	Chr4:156091361-156091388 (+)	14,046 bp
Tssr40756	Chr4:156093035-156093060 (+)	15,719 bp
Tssr40757	Chr4:156093073-156093089 (+)	15,752 bp
Tssr40758	Chr4:156093095-156093108 (+)	15,773 bp
Tssr40759	Chr4:156093115-156093123 (+)	15,790 bp
Tssr40760	Chr4:156093138-156093149 (+)	15,815 bp
Tssr40761	Chr4:156093153-156093163 (+)	15,829 bp
Tssr40762	Chr4:156093180-156093193 (+)	15,858 bp
Tssr40763	Chr4:156093285-156093307 (+)	15,967 bp
Tssr40764	Chr4:156093318-156093341 (+)	16,001 bp
Tssr40765	Chr4:156093604-156093688 (+)	16,317 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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