Rtcb (RNA 2',3'-cyclic phosphate and 5'-OH ligase) - Rat Genome Database

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Gene: Rtcb (RNA 2',3'-cyclic phosphate and 5'-OH ligase) Rattus norvegicus
Analyze
Symbol: Rtcb
Name: RNA 2',3'-cyclic phosphate and 5'-OH ligase
RGD ID: 1303261
Description: Predicted to enable RNA ligase (ATP) activity and vinculin binding activity. Predicted to be involved in tRNA exon ligation utilizing 2',3' cyclic phosphate of 5'-exon as source of linkage phosphate. Predicted to act upstream of or within in utero embryonic development and placenta development. Predicted to be located in cytosol; endoplasmic reticulum membrane; and nucleus. Predicted to be part of tRNA-splicing ligase complex. Predicted to be active in nucleus. Orthologous to human RTCB (RNA 2',3'-cyclic phosphate and 5'-OH ligase); PARTICIPATES IN tRNA maturation pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; Brodifacoum.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 3'-phosphate/5'-hydroxy nucleic acid ligase; hypothetical protein LOC362855; LOC362855; P55; RNA-splicing ligase RtcB homolog; tRNA-splicing ligase RtcB homolog
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: Rtcb-ps1  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2717,907,786 - 17,927,134 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl717,907,705 - 17,927,132 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx719,869,904 - 19,889,383 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0722,027,275 - 22,046,945 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0721,809,546 - 21,829,026 (+)NCBIRnor_WKY
Rnor_6.0723,913,830 - 23,933,191 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl723,913,830 - 23,933,191 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0724,063,354 - 24,082,716 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4720,045,978 - 20,065,340 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1720,059,163 - 20,079,411 (+)NCBI
Celera715,140,132 - 15,159,379 (+)NCBICelera
Cytogenetic Map7q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. Comprehensive gene review and curation RGD comprehensive gene curation
5. 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.
6. Handling tRNA introns, archaeal way and eukaryotic way. Yoshihisa T Front Genet. 2014 Jul 10;5:213. doi: 10.3389/fgene.2014.00213. eCollection 2014.
Additional References at PubMed
PMID:15163412   PMID:15489334   PMID:16854843   PMID:20510672   PMID:21311021   PMID:22658674   PMID:22681889   PMID:22871113   PMID:24608264   PMID:24625528   PMID:24870230   PMID:25087875  
PMID:28755400   PMID:29476059   PMID:30053369  


Genomics

Comparative Map Data
Rtcb
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2717,907,786 - 17,927,134 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl717,907,705 - 17,927,132 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx719,869,904 - 19,889,383 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0722,027,275 - 22,046,945 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0721,809,546 - 21,829,026 (+)NCBIRnor_WKY
Rnor_6.0723,913,830 - 23,933,191 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl723,913,830 - 23,933,191 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0724,063,354 - 24,082,716 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4720,045,978 - 20,065,340 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1720,059,163 - 20,079,411 (+)NCBI
Celera715,140,132 - 15,159,379 (+)NCBICelera
Cytogenetic Map7q13NCBI
RTCB
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382232,387,582 - 32,412,247 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl2232,387,582 - 32,412,248 (-)EnsemblGRCh38hg38GRCh38
GRCh372232,783,569 - 32,808,234 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362231,113,569 - 31,138,235 (-)NCBINCBI36Build 36hg18NCBI36
Celera2216,585,734 - 16,610,445 (-)NCBICelera
Cytogenetic Map22q12.3NCBI
HuRef2215,740,893 - 15,765,605 (-)NCBIHuRef
CHM1_12232,742,920 - 32,767,632 (-)NCBICHM1_1
T2T-CHM13v2.02232,851,498 - 32,876,163 (-)NCBIT2T-CHM13v2.0
Rtcb
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391085,774,501 - 85,793,657 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1085,774,501 - 85,793,687 (-)EnsemblGRCm39 Ensembl
GRCm381085,938,637 - 85,957,793 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1085,938,637 - 85,957,823 (-)EnsemblGRCm38mm10GRCm38
MGSCv371085,401,382 - 85,420,538 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361085,368,436 - 85,387,592 (-)NCBIMGSCv36mm8
Celera1087,913,234 - 87,932,391 (-)NCBICelera
Cytogenetic Map10C1NCBI
cM Map1041.81NCBI
Rtcb
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540541,360,370 - 41,375,215 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540541,360,370 - 41,375,215 (-)NCBIChiLan1.0ChiLan1.0
RTCB
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12231,248,280 - 31,273,030 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2231,248,280 - 31,273,030 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02213,394,160 - 13,418,862 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
RTCB
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11031,010,841 - 31,034,208 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1031,010,878 - 31,033,229 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1030,993,808 - 31,017,083 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01031,853,471 - 31,876,814 (+)NCBIROS_Cfam_1.0
UMICH_Zoey_3.11031,593,115 - 31,622,657 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01031,882,145 - 31,905,453 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01032,068,649 - 32,091,998 (+)NCBIUU_Cfam_GSD_1.0
Rtcb
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494514,324,021 - 14,343,299 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364927,334,154 - 7,356,797 (+)EnsemblSpeTri2.0
SpeTri2.0NW_0049364927,334,420 - 7,353,745 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RTCB
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl512,580,294 - 12,613,852 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1512,580,293 - 12,605,722 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2512,366,207 - 12,392,202 (+)NCBISscrofa10.2Sscrofa10.2susScr3
RTCB
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11915,216,939 - 15,243,259 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1915,216,556 - 15,243,132 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666045110,763,914 - 110,789,838 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rtcb
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247502,045,092 - 2,064,233 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247502,045,093 - 2,062,640 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rtcb
166 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:56
Count of miRNA genes:49
Interacting mature miRNAs:55
Transcripts:ENSRNOT00000006570
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
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7127829089Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7131962314Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7131962314Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)766427026029351Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)7946224658265113Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)7986646760460686Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)71557388960573889Rat
1582260Bw72Body weight QTL 723.20.0043body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
1582261Bw69Body weight QTL 693.20.0048body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
1582262Bw75Body weight QTL 7530.0038body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
2317059Aia15Adjuvant induced arthritis QTL 152.46joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)71700459862004598Rat

