Clip3 MGI Mouse Gene Detail - MGI:1923936 - CAP-GLY domain containing linker protein 3

Symbol

Clip3
Name

CAP-GLY domain containing linker protein 3
Synonyms

1500005P14Rik

Feature Type

protein coding gene
IDs

MGI:1923936
NCBI Gene: 76686
Alliance

gene page
Transcription Start Sites

12 TSS

Sequence Map

Chr7:29991153-30007792 bp, + strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 7, 17.37 cM, cytoband A3
Mapping Data

3 experiments

SNPs within 2kb

534 from dbSNP Build 142
Strain Annotations

18

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1923936	protein coding gene	Chr7:29991120-30007792 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0032011	protein coding gene	Chr7:29277069-29292905 (+)
A/J	MGP_AJ_G0031988	protein coding gene	Chr7:28502219-28517970 (+)
AKR/J	MGP_AKRJ_G0031921	protein coding gene	Chr7:29233900-29249643 (+)
BALB/cJ	MGP_BALBcJ_G0031995	protein coding gene	Chr7:28677605-28693551 (+)
C3H/HeJ	MGP_C3HHeJ_G0031714	protein coding gene	Chr7:29675436-29692246 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0032460	protein coding gene	Chr7:30220727-30245232 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0029511	protein coding gene	Chr7:29538350-29554029 (+)
CAST/EiJ	MGP_CASTEiJ_G0031048	protein coding gene	Chr7:22927559-22945475 (+)
CBA/J	MGP_CBAJ_G0031680	protein coding gene	Chr7:31683793-31704201 (+)
DBA/2J	MGP_DBA2J_G0031832	protein coding gene	Chr7:28231277-28247488 (+)
FVB/NJ	MGP_FVBNJ_G0031789	protein coding gene	Chr7:28349106-28365345 (+)
LP/J	MGP_LPJ_G0031913	protein coding gene	Chr7:29596407-29614309 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0031825	protein coding gene	Chr7:30933632-30954375 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0032489	protein coding gene	Chr7:28729371-28748570 (+)
PWK/PhJ	MGP_PWKPhJ_G0030774	protein coding gene	Chr7:23266249-23282294 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0030607	protein coding gene	Chr7:19733284-19748865 (+)
WSB/EiJ	MGP_WSBEiJ_G0031158	protein coding gene	Chr7:29112646-29129400 (+)

Human Ortholog

CLIP3, CAP-Gly domain containing linker protein 3

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

CLIP3, CAP-Gly domain containing linker protein 3
Synonyms

CLIPR-59, CLIPR59, RSNL1
Links

HGNC:24314

NCBI Gene ID: 25999

neXtProt AC: NX_Q96DZ5

UniProt: Q96DZ5
Chr Location

19q13.12; chr19:36014660-36033343 (-) GRCh38

MGI Vertebrate Homology

Clip3 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: CLIP3
Gene Tree

Clip3

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Phenotype Summary

9 phenotypes from 1 allele in 1 genetic background
4 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

6
Gene trapped

1
Targeted

5
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

19 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a knock-out allele exhibit impaired phrenic nerve-elicited muscle contraction, defects in diaphragm innervation, altered neuromuscular junction stability, abnormal motor innervation of other muscles, and complete neonatal lethality due to respiratory failure.

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All GO Annotations

38
GO References

5

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

811
Tissues

84
cDNA Data

99
Literature Summary

4

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas
Other Vertebrate Links

Xenbase clip3

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All Sequences

52
RefSeq

6
UniProt

4
CCDS

CCDS39880.1

Ensembl

ENSMUSG00000013921 (Evidence)
NCBI Gene

76686

			Length	Strain/Species	Flank
genomic	ENSMUSG00000013921	Ensembl Gene Model \| MGI Sequence Detail	16640	C57BL/6J	± kb
transcript	ENSMUST00000014065	Ensembl \| MGI Sequence Detail	3300	Not Applicable
polypeptide	ENSMUSP00000014065	Ensembl \| MGI Sequence Detail	547	Not Applicable

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UniProt

4 Sequences
Protein Ontology

PR:000005583 CAP-Gly domain-containing linker protein 3

(term hierarchy)
PDB

1WHH
InterPro Domains

IPR002110 Ankyrin repeat

IPR036770 Ankyrin repeat-containing domain superfamily

IPR000938 CAP Gly-rich domain

IPR036859 CAP Gly-rich domain superfamily

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All nucleic 101

cDNA 100

Other 1

Microarray probesets 5

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MGI:2142044

Summaries

All 33

Developmental Gene Expression 4

Gene Ontology 5

Phenotypes 4
Earliest

J:65060 Kawai J, et al., Functional annotation of a full-length mouse cDNA collection. Nature. 2001 Feb 8;409(6821):685-90
Latest

J:206108 Ren W, et al., DHHC17 palmitoylates ClipR-59 and modulates ClipR-59 association with the plasma membrane. Mol Cell Biol. 2013 Nov;33(21):4255-65

TSS for Clip3:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr65670	Chr7:29991084-29991193 (+)	-14 bp
Tssr65671	Chr7:29991196-29991204 (+)	47 bp
Tssr65672	Chr7:29991209-29991212 (+)	58 bp
Tssr65673	Chr7:29991228-29991232 (+)	77 bp
Tssr65674	Chr7:29991341-29991364 (+)	200 bp
Tssr65675	Chr7:29991366-29991393 (+)	227 bp
Tssr65676	Chr7:29991426-29991437 (+)	279 bp
Tssr65677	Chr7:29991570-29991594 (+)	429 bp
Tssr65678	Chr7:29991683-29991728 (+)	553 bp
Tssr65679	Chr7:29998368-29998385 (+)	7,224 bp
Tssr65680	Chr7:30002894-30002907 (+)	11,748 bp
Tssr65681	Chr7:30003331-30003351 (+)	12,188 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