Rttn (rotatin) - Rat Genome Database

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Gene: Rttn (rotatin) Rattus norvegicus
Analyze
Symbol: Rttn
Name: rotatin
RGD ID: 1306706
Description: Predicted to be involved in centriole replication; centriole-centriole cohesion; and ciliary basal body organization. Predicted to act upstream of or within determination of left/right symmetry. Predicted to be located in centrosome. Predicted to be active in centriole and ciliary basal body. Orthologous to human RTTN (rotatin); INTERACTS WITH bisphenol A; gentamycin; paracetamol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC291377
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21882,220,999 - 82,398,334 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1882,221,050 - 82,398,333 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1884,284,095 - 84,453,846 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01884,957,328 - 85,127,073 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01882,825,473 - 83,001,026 (+)NCBIRnor_WKY
Rnor_6.01886,071,884 - 86,247,486 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1886,071,662 - 86,247,486 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01885,110,453 - 85,286,009 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41885,830,884 - 86,012,604 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11885,950,678 - 86,085,700 (+)NCBI
Celera1880,771,824 - 80,948,867 (+)NCBICelera
Cytogenetic Map18q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
centriole  (IBA,ISO)
centrosome  (ISO)
ciliary basal body  (IBA,ISO)

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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11900971   PMID:22939636  


Genomics

Comparative Map Data
Rttn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21882,220,999 - 82,398,334 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1882,221,050 - 82,398,333 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1884,284,095 - 84,453,846 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01884,957,328 - 85,127,073 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01882,825,473 - 83,001,026 (+)NCBIRnor_WKY
Rnor_6.01886,071,884 - 86,247,486 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1886,071,662 - 86,247,486 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01885,110,453 - 85,286,009 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41885,830,884 - 86,012,604 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11885,950,678 - 86,085,700 (+)NCBI
Celera1880,771,824 - 80,948,867 (+)NCBICelera
Cytogenetic Map18q13NCBI
RTTN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381870,003,031 - 70,205,687 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1870,003,031 - 70,205,726 (-)EnsemblGRCh38hg38GRCh38
GRCh371867,670,267 - 67,872,923 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361865,822,020 - 66,023,942 (-)NCBINCBI36Build 36hg18NCBI36
Build 341865,822,020 - 66,023,942NCBI
Celera1864,518,916 - 64,720,330 (-)NCBICelera
Cytogenetic Map18q22.2NCBI
HuRef1864,389,979 - 64,591,919 (-)NCBIHuRef
CHM1_11867,666,254 - 67,868,184 (-)NCBICHM1_1
T2T-CHM13v2.01870,220,081 - 70,422,743 (-)NCBIT2T-CHM13v2.0
Rttn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391888,989,860 - 89,149,140 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1888,989,914 - 89,149,140 (+)EnsemblGRCm39 Ensembl
GRCm381888,971,736 - 89,131,014 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1888,971,790 - 89,131,016 (+)EnsemblGRCm38mm10GRCm38
MGSCv371889,141,182 - 89,300,406 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361889,105,983 - 89,265,207 (+)NCBIMGSCv36mm8
Celera1890,700,317 - 90,859,209 (+)NCBICelera
Cytogenetic Map18E4NCBI
Rttn
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540253,600,985 - 53,753,459 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540253,600,985 - 53,753,218 (-)NCBIChiLan1.0ChiLan1.0
RTTN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11866,674,250 - 66,874,390 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1866,674,597 - 66,874,104 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01863,381,953 - 63,584,937 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
