Clip3 (CAP-GLY domain containing linker protein 3) - Rat Genome Database

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Gene: Clip3 (CAP-GLY domain containing linker protein 3) Mus musculus
Analyze
Symbol: Clip3
Name: CAP-GLY domain containing linker protein 3
RGD ID: 1331911
MGI Page MGI
Description: Predicted to have ganglioside binding activity and microtubule plus-end binding activity. Involved in several processes, including fat cell differentiation; positive regulation of glucose transmembrane transport; and positive regulation of protein localization to plasma membrane. Localizes to plasma membrane and trans-Golgi network. Is expressed in several structures, including central nervous system; genitourinary system; and retina layer. Orthologous to human CLIP3 (CAP-Gly domain containing linker protein 3); INTERACTS WITH 1,2-dimethylhydrazine; 3,4-methylenedioxymethamphetamine; buta-1,3-diene.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: 1500005P14Rik; AI844915; CAP-Gly domain-containing linker protein 3; clip-170 related protein 59 kDa; CLIP-170-related 59 kDa protein; Clipr-59; cytoplasmic linker protein 170-related 59 kDa protein
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39729,991,120 - 30,007,792 (+)NCBIGRCm39mm39
GRCm39 Ensembl729,991,153 - 30,007,792 (+)Ensembl
GRCm38730,291,695 - 30,308,367 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl730,291,728 - 30,308,367 (+)EnsemblGRCm38mm10GRCm38
MGSCv37731,076,772 - 31,093,386 (+)NCBIGRCm37mm9NCBIm37
MGSCv36730,000,513 - 30,017,127 (+)NCBImm8
Celera724,888,679 - 24,904,486 (+)NCBICelera
Cytogenetic Map7B1NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Additional References at PubMed
PMID:8889548   PMID:10349636   PMID:11042159   PMID:11076861   PMID:12477932   PMID:14610273   PMID:15226823   PMID:16141072   PMID:16141073   PMID:18287559   PMID:19139280   PMID:21267068  
PMID:21873635   PMID:22689584   PMID:23482493   PMID:24001771   PMID:25572395   PMID:32581705  


Genomics

Comparative Map Data
Clip3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39729,991,120 - 30,007,792 (+)NCBIGRCm39mm39
GRCm39 Ensembl729,991,153 - 30,007,792 (+)Ensembl
GRCm38730,291,695 - 30,308,367 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl730,291,728 - 30,308,367 (+)EnsemblGRCm38mm10GRCm38
MGSCv37731,076,772 - 31,093,386 (+)NCBIGRCm37mm9NCBIm37
MGSCv36730,000,513 - 30,017,127 (+)NCBImm8
Celera724,888,679 - 24,904,486 (+)NCBICelera
Cytogenetic Map7B1NCBI
CLIP3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1936,014,660 - 36,033,343 (-)EnsemblGRCh38hg38GRCh38
GRCh381936,014,660 - 36,032,873 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371936,505,562 - 36,523,775 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361941,197,403 - 41,215,615 (-)NCBINCBI36hg18NCBI36
Celera1933,219,743 - 33,237,958 (-)NCBI
Cytogenetic Map19q13.12NCBI
HuRef1933,011,111 - 33,029,350 (-)NCBIHuRef
CHM1_11936,506,911 - 36,525,148 (-)NCBICHM1_1
Clip3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2185,547,170 - 85,563,187 (+)NCBI
Rnor_6.0 Ensembl190,962,707 - 90,978,907 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0188,750,453 - 88,766,453 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0192,100,103 - 92,116,122 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4185,238,779 - 85,253,538 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1185,316,889 - 85,331,362 (+)NCBI
Celera179,921,058 - 79,935,799 (+)NCBICelera
Cytogenetic Map1q21NCBI
Clip3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554682,560,953 - 2,575,291 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554682,560,953 - 2,575,073 (+)NCBIChiLan1.0ChiLan1.0
CLIP3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11941,681,432 - 41,699,680 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1941,681,432 - 41,699,680 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01932,932,915 - 32,951,047 (-)NCBIMhudiblu_PPA_v0panPan3
CLIP3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11116,657,613 - 116,670,738 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1116,657,657 - 116,669,667 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1116,063,388 - 116,076,437 (+)NCBI
ROS_Cfam_1.01117,260,885 - 117,273,887 (+)NCBI
UMICH_Zoey_3.11116,824,923 - 116,837,922 (+)NCBI
UNSW_CanFamBas_1.01116,448,500 - 116,461,488 (+)NCBI
UU_Cfam_GSD_1.01117,503,650 - 117,516,694 (+)NCBI
Clip3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934911,280,101 - 11,293,099 (-)NCBI
SpeTri2.0NW_00493692250,230 - 63,215 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLIP3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl645,390,658 - 45,418,873 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1645,390,656 - 45,418,866 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2640,793,340 - 40,809,756 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CLIP3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1630,925,756 - 30,943,736 (-)NCBI
ChlSab1.1 Ensembl630,925,623 - 30,944,071 (-)Ensembl
Vero_WHO_p1.0NW_0236660738,720,714 - 8,738,541 (-)NCBI
Clip3
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462479410,281,133 - 10,295,580 (-)NCBI

