CXCL13 (C-X-C motif chemokine ligand 13)

Gene: CXCL13 (C-X-C motif chemokine ligand 13) Sus scrofa

Analyze

Symbol:

CXCL13

Name:

C-X-C motif chemokine ligand 13

RGD ID:

13865318

Description:

ENCODES a protein that exhibits CCR10 chemokine receptor binding (ortholog); CXCR3 chemokine receptor binding (ortholog); CXCR5 chemokine receptor binding (ortholog); INVOLVED IN B cell chemotaxis (ortholog); B cell chemotaxis across high endothelial venule (ortholog); cell surface receptor signaling pathway (ortholog); ASSOCIATED WITH endometriosis (ortholog); Experimental Liver Cirrhosis (ortholog); genetic disease (ortholog); FOUND IN extracellular region (inferred); extracellular space (inferred); INTERACTS WITH deoxynivalenol; zearalenone

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

C-X-C motif chemokine 13

RGD Orthologs

Alliance Genes

More Info

more info ...

Latest Assembly:

Sscrofa11.1 - Pig Sscrofa11.1 Assembly

Position:

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1	8	73,071,261 - 73,077,342 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	8	77,268,254 - 77,274,314 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

endometriosis (ISO)

Experimental Liver Cirrhosis (ISO)

genetic disease (ISO)

malignant mesothelioma (ISO)

Recurrence (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

deoxynivalenol (EXP)

zearalenone (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

antimicrobial humoral immune response mediated by antimicrobial peptide (IBA)

B cell chemotaxis (ISO)

B cell chemotaxis across high endothelial venule (ISO)

cell chemotaxis (IEA)

cell surface receptor signaling pathway (ISO)

cell-cell signaling (ISO)

cellular response to lipopolysaccharide (IBA)

chemokine-mediated signaling pathway (IBA)

chemotaxis (IEA)

defense response (IEA)

defense response to bacterium (ISO)

endothelial cell chemotaxis to fibroblast growth factor (ISO)

immune response (IEA)

inflammatory response (IBA)

lymph node development (ISO)

lymphocyte chemotaxis across high endothelial venule (ISO)

negative regulation of endothelial cell chemotaxis to fibroblast growth factor (ISO)

neutrophil chemotaxis (IBA)

positive regulation of cell-cell adhesion mediated by integrin (ISO)

positive regulation of cytosolic calcium ion concentration (ISO)

positive regulation of integrin activation (ISO)

positive regulation of T cell chemotaxis (ISO)

signal transduction (IEA)

Cellular Component

extracellular region (IEA)

extracellular space (IBA,IEA)

Molecular Function

CCR10 chemokine receptor binding (ISO)

chemokine activity (IBA,IEA)

CXCR chemokine receptor binding (IBA)

CXCR3 chemokine receptor binding (ISO)

CXCR5 chemokine receptor binding (ISO)

cytokine activity (IEA)

fibroblast growth factor binding (ISO)

heparin binding (ISO)

receptor ligand activity (ISO)

References

Additional References at PubMed

PMID:14681463	PMID:17145712	PMID:22301074	PMID:30032202

Genomics

Comparative Map Data

CXCL13
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1	8	73,071,261 - 73,077,342 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	8	77,268,254 - 77,274,314 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

CXCL13
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	4	77,511,753 - 77,611,834 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	4	77,511,753 - 77,611,834 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	4	78,432,907 - 78,532,988 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	4	78,651,931 - 78,752,010 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	4	78,790,084 - 78,890,165	NCBI
Celera	4	75,734,287 - 75,834,362 (+)	NCBI		Celera
Cytogenetic Map	4	q21.1	NCBI
HuRef	4	74,184,783 - 74,284,964 (+)	NCBI		HuRef
CHM1_1	4	78,409,854 - 78,509,941 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	4	80,852,591 - 80,952,672 (+)	NCBI		T2T-CHM13v2.0

Cxcl13
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	5	96,104,785 - 96,108,927 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	5	96,104,810 - 96,108,927 (+)	Ensembl		GRCm39 Ensembl
GRCm38	5	95,956,939 - 95,961,068 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	5	95,956,951 - 95,961,068 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	5	96,385,958 - 96,390,087 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	5	96,197,241 - 96,201,370 (+)	NCBI		MGSCv36	mm8
Celera	5	93,306,539 - 93,310,668 (+)	NCBI		Celera
Cytogenetic Map	5	E3	NCBI
cM Map	5	47.29	NCBI

Cxcl13
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	14	13,912,858 - 13,917,920 (-)	NCBI		GRCr8
mRatBN7.2	14	13,608,894 - 13,613,965 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	14	13,608,902 - 13,613,933 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	14	13,576,171 - 13,581,214 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	14	14,876,016 - 14,881,059 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	14	13,592,498 - 13,597,541 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	14	15,253,146 - 15,258,221 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	14	15,253,125 - 15,258,207 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	14	15,193,472 - 15,198,546 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	14	15,126,332 - 15,131,368 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
Celera	14	13,649,303 - 13,654,347 (-)	NCBI		Celera
Cytogenetic Map	14	p22	NCBI

