Yipf2 (Yip1 domain family, member 2) - Rat Genome Database

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Gene: Yipf2 (Yip1 domain family, member 2) Rattus norvegicus
Analyze
Symbol: Yipf2
Name: Yip1 domain family, member 2
RGD ID: 1307512
Description: Predicted to enable small GTPase binding activity. Predicted to be involved in vesicle-mediated transport. Predicted to be located in Golgi medial cisterna; Golgi trans cisterna; and trans-Golgi network. Predicted to be active in Golgi apparatus. Orthologous to human YIPF2 (Yip1 domain family member 2); INTERACTS WITH 3,4-methylenedioxymethamphetamine; acetamide; acrylamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC363027; RGD1307512; similar to RIKEN cDNA 1300010K09; YIP1 family member 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8828,417,254 - 28,421,455 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl828,417,278 - 28,421,455 (-)EnsemblGRCr8
mRatBN7.2820,141,148 - 20,145,349 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl820,141,155 - 20,145,339 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx824,173,258 - 24,177,468 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0822,468,810 - 22,473,020 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0820,370,780 - 20,374,981 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0822,621,758 - 22,625,959 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl822,621,782 - 22,625,959 (-)Ensemblrn6Rnor6.0
Rnor_5.0822,675,712 - 22,679,913 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4820,694,350 - 20,698,551 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera821,532,460 - 21,536,661 (-)NCBICelera
RGSC_v3.1820,694,359 - 20,698,551 (-)NCBI
Cytogenetic Map8q13NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:15489334   PMID:28286305  


Genomics

Comparative Map Data
Yipf2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8828,417,254 - 28,421,455 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl828,417,278 - 28,421,455 (-)EnsemblGRCr8
mRatBN7.2820,141,148 - 20,145,349 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl820,141,155 - 20,145,339 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx824,173,258 - 24,177,468 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0822,468,810 - 22,473,020 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0820,370,780 - 20,374,981 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0822,621,758 - 22,625,959 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl822,621,782 - 22,625,959 (-)Ensemblrn6Rnor6.0
Rnor_5.0822,675,712 - 22,679,913 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4820,694,350 - 20,698,551 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera821,532,460 - 21,536,661 (-)NCBICelera
RGSC_v3.1820,694,359 - 20,698,551 (-)NCBI
Cytogenetic Map8q13NCBI
YIPF2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381910,922,193 - 10,928,639 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1910,918,919 - 10,928,681 (-)Ensemblhg38GRCh38
GRCh371911,032,869 - 11,039,315 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361910,894,444 - 10,900,357 (-)NCBIBuild 36Build 36hg18NCBI36
Celera1910,928,285 - 10,934,198 (-)NCBICelera
Cytogenetic Map19p13.2NCBI
HuRef1910,611,338 - 10,617,251 (-)NCBIHuRef
CHM1_11911,034,607 - 11,040,520 (-)NCBICHM1_1
T2T-CHM13v2.01911,049,196 - 11,055,650 (-)NCBIT2T-CHM13v2.0
Yipf2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39921,499,978 - 21,504,131 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl921,499,978 - 21,504,124 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38921,588,682 - 21,592,831 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl921,588,682 - 21,592,828 (-)Ensemblmm10GRCm38
MGSCv37921,393,126 - 21,397,190 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36921,339,084 - 21,343,148 (-)NCBIMGSCv36mm8
Celera918,858,302 - 18,862,366 (-)NCBICelera
Cytogenetic Map9A3NCBI
cM Map97.83NCBI
Yipf2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554951,997,720 - 2,006,264 (-)Ensembl
ChiLan1.0NW_0049554952,001,458 - 2,005,880 (-)NCBIChiLan1.0ChiLan1.0
YIPF2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22015,842,497 - 15,849,105 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11914,841,190 - 14,847,745 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01910,475,806 - 10,482,352 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11911,195,553 - 11,201,409 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1911,195,562 - 11,203,248 (-)EnsemblpanPan2panpan1.1
YIPF2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12050,326,437 - 50,331,038 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2050,325,271 - 50,331,031 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2050,199,791 - 50,204,961 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02050,848,514 - 50,853,681 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2050,847,352 - 50,853,676 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12050,057,866 - 50,063,037 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02050,485,152 - 50,490,324 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02050,726,756 - 50,731,927 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Yipf2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118209,228,218 - 209,234,338 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366591,120,483 - 1,126,403 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366591,120,365 - 1,126,418 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
YIPF2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl269,641,052 - 69,649,824 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1269,644,000 - 69,649,691 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2270,079,512 - 70,084,534 (-)NCBISscrofa10.2Sscrofa10.2susScr3
YIPF2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.169,915,133 - 9,927,917 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl69,916,223 - 9,927,902 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366607410,023,539 - 10,029,364 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Yipf2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248282,871,556 - 2,875,503 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248282,871,547 - 2,875,589 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Yipf2
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1817,851,616 - 17,863,085 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Yipf2
28 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:302
Count of miRNA genes:179
Interacting mature miRNAs:217
Transcripts:ENSRNOT00000012138
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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357398Slep3Serum leptin concentration QTL 33.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)81799410550763951Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)81699464261994642Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)81038254055382540Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)81296416557964165Rat
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)81595227960952279Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)81296416557964165Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)81799386262252873Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)81038254055382540Rat
9590084Insglur5Insulin/glucose ratio QTL 518.540.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)8132882639Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)81038254055382540Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)81699464261994642Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)81296416557964165Rat
2302367Slep5Serum leptin concentration QTL 53.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)81799410550763951Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)81038254055382540Rat

