Rai2 (retinoic acid induced 2) - Rat Genome Database

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Gene: Rai2 (retinoic acid induced 2) Rattus norvegicus
Analyze
Symbol: Rai2
Name: retinoic acid induced 2
RGD ID: 1560139
Description: Predicted to be involved in animal organ development. Predicted to be active in nucleus. Orthologous to human RAI2 (retinoic acid induced 2); INTERACTS WITH 6-propyl-2-thiouracil; acetamide; alpha-Zearalanol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC501555; retinoic acid-induced protein 2; RGD1560139; similar to Retinoic acid induced 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
GRCr8X36,580,406 - 36,642,943 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX36,573,917 - 36,643,240 (-)EnsemblGRCr8
mRatBN7.2X32,948,656 - 33,011,222 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX32,948,656 - 33,011,264 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX33,975,467 - 34,037,926 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X37,418,092 - 37,480,601 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X33,600,431 - 33,662,895 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X34,731,891 - 34,794,589 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX34,731,891 - 34,794,589 (-)Ensemblrn6Rnor6.0
Rnor_5.0X35,074,629 - 35,135,655 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X53,778,991 - 53,810,359 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX33,239,204 - 33,298,772 (-)NCBICelera
Cytogenetic MapXq14NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View
dextrocardia  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleus  (IBA)

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Rai2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X36,580,406 - 36,642,943 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX36,573,917 - 36,643,240 (-)EnsemblGRCr8
mRatBN7.2X32,948,656 - 33,011,222 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX32,948,656 - 33,011,264 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX33,975,467 - 34,037,926 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X37,418,092 - 37,480,601 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X33,600,431 - 33,662,895 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X34,731,891 - 34,794,589 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX34,731,891 - 34,794,589 (-)Ensemblrn6Rnor6.0
Rnor_5.0X35,074,629 - 35,135,655 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X53,778,991 - 53,810,359 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX33,239,204 - 33,298,772 (-)NCBICelera
Cytogenetic MapXq14NCBI
RAI2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X17,800,049 - 17,861,298 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX17,799,788 - 17,861,337 (-)Ensemblhg38GRCh38
GRCh37X17,818,169 - 17,879,418 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X17,728,092 - 17,730,428 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34X17,577,827 - 17,580,164NCBI
CeleraX21,937,489 - 21,998,776 (-)NCBICelera
Cytogenetic MapXp22.13NCBI
HuRefX15,576,074 - 15,613,134 (-)NCBIHuRef
CHM1_1X17,848,557 - 17,909,841 (-)NCBICHM1_1
T2T-CHM13v2.0X17,382,656 - 17,443,905 (-)NCBIT2T-CHM13v2.0
Rai2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X160,500,032 - 160,562,490 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX160,500,065 - 160,562,492 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38X161,717,036 - 161,779,494 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX161,717,069 - 161,779,496 (+)Ensemblmm10GRCm38
MGSCv37X158,154,968 - 158,217,426 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36X157,061,732 - 157,123,598 (+)NCBIMGSCv36mm8
CeleraX144,950,885 - 145,013,085 (+)NCBICelera
Cytogenetic MapXF4NCBI
cM MapX74.07NCBI
Rai2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955519494,463 - 553,839 (+)Ensembl
ChiLan1.0NW_004955519494,463 - 553,839 (+)NCBIChiLan1.0ChiLan1.0
RAI2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X19,598,224 - 19,659,714 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X19,601,616 - 19,663,121 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X10,423,258 - 10,484,740 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X17,791,701 - 17,936,223 (-)NCBIPanPan1.1PanPan1.1panPan2
RAI2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X13,871,795 - 14,021,908 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX13,723,958 - 14,112,454 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0X13,835,556 - 14,224,728 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX13,835,557 - 13,895,871 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X13,902,081 - 14,290,629 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X13,888,388 - 14,277,215 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X13,958,049 - 14,346,972 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Rai2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X7,011,228 - 7,084,787 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364707,016,665 - 7,018,254 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049364707,016,293 - 7,084,787 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RAI2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX14,244,317 - 14,309,143 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1X14,246,776 - 14,633,071 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X15,343,447 - 15,545,694 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RAI2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X16,250,538 - 16,312,788 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX16,250,911 - 16,252,503 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366605618,111,971 - 18,173,806 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rai2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248292,568,763 - 2,633,780 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248292,568,865 - 2,634,268 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Rai2
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1X22,942,360 - 23,003,753 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Rai2
149 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:426
Count of miRNA genes:232
Interacting mature miRNAs:291
Transcripts:ENSRNOT00000008703
Prediction methods:Microtar, Miranda, Pita, 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
1598873Memor2Memory QTL 22.5exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)X2447036044931007Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X400149344939387Rat
2290375Gluco34Glucose level QTL 342.75blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X2447036045082063Rat
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X197044046970440Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X811148653111486Rat