Cxcl13
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0	NW_004955433	2,123,190 - 2,129,119 (+)	NCBI	ChiLan1.0	ChiLan1.0

CXCL13
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	3	52,453,375 - 52,460,491 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	4	52,639,881 - 52,646,923 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	4	46,583,759 - 46,589,865 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	4	52,428,702 - 52,434,803 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	4	52,428,702 - 52,434,803 (-)	Ensembl	panpan1.1		panPan2

CXCL13
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	32	2,047,277 - 2,053,277 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	32	2,047,315 - 2,052,833 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	32	39,837,784 - 39,843,805 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	32	2,073,585 - 2,079,610 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	32	2,073,621 - 2,081,627 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	32	2,071,444 - 2,077,479 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	32	2,019,776 - 2,025,803 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	32	38,148,529 - 38,154,567 (-)	NCBI		UU_Cfam_GSD_1.0

Cxcl13
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024405285	10,191,903 - 10,197,633 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936676	1,309,625 - 1,313,933 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936676	1,309,625 - 1,314,532 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CXCL13
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	7	26,101,489 - 26,108,430 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	7	26,102,714 - 26,108,690 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666037	4,454,575 - 4,460,831 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Cxcl13
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla_female_1.0 Ensembl	NW_004624757	13,488,670 - 13,494,837 (-)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624757	13,488,787 - 13,494,831 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in CXCL13
226 total Variants

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	hemolymphoid system	musculoskeletal system	nervous system	reproductive system	respiratory system
High
Medium	4	2		5			1	3
Low	6				2	4
Below cutoff			1			13	1

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_003129101	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AEMK02000067	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AK237249	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AK347056	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CU928317	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GFLN01117773	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

XM_003129101 ⟹ XP_003129149

Type:

CODING

Position:

Pig Assembly	Chr	Position (strand)	Source
Sscrofa11.1	8	73,071,261 - 73,077,342 (+)	NCBI

Sequence:

show sequence

TCTAAATAAATAGGAGTCCCTGTGCTGAGAACCCACAGTTGGGACTCAAGAGCTGAAGTCTGAA
CTCCACCTTGAGGCAGAATGAGGTTCACACTGGGATCTCTGCTTCTCGTGCTGCTGCTGGCCTG
CAGCCTGTTCCCCATCCATGGTGTTCTGGAGACCAATGACACAAATTTGAAGTGTCAATGCCTC
CGAAGCACCTCGAACTGGGTCCCTATCCGCCTCATTGAAAAGATTCAAATCTGGCCTCCTGGGA
ATGGATGTCCAACCAGAGAAGTCATAGTCTGGATGACGAATAAGACAGCTATCTGCTTGAACCC
TCAAAGCAAACTGTTACAAAAACTAATAAACCTGATGTGGAGAAAAAAGACTTCTACAACTTTA
CCAGCTCCAGTGTCTAAGAAAAGCATTGCCTGACGCCAATAACCCCACCAAGGACACCTGCACG
CCTTTTCTTCCCACTCTGGATTTTAGTTTGGGGTTTGATTGGCTCTTTTCCAGAAGATCTTTCC
CATCCAAGCAAGCATGAGAATATATGCAAAAATTATCTTGCAGAAGCTGATGGGGCAAGCTTGA
GCTTTTTTTGAATATAGTGCCCCCCCTACTGACCATTTGCGTTCTTAGTCATCAGGGAGGAAAC
GTTCCTTGAGGATAGTTGTTTAGTTATAAATCACAGGGGTTTCTCTCCCAAAAAACATACCTGT
TGTAGAATGCTAAATTTTCCAAGAAAATAAGCCTTTGAGGATTTAAACCTTACATCTGAACATG
TGGCTTGAATTAAGGCGCAAATGATTGAAATGAATTTCAATCATTTTACACCCTAAGAAAAGCA
AGCCTCCGGAAGAGATTGAAAAAGCTGCCTGGGAAACCCATGGAGTTTCAGCCTGACAAGAGAC
AGAAGGTTCATGTCATAGCTACCCTTTGTTTAAAAGCTCACTCTTGAGAGGAATGGGGTCCTTC
TTCAACTTTTAAAGACTTTCTTTATCAGATTTATTGTCACAGATAAAGACGAATAGCTTCATAT
AGAGACTATTTAGGAAAAGCATATTTAGATGTATTCTCATACATTTGCTTTGATGAACTTTTTT
TTTAAATCACCTTTTGCACAGAGTATCTGGTGGGGGGGGCCCTCTGGTGTTCAATTCTTTAATG
CTTCCTATTAACCTAATGCTATTCAATAAACTTGAGCAATTGTTTTACTTAA

hide sequence

Protein Sequences


Protein RefSeqs	XP_003129149	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSSSCP00000039756
	ENSSSCP00000039756.1
	ENSSSCP00005045191.1
	ENSSSCP00015020124.1
	ENSSSCP00025009787.1
	ENSSSCP00030005867.1
	ENSSSCP00035026367.1
	ENSSSCP00040018133.1
	ENSSSCP00045000752.1
	ENSSSCP00045000758.1
	ENSSSCP00055023750.1
	ENSSSCP00055023777.1
	ENSSSCP00060012150.1
	ENSSSCP00065048413.1
	ENSSSCP00070006474.1

