Cxcl12 Gene Detail

Summary

• Symbol
  Cxcl12
• Name
  C-X-C motif chemokine ligand 12
• Synonyms
  PBSF, PBSF/SDF-1, Scyb12, Sdf1, SDF-1, Sdf1a, Sdf1b, TLSF-a, TLSF-b, TPAR1

• Feature Type
  protein coding gene
• IDs
  MGI:103556
  NCBI Gene: 20315
• Alliance
  gene page
• Transcription Start Sites
  55 TSS

Location &
Maps

• Sequence Map
  Chr6:117145496-117158328 bp, + strand

  From Ensembl annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 6, 54.81 cM, cytoband F1
• Mapping Data
  4 experiments

Strain
Comparison

• SNPs within 2kb
  351 from dbSNP Build 142
• Strain Annotations
  18
• RFLP
  6

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_103556	protein coding gene	Chr6:117145496-117158329 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0031177	protein coding gene	Chr6:119868254-119881078 (+)
A/J	MGP_AJ_G0031147	protein coding gene	Chr6:115264014-115276834 (+)
AKR/J	MGP_AKRJ_G0031077	protein coding gene	Chr6:118357842-118370666 (+)
BALB/cJ	MGP_BALBcJ_G0031157	protein coding gene	Chr6:115059791-115072614 (+)
C3H/HeJ	MGP_C3HHeJ_G0030552	protein coding gene	Chr6:65922611-65935437 (-)
C57BL/6NJ	MGP_C57BL6NJ_G0031615	protein coding gene	Chr6:122914398-122927229 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0028780	protein coding gene	Chr6:112232674-112245529 (+)
CAST/EiJ	MGP_CASTEiJ_G0030264	protein coding gene	Chr6:118732055-118749718 (+)
CBA/J	MGP_CBAJ_G0030841	protein coding gene	Chr6:127802285-127815113 (+)
DBA/2J	MGP_DBA2J_G0030997	protein coding gene	Chr6:114197485-114210307 (+)
FVB/NJ	MGP_FVBNJ_G0030949	protein coding gene	Chr6:113337261-113350093 (+)
LP/J	MGP_LPJ_G0031075	protein coding gene	Chr6:119888322-119901147 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0030983	protein coding gene	Chr6:131912179-131925008 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0031644	protein coding gene	Chr6:118396570-118409413 (+)
PWK/PhJ	MGP_PWKPhJ_G0029980	protein coding gene	Chr6:113180796-113198645 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0029808	protein coding gene	Chr6:117119540-117132395 (+)
WSB/EiJ	MGP_WSBEiJ_G0030347	protein coding gene	Chr6:118675468-118688328 (+)

Homology

• Human Ortholog
  CXCL12, C-X-C motif chemokine ligand 12

• Vertebrate Orthologs
  4

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  CXCL12, C-X-C motif chemokine ligand 12
  
• Synonyms
  IRH, PBSF, SCYB12, SDF1, TLSF, TPAR1
• Links
  HGNC:10672

  NCBI Gene ID: 6387

  neXtProt AC: NX_P48061

  UniProt: P48061

  
  
• Chr Location
  10q11.21; chr10:44370165-44386493 (-)  GRCh38

---

• MGI Vertebrate Homology
  Cxcl12 stringent orthology
  1 human;1 mouse;1 rat;2 zebrafish
  
• HCOP
  vertebrate homology predictions: CXCL12
• Gene Tree
  Cxcl12
  

Human Diseases

• Diseases
  4 with human CXCL12 associations

				Human Disease	Mouse Models
				breast carcinoma IDs breast carcinoma       DOID:3459 EFO:0000305 MESH:D001943 NCI:C4872 UMLS_CUI:C0678222
				diabetic angiopathy IDs diabetic angiopathy       DOID:11713 MESH:D003925 NCI:C35610 UMLS_CUI:C0011871 UMLS_CUI:C0011875
				human immunodeficiency virus infectious disease IDs human immunodeficiency virus infectious disease       DOID:526 ICD10CM:B20 ICD9CM:042 ICD9CM:042-042.99 MESH:D015658 NCI:C3108 UMLS_CUI:C0019693
				type 1 diabetes mellitus IDs type 1 diabetes mellitus       DOID:9744 ICD10CM:E10 KEGG:04940 MESH:D003922 NCI:C2986 OMIM:222100 UMLS_CUI:C0011854