Markers in Region
DXRat42  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr8X36,643,040 - 36,643,279 (+)Marker Load Pipeline
CeleraX33,298,885 - 33,299,123UniSTS
RH 3.4 MapX481.6RGD
RH 3.4 MapX481.6UniSTS
RH 2.0 Map21377.1RGD
SHRSP x BN MapX12.6999RGD
FHH x ACI MapX14.59RGD
Cytogenetic MapXq21UniSTS


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 67 153 91 90 59 28 59 6 291 128 11 132 80 92 31 14 14

Sequence


Ensembl Acc Id: ENSRNOT00000008703   ⟹   ENSRNOP00000008703
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX36,580,406 - 36,643,240 (-)Ensembl
mRatBN7.2 EnsemblX32,948,656 - 33,011,167 (-)Ensembl
Rnor_6.0 EnsemblX34,731,891 - 34,794,589 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000102368   ⟹   ENSRNOP00000096897
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX36,580,819 - 36,642,970 (-)Ensembl
mRatBN7.2 EnsemblX32,949,066 - 33,011,264 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000131492   ⟹   ENSRNOP00000098654
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX36,580,667 - 36,583,749 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000138563   ⟹   ENSRNOP00000101558
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX36,580,846 - 36,643,025 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000144033   ⟹   ENSRNOP00000099644
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX36,580,816 - 36,641,692 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000155249   ⟹   ENSRNOP00000105773
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX36,580,667 - 36,642,970 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000163197   ⟹   ENSRNOP00000103811
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX36,573,917 - 36,643,165 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000173711   ⟹   ENSRNOP00000108932
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX36,573,917 - 36,643,025 (-)Ensembl
RefSeq Acc Id: NM_001109316   ⟹   NP_001102786
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X36,580,406 - 36,642,896 (-)NCBI
mRatBN7.2X32,948,656 - 33,011,167 (-)NCBI
Rnor_6.0X34,731,891 - 34,794,589 (-)NCBI
Rnor_5.0X35,074,629 - 35,135,655 (-)NCBI
RGSC_v3.4X53,778,991 - 53,810,359 (-)RGD
CeleraX33,239,204 - 33,298,772 (-)RGD
Sequence:
RefSeq Acc Id: XM_039099966   ⟹   XP_038955894
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X36,580,816 - 36,642,942 (-)NCBI
mRatBN7.2X32,949,066 - 33,011,222 (-)NCBI
RefSeq Acc Id: XM_063280244   ⟹   XP_063136314
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X36,580,816 - 36,642,943 (-)NCBI
RefSeq Acc Id: XM_063280245   ⟹   XP_063136315
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X36,580,816 - 36,642,505 (-)NCBI
RefSeq Acc Id: XM_063280246   ⟹   XP_063136316
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X36,580,816 - 36,642,943 (-)NCBI
RefSeq Acc Id: XM_063280247   ⟹   XP_063136317
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X36,580,816 - 36,642,943 (-)NCBI
RefSeq Acc Id: XM_063280248   ⟹   XP_063136318
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X36,580,816 - 36,642,943 (-)NCBI
RefSeq Acc Id: NP_001102786   ⟸   NM_001109316
- UniProtKB: D3ZGZ4 (UniProtKB/TrEMBL),   A6K2P7 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000008703   ⟸   ENSRNOT00000008703
RefSeq Acc Id: XP_038955894   ⟸   XM_039099966
- Peptide Label: isoform X1
- UniProtKB: D3ZGZ4 (UniProtKB/TrEMBL),   A6K2P7 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000096897   ⟸   ENSRNOT00000102368
RefSeq Acc Id: XP_063136318   ⟸   XM_063280248
- Peptide Label: isoform X1
- UniProtKB: A6K2P7 (UniProtKB/TrEMBL),   D3ZGZ4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063136317   ⟸   XM_063280247
- Peptide Label: isoform X1
- UniProtKB: A6K2P7 (UniProtKB/TrEMBL),   D3ZGZ4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063136316   ⟸   XM_063280246
- Peptide Label: isoform X1
- UniProtKB: A6K2P7 (UniProtKB/TrEMBL),   D3ZGZ4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063136314   ⟸   XM_063280244
- Peptide Label: isoform X1
- UniProtKB: A6K2P7 (UniProtKB/TrEMBL),   D3ZGZ4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063136315   ⟸   XM_063280245
- Peptide Label: isoform X1
- UniProtKB: A6K2P7 (UniProtKB/TrEMBL),   D3ZGZ4 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000108932   ⟸   ENSRNOT00000173711
Ensembl Acc Id: ENSRNOP00000098654   ⟸   ENSRNOT00000131492
Ensembl Acc Id: ENSRNOP00000101558   ⟸   ENSRNOT00000138563
Ensembl Acc Id: ENSRNOP00000103811   ⟸   ENSRNOT00000163197
Ensembl Acc Id: ENSRNOP00000099644   ⟸   ENSRNOT00000144033
Ensembl Acc Id: ENSRNOP00000105773   ⟸   ENSRNOT00000155249

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZGZ4-F1-model_v2 AlphaFold D3ZGZ4 1-529 view protein structure

Transcriptome

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

Promoters
RGD ID:13701808
Promoter ID:EPDNEW_R12332
Type:single initiation site
Name:Rai2_1
Description:retinoic acid induced 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_6.0X34,794,599 - 34,794,659EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1560139 AgrOrtholog
BioCyc Gene G2FUF-2515 BioCyc
Ensembl Genes ENSRNOG00000006670 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000008703.5 UniProtKB/TrEMBL
  ENSRNOT00000102368.2 UniProtKB/TrEMBL
  ENSRNOT00000131492.1 UniProtKB/TrEMBL
  ENSRNOT00000138563 ENTREZGENE
  ENSRNOT00000138563.1 UniProtKB/TrEMBL
  ENSRNOT00000144033 ENTREZGENE
  ENSRNOT00000144033.1 UniProtKB/TrEMBL
  ENSRNOT00000155249.1 UniProtKB/TrEMBL
  ENSRNOT00000163197 ENTREZGENE
  ENSRNOT00000163197.1 UniProtKB/TrEMBL
  ENSRNOT00000173711.1 UniProtKB/TrEMBL
InterPro RAI2/SOBP UniProtKB/TrEMBL
KEGG Report rno:501555 UniProtKB/TrEMBL
NCBI Gene 501555 ENTREZGENE
PANTHER PTHR23186 UniProtKB/TrEMBL
  RETINOIC ACID-INDUCED PROTEIN 2 UniProtKB/TrEMBL
Pfam SOBP UniProtKB/TrEMBL
PhenoGen Rai2 PhenoGen
RatGTEx ENSRNOG00000006670 RatGTEx
UniProt A0A8I6AMS4_RAT UniProtKB/TrEMBL
  A0ABK0KWA7_RAT UniProtKB/TrEMBL
  A0ABK0LJM4_RAT UniProtKB/TrEMBL
  A0ABK0LLF7_RAT UniProtKB/TrEMBL
  A6K2P7 ENTREZGENE, UniProtKB/TrEMBL
  D3ZGZ4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-28 Rai2  retinoic acid induced 2  RGD1560139_predicted  similar to Retinoic acid induced 2 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1560139_predicted  similar to Retinoic acid induced 2 (predicted)  LOC501555  similar to Retinoic acid induced 2  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC501555  similar to Retinoic acid induced 2      Symbol and Name status set to provisional 70820 PROVISIONAL