RefSeq Acc Id:	XP_003129149 ⟸ XM_003129101
- UniProtKB:	A0A287A706 (UniProtKB/TrEMBL), A0A4X1SVT8 (UniProtKB/TrEMBL), A0A8D1E7E0 (UniProtKB/TrEMBL), A0A8D0TRN1 (UniProtKB/TrEMBL)
- Sequence:	show sequence MRFTLGSLLLVLLLACSLFPIHGVLETNDTNLKCQCLRSTSNWVPIRLIEKIQIWPPGNGCPTR EVIVWMTNKTAICLNPQSKLLQKLINLMWRKKTSTTLPAPVSKKSIA hide sequence

Protein Domains

Chemokine interleukin-8-like

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSSSCG00000036445	ENTREZGENE, UniProtKB/TrEMBL
	ENSSSCG00005044841	UniProtKB/TrEMBL
	ENSSSCG00015037947	UniProtKB/TrEMBL
	ENSSSCG00025017340	UniProtKB/TrEMBL
	ENSSSCG00030009531	UniProtKB/TrEMBL
	ENSSSCG00035048916	UniProtKB/TrEMBL
	ENSSSCG00040032131	UniProtKB/TrEMBL
	ENSSSCG00045000905	UniProtKB/TrEMBL
	ENSSSCG00055015137	UniProtKB/TrEMBL
	ENSSSCG00060020921	UniProtKB/TrEMBL
	ENSSSCG00065078246	UniProtKB/TrEMBL
	ENSSSCG00070004192	UniProtKB/TrEMBL
Ensembl Transcript	ENSSSCT00000049718	ENTREZGENE
	ENSSSCT00000049718.2	UniProtKB/TrEMBL
	ENSSSCT00005072292.1	UniProtKB/TrEMBL
	ENSSSCT00015050444.1	UniProtKB/TrEMBL
	ENSSSCT00025023405.1	UniProtKB/TrEMBL
	ENSSSCT00030013035.1	UniProtKB/TrEMBL
	ENSSSCT00035065145.1	UniProtKB/TrEMBL
	ENSSSCT00040043209.1	UniProtKB/TrEMBL
	ENSSSCT00045001315.1	UniProtKB/TrEMBL
	ENSSSCT00045001325.1	UniProtKB/TrEMBL
	ENSSSCT00055029829.1	UniProtKB/TrEMBL
	ENSSSCT00055029861.1	UniProtKB/TrEMBL
	ENSSSCT00060028363.1	UniProtKB/TrEMBL
	ENSSSCT00065108355.1	UniProtKB/TrEMBL
	ENSSSCT00070007875.1	UniProtKB/TrEMBL
Gene3D-CATH	2.40.50.40	UniProtKB/TrEMBL
InterPro	Chemokine_b/g/d	UniProtKB/TrEMBL
	Chemokine_CXC	UniProtKB/TrEMBL
	Chemokine_CXC_CS	UniProtKB/TrEMBL
	Chemokine_IL8-like_dom	UniProtKB/TrEMBL
	CXC_Chemokine_domain	UniProtKB/TrEMBL
	Interleukin_8-like_sf	UniProtKB/TrEMBL
KEGG Report	ssc:100524265	UniProtKB/TrEMBL
NCBI Gene	CXCL13	ENTREZGENE
PANTHER	C-X-C MOTIF CHEMOKINE 13	UniProtKB/TrEMBL
	SMALL INDUCIBLE CYTOKINE A	UniProtKB/TrEMBL
Pfam	IL8	UniProtKB/TrEMBL
PRINTS	INTERLEUKIN8	UniProtKB/TrEMBL
	SMALLCYTKCXC	UniProtKB/TrEMBL
PROSITE	PROKAR_LIPOPROTEIN	UniProtKB/TrEMBL
	SMALL_CYTOKINES_CXC	UniProtKB/TrEMBL
SMART	SCY	UniProtKB/TrEMBL
Superfamily-SCOP	SSF54117	UniProtKB/TrEMBL
UniProt	A0A287A706	ENTREZGENE, UniProtKB/TrEMBL
	A0A4X1SVT8	ENTREZGENE, UniProtKB/TrEMBL
	A0A8D0TRN1	ENTREZGENE, UniProtKB/TrEMBL
	A0A8D1E7E0	ENTREZGENE, UniProtKB/TrEMBL
	A0A8D1GA37_PIG	UniProtKB/TrEMBL
	A0A8D1U3B4_PIG	UniProtKB/TrEMBL
VGNC ID	VGNC:87104	ENTREZGENE

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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