Position Markers
UniSTS:235641  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38730,308,071 - 30,308,206UniSTSGRCm38
MGSCv37731,093,090 - 31,093,225UniSTSGRCm37
Celera724,904,190 - 24,904,325UniSTS
Cytogenetic Map7B1UniSTS
AI839550  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38730,314,203 - 30,314,284UniSTSGRCm38
MGSCv37731,099,222 - 31,099,303UniSTSGRCm37
Celera724,910,336 - 24,910,417UniSTS
Cytogenetic Map7B1UniSTS
Whitehead/MRC_RH7412.67UniSTS
AI844915  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38730,308,191 - 30,308,329UniSTSGRCm38
MGSCv37731,093,210 - 31,093,348UniSTSGRCm37
Celera724,904,310 - 24,904,448UniSTS
Cytogenetic Map7B1UniSTS
Whitehead/MRC_RH7414.12UniSTS
CLIPR-59__4586  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38730,307,576 - 30,308,364UniSTSGRCm38
MGSCv37731,092,595 - 31,093,383UniSTSGRCm37
Celera724,903,694 - 24,904,483UniSTS
Cytogenetic Map7B1UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1301572Sluc30_msusceptibility to lung cancer 30 (mouse)Not determined7269777136697919Mouse
1300722Sle3_msystemic lupus erythmatosus susceptibility 3 (mouse)Not determined7346321287493512Mouse
38501068Tip1_mtuberculosis immunophenotype 1, spleen CFU (mouse)7360000072900000Mouse
25314307Mlh1fc2_mMLH1 foci count 2 (mouse)76500000133900000Mouse
1357699Nhdlq6_mnon-HDL QTL 6 (mouse)Not determined71028944244289559Mouse
1558893Spir1_mStreptococcus pneumoniae infection resistance 1 (mouse)Not determined71060637344606511Mouse
10449139Eosn1_meosinophil differential 1 (mouse)71278145246781452Mouse
10449158Eosn3_meosinophil differential 3 (mouse)71278145246781452Mouse
4141566Femwf8_mfemur work to failure 8 (mouse)Not determined1333306047333196Mouse
11522751Cocia17_mcocaine-induced activity, QTL 17 (mouse)71343577947435779Mouse
25314314Sccor1_msynaptonemal complex length to mean MLH1 count ratio 1 (mouse)71360000047700000Mouse
1559016Drsi_mDCC-related Spp1 induction (mouse)Not determined71690336849509583Mouse
1301041Prnr2_mprion resistance 2 (mouse)Not determined71899486940024609Mouse
10412199Sst2_msusceptibility to tuberculosis 2 (mouse)Not determined718994869119886157Mouse
1301158Eae4_msusceptibility to experimental allergic encephalomyelitis 4 (mouse)Not determined719413473142366067Mouse
1301622Eae12_msusceptibility to experimental allergic encephalomyelitis 12 (mouse)Not determined71958059053580679Mouse
1301052Bhr6_mbronchial hyperresponsiveness 6 (mouse)Not determined72014282554142942Mouse
12904742Litsq2_mlitter size QTL 2 (mouse)72302446357024609Mouse
1301709Bdt4_mbone density traits 4 (mouse)Not determined72323914857239292Mouse
11354952Pdcc1_mplasmacytoid dentritic cell compartment 1 (mouse)72341710757417107Mouse
1301969Lbw5_mlupus NZB x NZW 5 (mouse)Not determined72719819161202351Mouse
7394747asp3_maudiogenic seizure prone 3 (mouse)Not determined72760637337142942Mouse
12790989Tgl6_mtriglyceride 6 (mouse)72789112561891125Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1836
Count of miRNA genes:651
Interacting mature miRNAs:804
Transcripts:ENSMUST00000014065, ENSMUST00000125935, ENSMUST00000126216, ENSMUST00000132844, ENSMUST00000144508, ENSMUST00000145253, ENSMUST00000150892
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSMUST00000014065   ⟹   ENSMUSP00000014065
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl730,291,753 - 30,308,367 (+)Ensembl
RefSeq Acc Id: ENSMUST00000125935
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl730,297,117 - 30,299,156 (+)Ensembl
RefSeq Acc Id: ENSMUST00000126216   ⟹   ENSMUSP00000123660
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl730,291,739 - 30,296,923 (+)Ensembl
RefSeq Acc Id: ENSMUST00000132844
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl730,303,902 - 30,307,304 (+)Ensembl
RefSeq Acc Id: ENSMUST00000144508   ⟹   ENSMUSP00000121276
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl730,291,958 - 30,296,934 (+)Ensembl
RefSeq Acc Id: ENSMUST00000145253
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl730,291,728 - 30,292,673 (+)Ensembl
RefSeq Acc Id: ENSMUST00000150892   ⟹   ENSMUSP00000123164
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl730,291,729 - 30,297,167 (+)Ensembl
RefSeq Acc Id: NM_001081114   ⟹   NP_001074583
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39729,991,120 - 30,007,792 (+)NCBI
GRCm38730,291,695 - 30,308,367 (+)NCBI
MGSCv37731,076,772 - 31,093,386 (+)RGD
Celera724,888,679 - 24,904,486 (+)RGD
cM Map7 ENTREZGENE
Sequence:
RefSeq Acc Id: NM_001360763   ⟹   NP_001347692
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39729,991,120 - 30,007,792 (+)NCBI
GRCm38730,291,695 - 30,308,367 (+)NCBI
Sequence:
RefSeq Acc Id: NM_001360764   ⟹   NP_001347693
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39729,991,120 - 30,007,792 (+)NCBI
GRCm38730,291,695 - 30,308,367 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001074583   ⟸   NM_001081114
- UniProtKB: B9EHT4 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001347692   ⟸   NM_001360763
RefSeq Acc Id: NP_001347693   ⟸   NM_001360764
RefSeq Acc Id: ENSMUSP00000123164   ⟸   ENSMUST00000150892
RefSeq Acc Id: ENSMUSP00000121276   ⟸   ENSMUST00000144508
RefSeq Acc Id: ENSMUSP00000014065   ⟸   ENSMUST00000014065
RefSeq Acc Id: ENSMUSP00000123660   ⟸   ENSMUST00000126216
Protein Domains
CAP-Gly