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

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  41 phenotypes from 10 alleles in 19 genetic backgrounds
  14 phenotypes from multigenic genotypes
  2 images
  166 phenotype references
  

• All Mutations and Alleles
  33
• Endonuclease-mediated
  5
• Gene trapped
  1
• Targeted
  25
• Transgenic
  2
• Find Mice (IMSR)
  25 strains or lines available
• Comparison Matrix
  Gene Expression + Phenotype
• Recombinase Activity
  Comparison Matrix Gene Expression + Recombinase Activity

Homozygous null mice display late embryonic lethality, impaired myelopoiesis, abnormal cerebellum development, abnormal germ cell migration, abnormal angiogenesis around the stomach, and ventricular septal defects.

Gene Ontology
(GO)
Classifications

• All GO Annotations
  75
• GO References
  20

Expression

• Assay Results
  1908
• Tissues
  503
• cDNA Data
  219
• Literature Summary
  177

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

• Other Mouse Links
  Allen Institute
  GENSAT
  GEO
  Expression Atlas
• Other Vertebrate Links
  GEISHA CXCL12
  Xenbase cxcl12
  ZFIN cxcl12a, cxcl12b

Sequences &
Gene Models

• All Sequences
  59
• RefSeq
  6
• UniProt
  2
• CCDS
  CCDS20463.1, CCDS39605.1, CCDS39606.1

• Ensembl
  ENSMUSG00000061353 (Evidence)
• NCBI Gene
  20315

Representative Sequences			Length	Strain/Species
genomic	ENSMUSG00000061353	Ensembl Gene Model | MGI Sequence Detail	12833	C57BL/6J
transcript	ENSMUST00000073043	Ensembl | MGI Sequence Detail	5627	Not Applicable
polypeptide	ENSMUSP00000072800	Ensembl | MGI Sequence Detail	119	Not Applicable

Protein
Information

• UniProt
  2 Sequences
• Protein Ontology
  PR:000006066 stromal cell-derived factor 1
  (term hierarchy)
• PDB
  6EHZ
• InterPro Domains
  IPR039809 Chemokine beta/gamma/delta
  IPR001811 Chemokine interleukin-8-like domain
  IPR036048 Chemokine interleukin-8-like superfamily
  IPR033899 CXC Chemokine domain

Molecular
Reagents

• All nucleic 254

  Genomic 2

  cDNA 220

  Primer pair 20

  Other 12

  
  

  Microarray probesets 8

Other
Accession IDs

MGD-MRK-16620, MGD-MRK-16621, MGD-MRK-24440, MGI:2141381

References

• Summaries
  All 526

  Developmental Gene Expression 177

  Gene Ontology 20

  Phenotypes 166
• Earliest
  J:17644 Tashiro K, et al., Signal sequence trap: a cloning strategy for secreted proteins and type I membrane proteins. Science. 1993 Jul 30;261(5121):600-3
• Latest
  J:353967 Thierry GR, et al., Non-classical monocytes scavenge the growth factor CSF1 from endothelial cells in the peripheral vascular tree to ensure survival and homeostasis. Immunity. 2024 Jul 27;

