Rcl1 (RNA terminal phosphate cyclase-like 1) - Rat Genome Database

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Gene: Rcl1 (RNA terminal phosphate cyclase-like 1) Rattus norvegicus
Analyze
Symbol: Rcl1
Name: RNA terminal phosphate cyclase-like 1
RGD ID: 1305320
Description: Predicted to enable RNA endonuclease activity. Predicted to be involved in endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) and ribosomal small subunit biogenesis. Predicted to act upstream of or within endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) and endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA). Predicted to be located in nuclear lumen. Predicted to be part of small-subunit processome. Predicted to be active in nucleolus. Orthologous to human RCL1 (RNA terminal phosphate cyclase like 1); PARTICIPATES IN ribosome biogenesis pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3-chloropropane-1,2-diol; acetamide.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Ab1-353; Ac1292; LOC309301; RNA 3'-terminal phosphate cyclase-like protein
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
GRCr81236,238,078 - 236,282,597 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1236,238,031 - 236,315,894 (+)EnsemblGRCr8
mRatBN7.21226,824,561 - 226,869,046 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1226,824,534 - 226,902,315 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1235,226,421 - 235,270,880 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01242,156,097 - 242,200,544 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01234,974,906 - 235,019,294 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01247,228,012 - 247,272,369 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1247,228,061 - 247,305,693 (+)Ensemblrn6Rnor6.0
Rnor_5.01254,467,399 - 254,544,970 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41232,766,489 - 232,787,901 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1223,999,296 - 224,020,801 (+)NCBICelera
RGSC_v3.11232,930,511 - 232,951,923 (+)NCBI
Cytogenetic Map1q52NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(-)-alpha-phellandrene  (ISO)
(-)-epigallocatechin 3-gallate  (ISO)
(1->4)-beta-D-glucan  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2-palmitoylglycerol  (ISO)
3-chloropropane-1,2-diol  (EXP)
4,4'-sulfonyldiphenol  (ISO)
acetamide  (EXP)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
Aflatoxin B2 alpha  (ISO)
all-trans-retinoic acid  (ISO)
alpha-phellandrene  (ISO)
antirheumatic drug  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
benzo[e]pyrene  (ISO)
beta-naphthoflavone  (ISO)
bisphenol A  (EXP,ISO)
buspirone  (EXP)
cadmium atom  (ISO)
cadmium dichloride  (ISO)
carbon nanotube  (ISO)
chlorpyrifos  (ISO)
chromium(6+)  (ISO)
ciguatoxin CTX1B  (ISO)
clofibrate  (ISO)
clomiphene  (ISO)
copper(II) sulfate  (ISO)
cyclosporin A  (ISO)
diarsenic trioxide  (ISO)
diethylstilbestrol  (ISO)
dioxygen  (EXP)
doxorubicin  (ISO)
estrone  (ISO)
folic acid  (ISO)
fulvestrant  (ISO)
genistein  (ISO)
gentamycin  (EXP)
glafenine  (EXP)
hexestrol  (ISO)
hydralazine  (ISO)
hydrogen peroxide  (ISO)
ivermectin  (ISO)
manganese atom  (ISO)
manganese(0)  (ISO)
manganese(II) chloride  (ISO)
mestranol  (ISO)
methapyrilene  (EXP,ISO)
N,N-diethyl-m-toluamide  (EXP)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP)
nitrates  (ISO)
paracetamol  (ISO)
paraquat  (EXP)
perfluorooctane-1-sulfonic acid  (ISO)
permethrin  (EXP)
phenobarbital  (ISO)
pirinixic acid  (ISO)
potassium chromate  (ISO)
propiconazole  (ISO)
raloxifene  (ISO)
senecionine  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (ISO)
temozolomide  (ISO)
tetrachloroethene  (ISO)
tetrachloromethane  (ISO)
trimellitic anhydride  (ISO)
triphenyl phosphate  (ISO)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
nucleolus  (IBA,IEA,ISO)
small-subunit processome  (IEA,ISO)

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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
5. GOA pipeline RGD automated data pipeline
6. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
7. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
8. Comprehensive gene review and curation RGD comprehensive gene curation
9. The roles of SSU processome components and surveillance factors in the initial processing of human ribosomal RNA. Sloan KE, etal., RNA. 2014 Apr;20(4):540-50. doi: 10.1261/rna.043471.113. Epub 2014 Feb 18.