Promoters
RGD ID:6892596
Promoter ID:EPDNEW_M9748
Type:initiation region
Name:Clip3_1
Description:Mus musculus CAP-GLY domain containing linker protein 3 , transcriptvariant 1, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M9749  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38730,291,692 - 30,291,752EPDNEW
RGD ID:6892598
Promoter ID:EPDNEW_M9749
Type:multiple initiation site
Name:Clip3_2
Description:Mus musculus CAP-GLY domain containing linker protein 3 , transcriptvariant 1, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M9748  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38730,291,923 - 30,291,983EPDNEW
RGD ID:6840845
Promoter ID:MM_KWN:49795
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   Brain,   MEF_B4,   MEF_B6
Transcripts:OTTMUST00000059549,   OTTMUST00000059550,   OTTMUST00000059551,   OTTMUST00000059552,   OTTMUST00000059553
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36731,076,396 - 31,076,896 (+)MPROMDB
RGD ID:6840849
Promoter ID:MM_KWN:49796
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Brain
Transcripts:OTTMUST00000059554
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36731,081,451 - 31,081,951 (+)MPROMDB
RGD ID:6840850
Promoter ID:MM_KWN:49797
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Brain
Transcripts:OTTMUST00000059555
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36731,088,101 - 31,088,802 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1923936 AgrOrtholog
Ensembl Genes ENSMUSG00000013921 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSMUSP00000014065 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUSP00000121276 UniProtKB/TrEMBL
  ENSMUSP00000123164 UniProtKB/TrEMBL
  ENSMUSP00000123660 UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000014065 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUST00000126216 UniProtKB/TrEMBL
  ENSMUST00000144508 UniProtKB/TrEMBL
  ENSMUST00000150892 UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.20 UniProtKB/Swiss-Prot
  2.30.30.190 UniProtKB/Swiss-Prot
InterPro Ankyrin_rpt UniProtKB/Swiss-Prot
  Ankyrin_rpt-contain_dom UniProtKB/Swiss-Prot
  Ankyrin_rpt-contain_sf UniProtKB/Swiss-Prot
  CAP-Gly_dom_sf UniProtKB/Swiss-Prot
  CAP-Gly_domain UniProtKB/Swiss-Prot
  CLIP3 UniProtKB/Swiss-Prot
KEGG Report mmu:76686 UniProtKB/Swiss-Prot
MGD MGI:1923936 ENTREZGENE
NCBI Gene 76686 ENTREZGENE
PANTHER PTHR18916:SF77 UniProtKB/Swiss-Prot
Pfam Ank_2 UniProtKB/Swiss-Prot
  CAP_GLY UniProtKB/Swiss-Prot
PhenoGen Clip3 PhenoGen
PROSITE ANK_REP_REGION UniProtKB/Swiss-Prot
  ANK_REPEAT UniProtKB/Swiss-Prot
  CAP_GLY_1 UniProtKB/Swiss-Prot
  CAP_GLY_2 UniProtKB/Swiss-Prot
SMART ANK UniProtKB/Swiss-Prot
  CAP_GLY UniProtKB/Swiss-Prot
Superfamily-SCOP SSF48403 UniProtKB/Swiss-Prot
  SSF74924 UniProtKB/Swiss-Prot
UniProt B9EHT4 ENTREZGENE, UniProtKB/Swiss-Prot
  D3YXY6_MOUSE UniProtKB/TrEMBL
  D3Z115_MOUSE UniProtKB/TrEMBL
  D3Z2W8_MOUSE UniProtKB/TrEMBL
UniProt Secondary Q7TNI1 UniProtKB/Swiss-Prot
  Q9DB67 UniProtKB/Swiss-Prot