TSS for Cxcl12:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr58390	Chr6:117145527-117145545 (+)	40 bp
Tssr58391	Chr6:117146960-117146966 (+)	1,467 bp
Tssr58392	Chr6:117148437-117148448 (+)	2,947 bp
Tssr58393	Chr6:117148449-117148467 (+)	2,962 bp
Tssr58394	Chr6:117148469-117148507 (+)	2,992 bp
Tssr58395	Chr6:117150453-117150466 (+)	4,964 bp
Tssr58396	Chr6:117150469-117150480 (+)	4,979 bp
Tssr58397	Chr6:117150507-117150515 (+)	5,015 bp
Tssr58398	Chr6:117150533-117150538 (+)	5,040 bp
Tssr58399	Chr6:117150555-117150567 (+)	5,065 bp
Tssr58400	Chr6:117150583-117150600 (+)	5,096 bp
Tssr58401	Chr6:117150619-117150634 (+)	5,131 bp
Tssr58402	Chr6:117150650-117150663 (+)	5,161 bp
Tssr58403	Chr6:117150668-117150681 (+)	5,179 bp
Tssr58404	Chr6:117150687-117150692 (+)	5,194 bp
Tssr58405	Chr6:117150729-117150748 (+)	5,243 bp
Tssr58406	Chr6:117150759-117150777 (+)	5,272 bp
Tssr58407	Chr6:117150790-117150799 (+)	5,299 bp
Tssr58408	Chr6:117150857-117150862 (+)	5,364 bp
Tssr58409	Chr6:117150879-117150890 (+)	5,389 bp
Tssr58410	Chr6:117150901-117150908 (+)	5,409 bp
Tssr58411	Chr6:117150917-117150939 (+)	5,432 bp
Tssr58412	Chr6:117150944-117150951 (+)	5,452 bp
Tssr58413	Chr6:117150957-117150975 (+)	5,470 bp
Tssr58414	Chr6:117150990-117150997 (+)	5,498 bp
Tssr58415	Chr6:117151005-117151015 (+)	5,514 bp
Tssr58416	Chr6:117151020-117151033 (+)	5,531 bp
Tssr58417	Chr6:117151074-117151087 (+)	5,585 bp
Tssr58418	Chr6:117151107-117151113 (+)	5,614 bp
Tssr58419	Chr6:117151126-117151133 (+)	5,634 bp
Tssr58420	Chr6:117151153-117151168 (+)	5,665 bp
Tssr58421	Chr6:117151172-117151192 (+)	5,686 bp
Tssr58422	Chr6:117151198-117151205 (+)	5,706 bp
Tssr58423	Chr6:117151206-117151226 (+)	5,720 bp
Tssr58424	Chr6:117151268-117151285 (+)	5,781 bp
Tssr58425	Chr6:117151313-117151324 (+)	5,823 bp
Tssr58426	Chr6:117151335-117151342 (+)	5,843 bp
Tssr58427	Chr6:117151362-117151376 (+)	5,873 bp
Tssr58428	Chr6:117151377-117151387 (+)	5,886 bp
Tssr58429	Chr6:117151442-117151465 (+)	5,958 bp
Tssr58430	Chr6:117151487-117151496 (+)	5,996 bp
Tssr58431	Chr6:117151583-117151595 (+)	6,093 bp
Tssr58432	Chr6:117151656-117151676 (+)	6,170 bp
Tssr58433	Chr6:117151692-117151701 (+)	6,201 bp
Tssr58434	Chr6:117152130-117152148 (+)	6,643 bp
Tssr58435	Chr6:117155656-117155668 (+)	10,166 bp
Tssr58436	Chr6:117155673-117155686 (+)	10,184 bp
Tssr58437	Chr6:117155748-117155762 (+)	10,259 bp
Tssr58438	Chr6:117155921-117155929 (+)	10,429 bp
Tssr58439	Chr6:117155944-117155951 (+)	10,452 bp
Tssr58440	Chr6:117155977-117156005 (+)	10,495 bp
Tssr58441	Chr6:117156169-117156196 (+)	10,687 bp
Tssr58442	Chr6:117156616-117156622 (+)	11,123 bp
Tssr58443	Chr6:117156932-117156944 (+)	11,442 bp
Tssr58444	Chr6:117157856-117157868 (+)	12,366 bp