Markers in Region
RH129545  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2717,926,905 - 17,927,088 (+)MAPPERmRatBN7.2
mRatBN7.2752,671,555 - 52,671,876 (+)MAPPERmRatBN7.2
Rnor_6.0760,071,946 - 60,072,265NCBIRnor6.0
Rnor_6.0723,932,963 - 23,933,145NCBIRnor6.0
Rnor_5.0760,072,239 - 60,072,558UniSTSRnor5.0
Rnor_5.0724,082,488 - 24,082,670UniSTSRnor5.0
RGSC_v3.4720,065,112 - 20,065,294UniSTSRGSC3.4
RGSC_v3.4756,370,005 - 56,370,324UniSTSRGSC3.4
Celera749,447,402 - 49,447,721UniSTS
Celera715,159,151 - 15,159,333UniSTS
Cytogenetic Map7q22UniSTS
Cytogenetic Map7q13UniSTS
RH136031  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2752,671,116 - 52,671,323 (+)MAPPERmRatBN7.2
Rnor_6.0760,071,507 - 60,071,713NCBIRnor6.0
Rnor_5.0760,071,800 - 60,072,006UniSTSRnor5.0
RGSC_v3.4756,369,566 - 56,369,772UniSTSRGSC3.4
Celera749,446,963 - 49,447,169UniSTS
Cytogenetic Map7q22UniSTS
Cytogenetic Map7q13UniSTS


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 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000006570   ⟹   ENSRNOP00000006570
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl717,907,705 - 17,927,132 (+)Ensembl
Rnor_6.0 Ensembl723,913,830 - 23,933,191 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000103817   ⟹   ENSRNOP00000093665
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl717,907,786 - 17,927,126 (+)Ensembl
RefSeq Acc Id: NM_207614   ⟹   NP_997497
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2717,907,786 - 17,927,134 (+)NCBI
Rnor_6.0723,913,830 - 23,933,191 (+)NCBI
Rnor_5.0724,063,354 - 24,082,716 (+)NCBI
RGSC_v3.4720,045,978 - 20,065,340 (+)RGD
Celera715,140,132 - 15,159,379 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_997497 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH78924 (Get FASTA)   NCBI Sequence Viewer  
  AAS78621 (Get FASTA)   NCBI Sequence Viewer  
  EDM17118 (Get FASTA)   NCBI Sequence Viewer  
  Q6AYT3 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_997497   ⟸   NM_207614
- UniProtKB: Q6PX76 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000006570   ⟸   ENSRNOT00000006570
RefSeq Acc Id: ENSRNOP00000093665   ⟸   ENSRNOT00000103817

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6AYT3-F1-model_v2 AlphaFold Q6AYT3 1-505 view protein structure

Transcriptome

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

Promoters
RGD ID:13695093
Promoter ID:EPDNEW_R5618
Type:initiation region
Name:Rtcb_1
Description:RNA 2',3'-cyclic phosphate and 5'-OH ligase
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_6.0723,913,785 - 23,913,845EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1303261 AgrOrtholog
BioCyc Gene G2FUF-34638 BioCyc
Ensembl Genes ENSRNOG00000004813 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000006570 ENTREZGENE
  ENSRNOP00000006570.4 UniProtKB/TrEMBL
  ENSRNOP00000093665.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006570 ENTREZGENE
  ENSRNOT00000006570.6 UniProtKB/TrEMBL
  ENSRNOT00000103817.1 UniProtKB/TrEMBL
Gene3D-CATH 3.90.1860.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7106266 IMAGE-MGC_LOAD
InterPro RtcB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RtcB-like_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RtcB_euk UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:362855 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93713 IMAGE-MGC_LOAD
NCBI Gene 362855 ENTREZGENE
PANTHER PTHR11118 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam RtcB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Rtcb PhenoGen
PROSITE UPF0027 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF103365 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I6AI02_RAT UniProtKB/TrEMBL
  A0A8L2Q3K4_RAT UniProtKB/TrEMBL
  Q6AYT3 ENTREZGENE
  Q6PX76 ENTREZGENE
  RTCB_RAT UniProtKB/Swiss-Prot
UniProt Secondary Q6PX76 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-06-05 Rtcb  RNA 2',3'-cyclic phosphate and 5'-OH ligase  LOC362855  P55  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-09-30 LOC362855        Symbol and Name status set to provisional 70820 PROVISIONAL