RTTN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.118,180,831 - 8,326,947 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl18,180,888 - 8,323,346 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha19,191,081 - 9,333,849 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.018,010,620 - 8,153,335 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl18,010,620 - 8,153,597 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.118,032,050 - 8,174,811 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.017,992,299 - 8,135,078 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.018,202,269 - 8,345,164 (+)NCBIUU_Cfam_GSD_1.0
Rttn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494421,997,733 - 22,069,016 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049369641,369 - 71,142 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RTTN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1152,689,504 - 152,833,946 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11152,688,305 - 152,833,969 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21169,083,952 - 169,146,612 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RTTN
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1189,574,647 - 9,770,940 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl189,575,159 - 9,772,596 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606016,043,053 - 16,239,698 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rttn
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462480611,058,880 - 11,266,289 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462480611,058,138 - 11,266,639 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rttn
509 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:76
Count of miRNA genes:55
Interacting mature miRNAs:73
Transcripts:ENSRNOT00000058160
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1578661Bss20Bone structure and strength QTL 203.7femur morphology trait (VT:0000559)femoral neck cross-sectional area (CMO:0001697)181179151883218561Rat
1578667Bss21Bone structure and strength QTL 213.5femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)181179151883218561Rat
1600373Mamtr6Mammary tumor resistance QTL 6mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)181927890183218561Rat
1331741Bp232Blood pressure QTL 2323.59112arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)182137289383213037Rat
2303120Mamtr8Mammary tumor resistance QTL 80.001mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)183135940883218561Rat
61367Iddm4Insulin dependent diabetes mellitus QTL 42.330.0074blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)183819245583192455Rat
1598826Anxrr20Anxiety related response QTL 203.04body movement coordination trait (VT:0005424)number of rearing movements in an experimental apparatus (CMO:0001752)184143297183828827Rat
6893683Bw110Body weight QTL 1102.70.002body mass (VT:0001259)body weight (CMO:0000012)184334502283828827Rat
8694366Abfw8Abdominal fat weight QTL 86.380.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)184664067583828827Rat
8694432Bw165Body weight QTL 1653.810.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)184664067583828827Rat
9589041Epfw12Epididymal fat weight QTL 1217.080.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)184664067583828827Rat
2303571Bw92Body weight QTL 923body mass (VT:0001259)body weight (CMO:0000012)184852004483828827Rat
2303584Gluco55Glucose level QTL 552blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)184852004483828827Rat
738008Hcar14Hepatocarcinoma resistance QTL 144.3liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion number (CMO:0001462)185146473383218561Rat
1298072Cia26Collagen induced arthritis QTL 263.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)185470976983828827Rat
724542Kidm2Kidney mass QTL 22.6kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)185917211583828827Rat
6903353Bp353Blood pressure QTL 3532.8arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)185979647883828827Rat
6903356Bp354Blood pressure QTL 3544.6arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)185979647883828827Rat