10. 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.
Additional References at PubMed
PMID:10790377   PMID:25190460  


Genomics

Comparative Map Data
Rcl1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81236,238,078 - 236,282,597 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1236,238,031 - 236,315,894 (+)EnsemblGRCr8
mRatBN7.21226,824,561 - 226,869,046 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1226,824,534 - 226,902,315 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1235,226,421 - 235,270,880 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01242,156,097 - 242,200,544 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01234,974,906 - 235,019,294 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01247,228,012 - 247,272,369 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1247,228,061 - 247,305,693 (+)Ensemblrn6Rnor6.0
Rnor_5.01254,467,399 - 254,544,970 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41232,766,489 - 232,787,901 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1223,999,296 - 224,020,801 (+)NCBICelera
RGSC_v3.11232,930,511 - 232,951,923 (+)NCBI
Cytogenetic Map1q52NCBI
RCL1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3894,792,944 - 4,861,066 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl94,792,944 - 4,885,917 (+)Ensemblhg38GRCh38
GRCh3794,792,944 - 4,861,066 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3694,782,834 - 4,851,064 (+)NCBIBuild 36Build 36hg18NCBI36
Build 3494,782,936 - 4,851,061NCBI
Celera94,718,433 - 4,786,663 (+)NCBICelera
Cytogenetic Map9p24.1NCBI
HuRef94,748,408 - 4,816,670 (+)NCBIHuRef
CHM1_194,793,011 - 4,861,300 (+)NCBICHM1_1
T2T-CHM13v2.094,798,060 - 4,866,205 (+)NCBIT2T-CHM13v2.0
Rcl1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391929,078,761 - 29,121,251 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1929,078,775 - 29,121,329 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381929,101,375 - 29,143,851 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1929,101,375 - 29,143,929 (+)Ensemblmm10GRCm38
MGSCv371929,175,865 - 29,218,333 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361929,167,372 - 29,209,840 (+)NCBIMGSCv36mm8
Celera1929,876,695 - 29,919,293 (+)NCBICelera
Cytogenetic Map19C1NCBI
cM Map1923.61NCBI
Rcl1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554349,073,525 - 9,137,678 (+)Ensembl
ChiLan1.0NW_0049554349,073,643 - 9,137,387 (+)NCBIChiLan1.0ChiLan1.0
RCL1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v211119,696,086 - 119,764,574 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan19119,702,033 - 119,770,521 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v094,626,981 - 4,695,444 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.194,813,750 - 4,881,423 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl94,813,750 - 4,881,423 (+)EnsemblpanPan2panpan1.1
RCL1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1193,144,164 - 93,204,233 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl193,142,635 - 93,435,997 (+)NCBIcanFam3CanFam3.1
ROS_Cfam_1.0193,699,300 - 93,759,439 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl193,699,315 - 93,758,830 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1193,330,324 - 93,390,234 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0193,053,846 - 93,113,777 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0193,819,427 - 93,879,366 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Rcl1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947140,722,497 - 140,798,366 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936503373,934 - 450,596 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936503375,191 - 450,596 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RCL1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1217,142,966 - 217,204,965 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11217,142,965 - 217,204,960 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21242,978,606 - 243,040,553 (-)NCBISscrofa10.2Sscrofa10.2susScr3
RCL1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11274,688,284 - 74,754,184 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1274,687,071 - 74,754,045 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366635226,167 - 80,993 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rcl1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247369,545,433 - 9,609,887 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247369,545,580 - 9,609,897 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Rcl1
