Yipf6 (Yip1 domain family, member 6) - Rat Genome Database

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Gene: Yipf6 (Yip1 domain family, member 6) Rattus norvegicus
Analyze
Symbol: Yipf6
Name: Yip1 domain family, member 6
RGD ID: 1566154
Description: Predicted to enable identical protein binding activity. Predicted to be involved in endoplasmic reticulum to Golgi vesicle-mediated transport. Predicted to act upstream of or within intestinal epithelial cell development. Predicted to be located in COPII-coated ER to Golgi transport vesicle and Golgi apparatus. Predicted to be active in trans-Golgi network. Orthologous to human YIPF6 (Yip1 domain family member 6); INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; acrylamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: MGC116126; similar to RIKEN cDNA A430107J06; YIP1 family member 6
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
GRCr8X68,079,754 - 68,091,845 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX68,079,860 - 68,090,530 (+)EnsemblGRCr8
mRatBN7.2X64,039,602 - 64,051,715 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX64,040,952 - 64,054,702 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX65,524,701 - 65,532,965 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X69,025,050 - 69,033,314 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X66,586,007 - 66,594,271 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X68,625,760 - 68,637,780 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX68,626,185 - 68,637,416 (+)Ensemblrn6Rnor6.0
Rnor_5.0X69,499,397 - 69,511,418 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X86,941,818 - 86,950,082 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX64,417,679 - 64,425,943 (+)NCBICelera
Cytogenetic MapXq22NCBI
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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. 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:22802641   PMID:28286305  


Genomics

Comparative Map Data
Yipf6
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X68,079,754 - 68,091,845 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX68,079,860 - 68,090,530 (+)EnsemblGRCr8
mRatBN7.2X64,039,602 - 64,051,715 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX64,040,952 - 64,054,702 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX65,524,701 - 65,532,965 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X69,025,050 - 69,033,314 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X66,586,007 - 66,594,271 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X68,625,760 - 68,637,780 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX68,626,185 - 68,637,416 (+)Ensemblrn6Rnor6.0
Rnor_5.0X69,499,397 - 69,511,418 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X86,941,818 - 86,950,082 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX64,417,679 - 64,425,943 (+)NCBICelera
Cytogenetic MapXq22NCBI
YIPF6
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X68,499,051 - 68,537,282 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX68,498,562 - 68,537,282 (+)Ensemblhg38GRCh38
GRCh37X67,718,893 - 67,757,124 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X67,635,611 - 67,669,026 (+)NCBIBuild 36Build 36hg18NCBI36
CeleraX68,070,045 - 68,103,397 (+)NCBICelera
Cytogenetic MapXq12-q13.1NCBI
HuRefX61,546,257 - 61,584,629 (+)NCBIHuRef
CHM1_1X67,611,366 - 67,649,863 (+)NCBICHM1_1
T2T-CHM13v2.0X66,932,508 - 66,970,741 (+)NCBIT2T-CHM13v2.0
Yipf6
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X97,979,922 - 97,992,627 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX97,979,922 - 97,992,623 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38X98,936,316 - 98,949,021 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX98,936,316 - 98,949,017 (+)Ensemblmm10GRCm38
MGSCv37X96,133,120 - 96,144,360 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36X95,140,500 - 95,151,740 (+)NCBIMGSCv36mm8
CeleraX85,879,308 - 85,890,754 (+)NCBICelera
Cytogenetic MapXC3NCBI
cM MapX43.19NCBI
Yipf6
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554758,084,886 - 8,101,624 (+)Ensembl
ChiLan1.0NW_0049554758,085,017 - 8,101,624 (+)NCBIChiLan1.0ChiLan1.0
YIPF6
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X68,146,112 - 68,225,060 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X68,149,708 - 68,227,390 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X57,738,236 - 57,815,002 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X67,803,914 - 67,879,812 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX67,803,940 - 67,839,711 (+)EnsemblpanPan2panpan1.1
YIPF6
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X53,026,414 - 53,049,619 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX53,026,609 - 53,045,376 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_TashaX43,840,826 - 43,864,105 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0X53,986,027 - 54,009,311 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX53,986,275 - 54,009,309 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X51,960,734 - 51,984,014 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X53,286,087 - 53,309,366 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X53,213,136 - 53,236,425 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Yipf6
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X49,041,150 - 49,064,654 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936777169,080 - 193,231 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936777169,794 - 193,155 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
YIPF6
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX54,661,829 - 54,687,976 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1X54,661,771 - 54,687,988 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X61,698,587 - 61,724,762 (+)NCBISscrofa10.2Sscrofa10.2susScr3
YIPF6
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X58,345,915 - 58,381,517 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX58,346,203 - 58,379,743 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_023666065186,978 - 267,810 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Yipf6
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248911,802,679 - 1,838,666 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248911,802,679 - 1,832,450 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Yipf6
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1X56,929,235 - 56,943,065 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Yipf6
15 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:614
Count of miRNA genes:297
Interacting mature miRNAs:374
Transcripts:ENSRNOT00000008705
Prediction methods:Microtar, Miranda, Pita
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
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX45182909117740458Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between duration of physical contact or close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X4493088389930883Rat


