cxcl12b chemokine (C-X-C motif) ligand 12b (stromal cell-derived factor 1) [Danio rerio (zebrafish)] - Gene

Summary

Official Symbol: cxcl12bprovided by ZNC
Official Full Name: chemokine (C-X-C motif) ligand 12b (stromal cell-derived factor 1)provided by ZNC
Primary source: ZFIN:ZDB-GENE-030721-1
See related: Ensembl:ENSDARG00000055100 AllianceGenome:ZFIN:ZDB-GENE-030721-1
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Danio rerio
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Actinopterygii; Neopterygii; Teleostei; Ostariophysi; Cypriniformes; Danionidae; Danioninae; Danio
Also known as: SDF1b; sdf-1b; cxc112b; zgc:136720
Summary: Enables chemoattractant activity. Acts upstream of or within with a positive effect on Kupffer's vesicle development. Acts upstream of or within several processes, including blood vessel morphogenesis; induction of positive chemotaxis; and nervous system development. Predicted to be located in extracellular space. Is expressed in several structures, including cardiovascular system; central nervous system; endoderm; head; and mesoderm. Human ortholog(s) of this gene implicated in breast carcinoma; diabetic angiopathy; human immunodeficiency virus infectious disease; and type 1 diabetes mellitus. Orthologous to human CXCL12 (C-X-C motif chemokine ligand 12). [provided by Alliance of Genome Resources, Apr 2022]
Orthologs: all
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Genomic context

Location:: chromosome: 22

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCz11 (GCF_000002035.6)	22	NC_007133.7 (26929559..26945511, complement)
105	previous assembly	GRCz10 (GCF_000002035.5)	22	NC_007133.6 (27067107..27083059, complement)

Chromosome 22 - NC_007133.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
Description: Sequencing the Zebrafish transcriptome from a range of tissues and developmental stages
BioProject: PRJEB1986
Analysis date: Fri Dec 8 19:48:10 2017

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Zebrafish mutants for the chemokine receptor cxcr4a or its ligand cxcl12b establish a decreased number of arterial-venous connections, leading to the formation of an unperfused and interconnected blood vessel network.
Title: Arterial-venous network formation during brain vascularization involves hemodynamic regulation of chemokine signaling.
findings show that the chemokine Cxcl12b and its receptor Cxcr4a restrict anterior migration of the endoderm during zebrafish gastrulation, thereby coordinating its movements with those of the mesoderm
Title: Chemokine signaling controls endodermal migration during zebrafish gastrulation.

Submit: New GeneRIF Correction

General gene information

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Markers

AI477993 (e-PCR)
- UniSTS:206420

fc19e04.x1 (e-PCR)
- UniSTS:192929

fc19e04.x1 (e-PCR)
- UniSTS:192930

fa03a02.s1 (e-PCR)
- UniSTS:202154

Gene Ontology Provided by ZFIN

Function	Evidence Code	Pubs
enables chemoattractant activity	IBA Inferred from Biological aspect of Ancestor more info
enables chemoattractant activity	IDA Inferred from Direct Assay more info	PubMed
enables chemokine activity	IEA Inferred from Electronic Annotation more info
enables cytokine activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
acts_upstream_of_or_within_positive_effect Kupffer's vesicle development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within_positive_effect Kupffer's vesicle development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in axon guidance	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within cell migration involved in gastrulation	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within cell migration involved in gastrulation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cell migration involved in sprouting angiogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within cell migration involved in sprouting angiogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within cell morphogenesis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within chemotaxis	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within defense response	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within hemopoiesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within immune response	IEA Inferred from Electronic Annotation more info
involved_in induction of positive chemotaxis	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within induction of positive chemotaxis	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within lymphoid lineage cell migration into thymus	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within lymphoid lineage cell migration into thymus	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuron migration	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within neuron migration	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of cell migration	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within regulation of intracellular pH	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within retinal ganglion cell axon guidance	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within sprouting angiogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within trigeminal sensory nucleus development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within vasculogenesis	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in extracellular region	IEA Inferred from Electronic Annotation more info
located_in extracellular space	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: chemokine (C-X-C motif) ligand 12b (stromal cell-derived factor 1)

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001320414.1 → NP_001307343.1 chemokine (C-X-C motif) ligand 12b (stromal cell-derived factor 1) precursor

Status: VALIDATED

Source sequence(s)

AL953841, BC115240, CK141919, CN506496, DT074803, EB765600, EB901237

UniProtKB/TrEMBL

A0A0B5JF80, Q6V9B5

Related

ENSDARP00000071878.4, ENSDART00000077411.5

Conserved Domains (1) summary

cd00273
Location:29 → 89

Chemokine_CXC; Chemokine_CXC: 1 of 4 subgroup designations based on the arrangement of the two N-terminal cysteine residues; includes a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity; many members ...