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 have oxidoreductase activity and zinc ion binding activity. Predicted to be involved in regulation of dendrite development. Predicted to localize to mitochondrial outer membrane. 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; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also 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 Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22047,382,251 - 47,422,747 (+)NCBI
Rnor_6.0 Ensembl2048,881,194 - 48,925,081 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02048,881,124 - 48,924,921 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02050,523,639 - 50,566,520 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42047,818,499 - 47,857,762 (+)NCBIRGSC3.4rn4RGSC3.4
Celera2052,570,670 - 52,611,426 (-)NCBICelera
Cytogenetic Map20q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:12477932   PMID:14651853   PMID:18614015   PMID:22871113   PMID:26593267  


Genomics

Comparative Map Data
Rtn4ip1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22047,382,251 - 47,422,747 (+)NCBI
Rnor_6.0 Ensembl2048,881,194 - 48,925,081 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02048,881,124 - 48,924,921 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02050,523,639 - 50,566,520 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42047,818,499 - 47,857,762 (+)NCBIRGSC3.4rn4RGSC3.4
Celera2052,570,670 - 52,611,426 (-)NCBICelera
Cytogenetic Map20q13NCBI
RTN4IP1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl6106,570,771 - 106,629,498 (-)EnsemblGRCh38hg38GRCh38
GRCh386106,559,237 - 106,630,921 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh376107,018,646 - 107,078,366 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 366107,125,596 - 107,184,066 (-)NCBINCBI36hg18NCBI36
Build 346107,126,544 - 107,184,045NCBI
Celera6107,639,823 - 107,698,287 (-)NCBI
Cytogenetic Map6q21NCBI
HuRef6104,465,727 - 104,524,482 (-)NCBIHuRef
CHM1_16107,280,912 - 107,341,130 (-)NCBICHM1_1
Rtn4ip1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391043,777,772 - 43,823,860 (+)NCBIGRCm39mm39
GRCm39 Ensembl1043,777,803 - 43,833,197 (+)Ensembl
GRCm381043,901,807 - 43,947,863 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1043,901,807 - 43,957,201 (+)EnsemblGRCm38mm10GRCm38
MGSCv371043,621,613 - 43,667,668 (+)NCBIGRCm37mm9NCBIm37
MGSCv361043,590,222 - 43,636,277 (+)NCBImm8
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
PanPan1.16108,258,745 - 108,316,191 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6108,258,745 - 108,315,214 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v06104,368,222 - 104,444,583 (-)NCBIMhudiblu_PPA_v0panPan3
RTN4IP1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1263,926,799 - 63,972,369 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11263,926,803 - 63,972,417 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Rtn4ip1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365643,104,652 - 3,149,100 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RTN4IP1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl172,762,840 - 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 - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11367,188,707 - 67,243,288 (+)NCBI
ChlSab1.1 Ensembl1367,189,318 - 67,243,925 (+)Ensembl
Rtn4ip1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462478015,606,146 - 15,705,320 (+)NCBI

Position Markers
BF401461  
Rat AssemblyChrPosition (strand)SourceJBrowse
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


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)20410895649108956Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201383430956205956Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201383430956205956Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201782709656205956Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201887215049108956Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)202085847056205956Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202660884356205956Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202660884356205956Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202660884356205956Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202671232356205956Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)203091348156205956Rat

miRNA Target Status

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.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 31 16 10 16 2 5 48 33 28 2 2
Low 26 25 9 25 6 6 26 2 13 9 6
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000000304   ⟹   ENSRNOP00000000304
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
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_006256589   ⟹   XP_006256651
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02048,881,197 - 48,924,921 (+)NCBI
Rnor_5.02050,523,639 - 50,566,520 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006256590   ⟹   XP_006256652
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02048,881,197 - 48,909,556 (+)NCBI
Rnor_5.02050,523,639 - 50,566,520 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008772999   ⟹   XP_008771221
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02048,881,124 - 48,924,921 (+)NCBI
Sequence:
RefSeq Acc Id: XR_005497272
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22047,382,251 - 47,421,030 (+)NCBI
RefSeq Acc Id: XR_005497273
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22047,382,251 - 47,422,747 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001101114 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI66465 (Get FASTA)   NCBI Sequence Viewer  
  EDL99682 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001101114   ⟸   NM_001107644
- UniProtKB: B2GUZ6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256651   ⟸   XM_006256589
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006256652   ⟸   XM_006256590
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_008771221   ⟸   XM_008772999
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000000304   ⟸   ENSRNOT00000000304
Protein Domains
PKS_ER

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

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 50551649 50551650 C T snv COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), SHR/NCrlPrin (KNAW), SHR/NHsd (KNAW), MNS/Gib (KNAW), SHR/OlaIpcvPrin (KNAW), SHRSP/Gcrc (KNAW), WKY/Gcrc (KNAW), SHR/OlaIpcv (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 48909214 48909215 C T snv COP/CrCrl (MCW & UW), GH/OmrMcwi (MCW), WKY/Gcrc (RGD), SHR/NHsd (RGD), SHRSP/Gcrc (RGD), MNS/Gib (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1563384 AgrOrtholog
Ensembl Genes ENSRNOG00000000279 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000000304 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000304 ENTREZGENE, 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
KEGG Report rno:309912 UniProtKB/TrEMBL
MGC_CLONE MGC:187808 IMAGE-MGC_LOAD
NCBI Gene 309912 ENTREZGENE
Pfam ADH_N UniProtKB/TrEMBL
PhenoGen Rtn4ip1 PhenoGen
PROSITE QOR_ZETA_CRYSTAL UniProtKB/TrEMBL
SMART PKS_ER UniProtKB/TrEMBL
Superfamily-SCOP GroES_like UniProtKB/TrEMBL
  SSF51735 UniProtKB/TrEMBL
UniProt B2GUZ6 ENTREZGENE, 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