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 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000008705   ⟹   ENSRNOP00000008705
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX64,040,952 - 64,047,933 (+)Ensembl
Rnor_6.0 EnsemblX68,627,329 - 68,635,593 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000076699   ⟹   ENSRNOP00000068227
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX68,627,313 - 68,637,027 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000076795   ⟹   ENSRNOP00000068121
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX68,079,860 - 68,090,530 (+)Ensembl
mRatBN7.2 EnsemblX64,041,195 - 64,054,702 (+)Ensembl
Rnor_6.0 EnsemblX68,627,329 - 68,632,512 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000090942   ⟹   ENSRNOP00000072895
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX68,626,185 - 68,637,416 (+)Ensembl
RefSeq Acc Id: NM_001025747   ⟹   NP_001020918
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X68,081,394 - 68,089,658 (+)NCBI
mRatBN7.2X64,041,194 - 64,049,458 (+)NCBI
Rnor_6.0X68,627,329 - 68,635,593 (+)NCBI
Rnor_5.0X69,499,397 - 69,511,418 (+)NCBI
RGSC_v3.4X86,941,818 - 86,950,082 (+)RGD
CeleraX64,417,679 - 64,425,943 (+)RGD
Sequence:
RefSeq Acc Id: XM_006257077   ⟹   XP_006257139
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X68,079,754 - 68,091,845 (+)NCBI
mRatBN7.2X64,039,602 - 64,051,715 (+)NCBI
Rnor_6.0X68,625,760 - 68,637,780 (+)NCBI
Rnor_5.0X69,499,397 - 69,511,418 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039099896   ⟹   XP_038955824
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X68,081,393 - 68,091,845 (+)NCBI
mRatBN7.2X64,041,181 - 64,051,715 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001020918 (Get FASTA)   NCBI Sequence Viewer  
  XP_006257139 (Get FASTA)   NCBI Sequence Viewer  
  XP_038955824 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH97987 (Get FASTA)   NCBI Sequence Viewer  
  EDL95952 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000068121
  ENSRNOP00000068121.2
GenBank Protein Q4QQU5 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001020918   ⟸   NM_001025747
- UniProtKB: Q4QQU5 (UniProtKB/Swiss-Prot),   A6IQ61 (UniProtKB/TrEMBL),   A0A8L2Q3E7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006257139   ⟸   XM_006257077
- Peptide Label: isoform X1
- UniProtKB: Q4QQU5 (UniProtKB/Swiss-Prot),   A6IQ61 (UniProtKB/TrEMBL),   A0A8L2Q3E7 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000008705   ⟸   ENSRNOT00000008705
Ensembl Acc Id: ENSRNOP00000072895   ⟸   ENSRNOT00000090942
Ensembl Acc Id: ENSRNOP00000068227   ⟸   ENSRNOT00000076699
Ensembl Acc Id: ENSRNOP00000068121   ⟸   ENSRNOT00000076795
RefSeq Acc Id: XP_038955824   ⟸   XM_039099896
- Peptide Label: isoform X2
Protein Domains
Yip1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q4QQU5-F1-model_v2 AlphaFold Q4QQU5 1-236 view protein structure

Transcriptome

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

Promoters
RGD ID:13701858
Promoter ID:EPDNEW_R12380
Type:multiple initiation site
Name:Yipf6_1
Description:Yip1 domain family, member 6
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_6.0X68,627,316 - 68,627,376EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1566154 AgrOrtholog
BioCyc Gene G2FUF-2157 BioCyc
Ensembl Genes ENSRNOG00000006642 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000076795 ENTREZGENE
  ENSRNOT00000076795.3 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7444864 IMAGE-MGC_LOAD
InterPro Yip1 UniProtKB/Swiss-Prot
  Yip1/4-like UniProtKB/Swiss-Prot
KEGG Report rno:363476 UniProtKB/Swiss-Prot
MGC_CLONE MGC:116126 IMAGE-MGC_LOAD
NCBI Gene 363476 ENTREZGENE
PANTHER PROTEIN YIPF6 UniProtKB/Swiss-Prot
  PTHR21236 UniProtKB/Swiss-Prot
Pfam Yip1 UniProtKB/Swiss-Prot
PhenoGen Yipf6 PhenoGen
RatGTEx ENSRNOG00000006642 RatGTEx
UniProt A0A096MJG6_RAT UniProtKB/TrEMBL
  A0A8L2Q3E7 ENTREZGENE
  A6IQ61 ENTREZGENE, UniProtKB/TrEMBL
  Q4QQU5 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-03-30 Yipf6  Yip1 domain family, member 6  MGC116126  similar to RIKEN cDNA A430107J06  Symbol and Name updated 1299863 APPROVED
2006-02-09 MGC116126  similar to RIKEN cDNA A430107J06      Symbol and Name status set to provisional 70820 PROVISIONAL