Markers in Region
UniSTS:237862  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21882,398,010 - 82,398,238 (+)MAPPERmRatBN7.2
Rnor_6.01886,247,164 - 86,247,391NCBIRnor6.0
Rnor_5.01885,285,687 - 85,285,914UniSTSRnor5.0
RGSC_v3.41886,012,282 - 86,012,509UniSTSRGSC3.4
Celera1880,948,545 - 80,948,772UniSTS
Cytogenetic Map18q13UniSTS


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 7 15 10 2 11 6
Low 3 42 49 40 4 40 8 11 64 33 30 5 8
Below cutoff 1 1 1 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000058160   ⟹   ENSRNOP00000054965
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1882,221,252 - 82,398,333 (+)Ensembl
Rnor_6.0 Ensembl1886,116,044 - 86,247,486 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000064901   ⟹   ENSRNOP00000063323
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1886,071,662 - 86,112,594 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000076159   ⟹   ENSRNOP00000068057
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1882,221,050 - 82,398,333 (+)Ensembl
Rnor_6.0 Ensembl1886,116,055 - 86,247,156 (+)Ensembl
RefSeq Acc Id: NM_001170436   ⟹   NP_001163907
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21882,221,252 - 82,398,333 (+)NCBI
Rnor_6.01886,071,884 - 86,247,486 (+)NCBI
Rnor_5.01885,110,453 - 85,286,009 (+)NCBI
RGSC_v3.41885,830,884 - 86,012,604 (+)RGD
Celera1880,771,824 - 80,948,867 (+)RGD
Sequence:
RefSeq Acc Id: XM_039096615   ⟹   XP_038952543
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21882,221,000 - 82,398,334 (+)NCBI
RefSeq Acc Id: XM_039096616   ⟹   XP_038952544
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21882,221,000 - 82,398,334 (+)NCBI
RefSeq Acc Id: XM_039096617   ⟹   XP_038952545
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21882,221,000 - 82,398,334 (+)NCBI
RefSeq Acc Id: XM_039096618   ⟹   XP_038952546
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21882,222,908 - 82,398,334 (+)NCBI
RefSeq Acc Id: XM_039096619   ⟹   XP_038952547
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21882,223,681 - 82,398,334 (+)NCBI
RefSeq Acc Id: XM_039096620   ⟹   XP_038952548
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21882,222,908 - 82,398,334 (+)NCBI
RefSeq Acc Id: XM_039096621   ⟹   XP_038952549
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21882,220,999 - 82,362,035 (+)NCBI
RefSeq Acc Id: XM_039096622   ⟹   XP_038952550
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21882,276,071 - 82,398,334 (+)NCBI
RefSeq Acc Id: XR_005495995
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21882,221,000 - 82,338,607 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001163907   ⟸   NM_001170436
- Sequence:
RefSeq Acc Id: ENSRNOP00000054965   ⟸   ENSRNOT00000058160
RefSeq Acc Id: ENSRNOP00000063323   ⟸   ENSRNOT00000064901
RefSeq Acc Id: ENSRNOP00000068057   ⟸   ENSRNOT00000076159
RefSeq Acc Id: XP_038952549   ⟸   XM_039096621
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038952543   ⟸   XM_039096615
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038952545   ⟸   XM_039096617
- Peptide Label: isoform X3
- UniProtKB: D3ZS92 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038952544   ⟸   XM_039096616
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038952548   ⟸   XM_039096620
- Peptide Label: isoform X5
- UniProtKB: A0A096MJA7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038952546   ⟸   XM_039096618
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038952547   ⟸   XM_039096619
- Peptide Label: isoform X5
- UniProtKB: A0A096MJA7 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038952550   ⟸   XM_039096622
- Peptide Label: isoform X7
Protein Domains
RTTN_N

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZS92-F1-model_v2 AlphaFold D3ZS92 1-1629 view protein structure

Transcriptome

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

Promoters
RGD ID:13700897
Promoter ID:EPDNEW_R11421
Type:single initiation site
Name:Rttn_1
Description:rotatin
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_6.01886,071,888 - 86,071,948EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306706 AgrOrtholog
BioCyc Gene G2FUF-6692 BioCyc
Ensembl Genes ENSRNOG00000038200 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000054965 ENTREZGENE
  ENSRNOP00000054965.5 UniProtKB/TrEMBL
  ENSRNOP00000068057 ENTREZGENE
  ENSRNOP00000068057.2 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000058160 ENTREZGENE
  ENSRNOT00000058160.6 UniProtKB/TrEMBL
  ENSRNOT00000076159 ENTREZGENE
  ENSRNOT00000076159.2 UniProtKB/TrEMBL
Gene3D-CATH 1.25.10.10 UniProtKB/TrEMBL
InterPro ARM-like UniProtKB/TrEMBL
  ARM-type_fold UniProtKB/TrEMBL
  Rotatin UniProtKB/TrEMBL
  Rotatin_N UniProtKB/TrEMBL
NCBI Gene 291377 ENTREZGENE
PANTHER PTHR31691 UniProtKB/TrEMBL
Pfam RTTN_N UniProtKB/TrEMBL
PhenoGen Rttn PhenoGen
Superfamily-SCOP SSF48371 UniProtKB/TrEMBL
UniProt A0A096MJA7 ENTREZGENE, UniProtKB/TrEMBL
  D3ZS92 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Rttn  rotatin   Rttn_predicted  rotatin (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Rttn_predicted  rotatin (predicted)      Symbol and Name status set to approved 70820 APPROVED