Markers in Region
RH132083  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2820,141,659 - 20,141,845 (+)MAPPERmRatBN7.2
Rnor_6.0822,622,270 - 22,622,455NCBIRnor6.0
Rnor_5.0822,676,224 - 22,676,409UniSTSRnor5.0
RGSC_v3.4820,694,862 - 20,695,047UniSTSRGSC3.4
Celera821,532,972 - 21,533,157UniSTS
RH 3.4 Map8180.7UniSTS
Cytogenetic Map8q13UniSTS
RH133576  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2820,141,434 - 20,141,616 (+)MAPPERmRatBN7.2
Rnor_6.0822,622,045 - 22,622,226NCBIRnor6.0
Rnor_5.0822,675,999 - 22,676,180UniSTSRnor5.0
RGSC_v3.4820,694,637 - 20,694,818UniSTSRGSC3.4
Celera821,532,747 - 21,532,928UniSTS
RH 3.4 Map8181.3UniSTS
Cytogenetic Map8q13UniSTS
Carm1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2820,141,241 - 20,141,716 (+)MAPPERmRatBN7.2
Rnor_6.0822,621,852 - 22,622,326NCBIRnor6.0
Rnor_5.0822,675,806 - 22,676,280UniSTSRnor5.0
RGSC_v3.4820,694,444 - 20,694,918UniSTSRGSC3.4
Celera821,532,554 - 21,533,028UniSTS
Cytogenetic Map8q13UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 161 91 90 59 92 59 6 356 192 11 140 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000012138   ⟹   ENSRNOP00000012138
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl828,417,278 - 28,421,455 (-)Ensembl
mRatBN7.2 Ensembl820,141,155 - 20,145,339 (-)Ensembl
Rnor_6.0 Ensembl822,621,782 - 22,625,959 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000116283   ⟹   ENSRNOP00000087888
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl820,141,155 - 20,145,339 (-)Ensembl
RefSeq Acc Id: NM_001014208   ⟹   NP_001014230
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8828,417,254 - 28,421,455 (-)NCBI
mRatBN7.2820,141,148 - 20,145,349 (-)NCBI
Rnor_6.0822,621,758 - 22,625,959 (-)NCBI
Rnor_5.0822,675,712 - 22,679,913 (-)NCBI
RGSC_v3.4820,694,350 - 20,698,551 (-)RGD
Celera821,532,460 - 21,536,661 (-)RGD
Sequence:
RefSeq Acc Id: NP_001014230   ⟸   NM_001014208
- UniProtKB: Q5XIT3 (UniProtKB/Swiss-Prot),   A6JNT4 (UniProtKB/TrEMBL),   A0A8I6A8N0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000012138   ⟸   ENSRNOT00000012138
Ensembl Acc Id: ENSRNOP00000087888   ⟸   ENSRNOT00000116283
Protein Domains
Yip1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5XIT3-F1-model_v2 AlphaFold Q5XIT3 1-311 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13695784
Promoter ID:EPDNEW_R6309
Type:initiation region
Name:Yipf2_1
Description:Yip1 domain family, member 2
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0822,625,931 - 22,625,991EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307512 AgrOrtholog
BioCyc Gene G2FUF-31414 BioCyc
Ensembl Genes ENSRNOG00000022043 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000012138 ENTREZGENE
  ENSRNOT00000012138.6 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7131986 IMAGE-MGC_LOAD
InterPro Yip1 UniProtKB/Swiss-Prot
  Yip5/YIPF1/YIPF2 UniProtKB/Swiss-Prot
KEGG Report rno:363027 UniProtKB/Swiss-Prot
MGC_CLONE MGC:94285 IMAGE-MGC_LOAD
NCBI Gene 363027 ENTREZGENE
PANTHER PROTEIN YIPF2 UniProtKB/Swiss-Prot
  PTHR12822 UniProtKB/Swiss-Prot
Pfam Yip1 UniProtKB/Swiss-Prot
PhenoGen Yipf2 PhenoGen
RatGTEx ENSRNOG00000022043 RatGTEx
UniProt A0A8I6A8N0 ENTREZGENE, UniProtKB/TrEMBL
  A6JNT2_RAT UniProtKB/TrEMBL
  A6JNT4 ENTREZGENE, UniProtKB/TrEMBL
  A6JNT5_RAT UniProtKB/TrEMBL
  Q5XIT3 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 Yipf2  Yip1 domain family, member 2  RGD1307512  similar to RIKEN cDNA 1300010K09  Symbol and Name updated 1299863 APPROVED
2005-12-06 RGD1307512  similar to RIKEN cDNA 1300010K09  RGD1307512_predicted  similar to RIKEN cDNA 1300010K09 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1307512_predicted  similar to RIKEN cDNA 1300010K09 (predicted)  LOC363027_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC363027_predicted  similar to RIKEN cDNA 1300010K09 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL