Rtn4ip1 (reticulon 4 interacting protein 1) - Rat Genome Database

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Gene: Rtn4ip1 (reticulon 4 interacting protein 1) Rattus norvegicus
Analyze
Symbol: Rtn4ip1
Name: reticulon 4 interacting protein 1
RGD ID: 1563384
Description: Predicted to enable NADPH dehydrogenase (quinone) activity. Predicted to be involved in regulation of dendrite development and ubiquinone biosynthetic process. Predicted to be located in mitochondrial outer membrane. Predicted to be active in mitochondrial matrix. Human ortholog(s) of this gene implicated in optic atrophy 10. Orthologous to human RTN4IP1 (reticulon 4 interacting protein 1); INTERACTS WITH 2,2',5,5'-tetrachlorobiphenyl; 6-propyl-2-thiouracil; alpha-Zearalanol.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC309912; reticulon-4-interacting protein 1, mitochondrial; RGD1563384; similar to NOGO-interacting mitochondrial protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Candidate Gene For: Scl83
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82048,964,903 - 49,004,235 (+)NCBIGRCr8
mRatBN7.22047,382,251 - 47,422,747 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2047,382,234 - 47,422,338 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2049,105,866 - 49,144,126 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02048,755,740 - 48,794,000 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02049,437,837 - 49,477,141 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02048,881,124 - 48,924,921 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2048,881,194 - 48,925,081 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02050,523,639 - 50,566,520 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42047,818,499 - 47,857,762 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2052,570,670 - 52,611,426 (-)NCBICelera
Cytogenetic Map20q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:14651853   PMID:18614015   PMID:22871113   PMID:26593267   PMID:34800366  


Genomics

Comparative Map Data
Rtn4ip1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82048,964,903 - 49,004,235 (+)NCBIGRCr8
mRatBN7.22047,382,251 - 47,422,747 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2047,382,234 - 47,422,338 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2049,105,866 - 49,144,126 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02048,755,740 - 48,794,000 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02049,437,837 - 49,477,141 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02048,881,124 - 48,924,921 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2048,881,194 - 48,925,081 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02050,523,639 - 50,566,520 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42047,818,499 - 47,857,762 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2052,570,670 - 52,611,426 (-)NCBICelera
Cytogenetic Map20q13NCBI
RTN4IP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386106,570,771 - 106,630,491 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6106,570,771 - 106,629,498 (-)EnsemblGRCh38hg38GRCh38
GRCh376107,018,646 - 107,078,366 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 366107,125,596 - 107,184,066 (-)NCBINCBI36Build 36hg18NCBI36
Build 346107,126,544 - 107,184,045NCBI
Celera6107,639,823 - 107,698,287 (-)NCBICelera
Cytogenetic Map6q21NCBI
HuRef6104,465,727 - 104,524,482 (-)NCBIHuRef
CHM1_16107,281,169 - 107,340,137 (-)NCBICHM1_1
T2T-CHM13v2.06107,746,918 - 107,806,978 (-)NCBIT2T-CHM13v2.0
Rtn4ip1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391043,777,772 - 43,823,860 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1043,777,803 - 43,833,197 (+)EnsemblGRCm39 Ensembl
GRCm381043,901,807 - 43,947,863 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1043,901,807 - 43,957,201 (+)EnsemblGRCm38mm10GRCm38
MGSCv371043,621,613 - 43,667,668 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361043,590,222 - 43,636,277 (+)NCBIMGSCv36mm8
Celera1044,773,738 - 44,819,793 (+)NCBICelera
Cytogenetic Map10B2NCBI
cM Map1023.12NCBI
Rtn4ip1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541131,902,848 - 31,950,645 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541131,902,848 - 31,950,645 (-)NCBIChiLan1.0ChiLan1.0
RTN4IP1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25126,573,847 - 126,650,896 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16124,461,121 - 124,538,122 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06104,368,222 - 104,444,583 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16108,258,745 - 108,316,191 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6108,258,745 - 108,315,214 (-)Ensemblpanpan1.1panPan2
RTN4IP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11263,926,803 - 63,972,417 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1263,926,799 - 63,972,369 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1263,714,058 - 63,759,670 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01264,770,070 - 64,815,694 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1264,770,083 - 64,815,636 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11264,131,057 - 64,176,626 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01263,973,679 - 64,019,259 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01264,247,452 - 64,293,044 (-)NCBIUU_Cfam_GSD_1.0
Rtn4ip1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494698,829,816 - 98,874,266 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365643,104,163 - 3,149,072 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365643,104,652 - 3,149,100 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RTN4IP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl172,762,855 - 72,815,540 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1172,763,453 - 72,816,450 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2182,062,555 - 82,112,789 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RTN4IP1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11367,188,707 - 67,243,288 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1367,189,318 - 67,243,925 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604039,524,695 - 39,579,756 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rtn4ip1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462478015,664,836 - 15,705,320 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462478015,606,146 - 15,705,320 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rtn4ip1
663 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:57
Count of miRNA genes:49
Interacting mature miRNAs:54
Transcripts:ENSRNOT00000000304
Prediction methods: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
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201761783247606836Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202510672254435887Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202520973454435887Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)201919072154435887Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202510672254435887Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201769755054435887Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)202924438854435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202510672254435887Rat

Markers in Region
BF401461  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22047,398,057 - 47,398,163 (+)MAPPERmRatBN7.2
Rnor_6.02048,896,993 - 48,897,098NCBIRnor6.0
Rnor_5.02050,539,428 - 50,539,533UniSTSRnor5.0
RGSC_v3.42047,834,273 - 47,834,378UniSTSRGSC3.4
Celera2052,595,547 - 52,595,652UniSTS
RH 3.4 Map20492.93UniSTS
Cytogenetic Map20q13UniSTS


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
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000000304   ⟹   ENSRNOP00000000304
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2047,382,234 - 47,422,338 (+)Ensembl
Rnor_6.0 Ensembl2048,881,194 - 48,925,081 (+)Ensembl
RefSeq Acc Id: NM_001107644   ⟹   NP_001101114
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82048,964,935 - 49,004,235 (+)NCBI
mRatBN7.22047,382,283 - 47,421,587 (+)NCBI
Rnor_6.02048,881,219 - 48,924,167 (+)NCBI
Rnor_5.02050,523,639 - 50,566,520 (+)NCBI
RGSC_v3.42047,818,499 - 47,857,762 (+)RGD
Celera2052,570,670 - 52,611,426 (-)RGD
Sequence:
RefSeq Acc Id: XM_063279188   ⟹   XP_063135258
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82048,964,903 - 48,993,691 (+)NCBI
RefSeq Acc Id: XM_063279189   ⟹   XP_063135259
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82048,964,903 - 48,987,475 (+)NCBI
RefSeq Acc Id: XM_063279190   ⟹   XP_063135260
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82048,964,903 - 48,987,814 (+)NCBI
RefSeq Acc Id: NP_001101114   ⟸   NM_001107644
- UniProtKB: B2GUZ6 (UniProtKB/TrEMBL),   A6K6W3 (UniProtKB/TrEMBL),   F7ESF4 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000000304   ⟸   ENSRNOT00000000304
RefSeq Acc Id: XP_063135258   ⟸   XM_063279188
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063135260   ⟸   XM_063279190
- Peptide Label: isoform X3
RefSeq Acc Id: XP_063135259   ⟸   XM_063279189
- Peptide Label: isoform X2
Protein Domains
Enoyl reductase (ER)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B2GUZ6-F1-model_v2 AlphaFold B2GUZ6 1-396 view protein structure

Transcriptome

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

Promoters
RGD ID:13701681
Promoter ID:EPDNEW_R12205
Type:initiation region
Name:Rtn4ip1_1
Description:reticulon 4 interacting protein 1
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_6.02048,881,185 - 48,881,245EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1563384 AgrOrtholog
BioCyc Gene G2FUF-3308 BioCyc
Ensembl Genes ENSRNOG00000000279 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000304.8 UniProtKB/TrEMBL
  ENSRNOT00000132854 ENTREZGENE
Gene3D-CATH Medium-chain alcohol dehydrogenases, catalytic domain UniProtKB/TrEMBL
  NAD(P)-binding Rossmann-like Domain UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:9030981 IMAGE-MGC_LOAD
InterPro ADH_GroES-like UniProtKB/TrEMBL
  GroES-like UniProtKB/TrEMBL
  NAD(P)-bd_dom_sf UniProtKB/TrEMBL
  PKS_ER UniProtKB/TrEMBL
  Quin_OxRdtase/zeta-crystal_CS UniProtKB/TrEMBL
  RTN4I1 UniProtKB/TrEMBL
  YIM1/Zinc_Alcohol_DH_Fams UniProtKB/TrEMBL
KEGG Report rno:309912 UniProtKB/TrEMBL
MGC_CLONE MGC:187808 IMAGE-MGC_LOAD
NCBI Gene 309912 ENTREZGENE
PANTHER ALCOHOL DEHYDROGENASE RELATED UniProtKB/TrEMBL
  RETICULON-4-INTERACTING PROTEIN 1, MITOCHONDRIAL UniProtKB/TrEMBL
Pfam ADH_N UniProtKB/TrEMBL
  ADH_zinc_N_2 UniProtKB/TrEMBL
PhenoGen Rtn4ip1 PhenoGen
PROSITE QOR_ZETA_CRYSTAL UniProtKB/TrEMBL
RatGTEx ENSRNOG00000000279 RatGTEx
SMART PKS_ER UniProtKB/TrEMBL
Superfamily-SCOP GroES_like UniProtKB/TrEMBL
  SSF51735 UniProtKB/TrEMBL
UniProt A6K6W3 ENTREZGENE, UniProtKB/TrEMBL
  B2GUZ6 ENTREZGENE
  F7ESF4 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary B2GUZ6 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-07 Rtn4ip1  reticulon 4 interacting protein 1  RGD1563384_predicted  similar to NOGO-interacting mitochondrial protein (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1563384_predicted  similar to NOGO-interacting mitochondrial protein (predicted)  LOC309912  similar to NOGO-interacting mitochondrial protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC309912  similar to NOGO-interacting mitochondrial protein      Symbol and Name status set to provisional 70820 PROVISIONAL