Clcf1 MGI Mouse Gene Detail - MGI:1930088 - cardiotrophin-like cytokine factor 1

Symbol

Clcf1
Name

cardiotrophin-like cytokine factor 1
Synonyms

Bsf3, CLC, NNT-1/BSF-3

Feature Type

protein coding gene
IDs

MGI:1930088
NCBI Gene: 56708
Alliance

gene page
Transcription Start Sites

2 TSS

Sequence Map

Chr19:4264479-4273548 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 19, 3.91 cM, cytoband A
Mapping Data

1 experiment

SNPs within 2kb

157 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1930088	protein coding gene	Chr19:4264292-4273548 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0024657	protein coding gene	Chr19:1058549-1067800 (+)
A/J	MGP_AJ_G0024623	protein coding gene	Chr19:1016804-1026067 (+)
AKR/J	MGP_AKRJ_G0024596	protein coding gene	Chr19:1045145-1054399 (+)
BALB/cJ	MGP_BALBcJ_G0024623	protein coding gene	Chr19:1007290-1016564 (+)
C3H/HeJ	MGP_C3HHeJ_G0024391	protein coding gene	Chr19:1041880-1051163 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0025071	protein coding gene	Chr19:1095417-1104681 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0022500	protein coding gene	Chr19:959466-969583 (+)
CAST/EiJ	MGP_CASTEiJ_G0023863	protein coding gene	Chr19:1055638-1064938 (+)
CBA/J	MGP_CBAJ_G0024362	protein coding gene	Chr19:1159196-1168469 (+)
DBA/2J	MGP_DBA2J_G0024490	protein coding gene	Chr19:977100-986352 (+)
FVB/NJ	MGP_FVBNJ_G0024457	protein coding gene	Chr19:986566-995804 (+)
LP/J	MGP_LPJ_G0024576	protein coding gene	Chr19:1051730-1060981 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0024487	protein coding gene	Chr19:1099810-1109060 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0025118	protein coding gene	Chr19:1042556-1051810 (+)
PWK/PhJ	MGP_PWKPhJ_G0023609	protein coding gene	Chr19:1030416-1039766 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0023414	protein coding gene	Chr19:1023868-1033825 (+)
WSB/EiJ	MGP_WSBEiJ_G0023925	protein coding gene	Chr19:1030316-1040926 (+)

Human Ortholog

CLCF1, cardiotrophin like cytokine factor 1

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

CLCF1, cardiotrophin like cytokine factor 1
Synonyms

BSF-3, BSF3, CISS2, CLC, NNT-1, NNT1, NR6
Links

HGNC:17412

NCBI Gene ID: 23529

neXtProt AC: NX_Q9UBD9

UniProt: Q9UBD9
Chr Location

11q13.2; chr11:67364168-67374177 (-) GRCh38

MGI Vertebrate Homology

Clcf1 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: CLCF1
Gene Tree

Clcf1

Diseases

1 with human CLCF1 associations

				Human Disease	Mouse Models
				cold-induced sweating syndrome 2 IDs cold-induced sweating syndrome 2 DOID:0080330 OMIM:610313

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

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Phenotype Summary

11 phenotypes from 3 alleles in 3 genetic backgrounds
11 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

7
Endonuclease-mediated

3
Targeted

4
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

13 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a knock-out allele exhibit postnatal lethality associated with a failure to suckle and decreased facial and spinal motor neurons.

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All GO Annotations

43
GO References

12

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

750
Tissues

37
cDNA Data

14
Literature Summary

8

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase clcf1

ZFIN clcf1

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All Sequences

51
RefSeq

6
UniProt

5
CCDS

CCDS29423.1

Ensembl

ENSMUSG00000040663 (Evidence)
NCBI Gene

56708

			Length	Strain/Species	Flank
genomic	56708	NCBI Gene Model \| MGI Sequence Detail	9070	C57BL/6J	± kb
transcript	NM_001310039	RefSeq \| MGI Sequence Detail	1796	C57BL/6
polypeptide	Q9QZM3	UniProt \| EBI \| MGI Sequence Detail	225	Not Applicable

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UniProt

5 Sequences
Protein Ontology

PR:000005527 cardiotrophin-like cytokine factor 1

(term hierarchy)
InterPro Domains

IPR009079 Four-helical cytokine-like, core

IPR010681 Plethodontid receptivity factor PRF/cardiotrophin-like
GlyGen

Q9QZM3 1 site

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All nucleic 17

cDNA 14

Primer pair 3

Microarray probesets 5

Summaries

All 47

Developmental Gene Expression 8

Gene Ontology 12

Phenotypes 11
Earliest

J:57927 Senaldi G, et al., Novel neurotrophin-1/B cell-stimulating factor-3: a cytokine of the IL-6 family. Proc Natl Acad Sci U S A. 1999 Sep 28;96(20):11458-63
Latest

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

TSS for Clcf1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr154303	Chr19:4264470-4264486 (+)	-1 bp
Tssr154304	Chr19:4265886-4265901 (+)	1,415 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)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 11/12/2024 MGI 6.24