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1229,160,064 - 29,203,851 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Rcl1
383 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:356
Count of miRNA genes:226
Interacting mature miRNAs:252
Transcripts:ENSRNOT00000020809, ENSRNOT00000048910
Prediction methods:Microtar, 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
8693637Alc29Alcohol consumption QTL 292.70.258drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)1217412367243666627Rat
1578778Pur4Proteinuria QTL 43.30.003urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1160111531262090437Rat
1354646Kidm18Kidney mass QTL 185.7kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1160573753266453731Rat
1357335Bw39Body weight QTL 393.3body mass (VT:0001259)body weight (CMO:0000012)1207243873252243873Rat
1354652Kidm20Kidney mass QTL 204.3kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1186658830266453731Rat
2293674Bss39Bone structure and strength QTL 397.10.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)1210980612255980612Rat
61455Niddm7Non-insulin dependent diabetes mellitus QTL 75.5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1223964326248681945Rat
61327Eae7Experimental allergic encephalomyelitis QTL 75.6body mass (VT:0001259)change in body weight (CMO:0002045)1226175591270518180Rat
1600395Niddm69Non-insulin dependent diabetes mellitus QTL 694.140.0002blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1205233991267096252Rat
1578763Kidm29Kidney mass QTL 293.30.0001kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1218829748263829748Rat
1354624Cm35Cardiac mass QTL355.7heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1186658830266453731Rat
1600396Niddm68Non-insulin dependent diabetes mellitus QTL 684.970.0003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1205233991267096252Rat
1600397Edcs4Endometrial carcinoma susceptibility QTL 42.2uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)1176288899270518180Rat
631838Niddm36Non-insulin dependent diabetes mellitus QTL 360.01insulin secretion trait (VT:0003564)calculated pancreatic islet insulin release measurement (CMO:0001217)1193964073238964073Rat
8693661Alc34Alcohol consumption QTL 342.20.611drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)1217412367238041033Rat
1549837Hcar15Hepatocarcinoma resistance QTL 150.05liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1162548015270518180Rat
152025235Bw194Body weight QTL 1944.86body mass (VT:0001259)1132966869252856240Rat
1600388Niddm67Non-insulin dependent diabetes mellitus QTL 675.840.000004blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1205233991267096252Rat
2293694Bss38Bone structure and strength QTL 387.050.0001femur strength trait (VT:0010010)femur stiffness (CMO:0001674)1210980612255980612Rat
1598853Memor3Memory QTL 34.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)1152919152268496042Rat
1578759Uae30Urinary albumin excretion QTL 303.30.003urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1160111531262090437Rat
1300145Rf7Renal function QTL 72.96urine creatinine amount (VT:0010540)urine creatinine level (CMO:0000125)1194575422239575422Rat
8655655Arrd2Age-related retinal degeneration QTL 27.79retinal layer morphology trait (VT:0003727)percentage of study population developing retinopathy during a period of time (CMO:0002453)1193400541238400541Rat
734767Niddm57Non-insulin dependent diabetes mellitus QTL 57body mass (VT:0001259)body weight (CMO:0000012)1233480549270108840Rat
1358898Bp255Blood pressure QTL 2553.6arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1200449456256003563Rat
631215Stl8Serum triglyceride level QTL 89.270.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1234540191270518180Rat
7771612Cm80Cardiac mass QTL 808.4heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)1146080545243492863Rat
631843Bw116Body weight QTL 1164.10.016abdominal adipose amount (VT:1000220)abdominal fat pad weight (CMO:0000088)1233480549270108840Rat
731175Uae20Urinary albumin excretion QTL 203.50.0018urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1207163993269633915Rat
2300175Bmd40Bone mineral density QTL 4015.40.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)1210980612255980612Rat
1354661Bw33Body weight QTL 335.2body mass (VT:0001259)body weight (CMO:0000012)1160573753266453731Rat
724538Kidm1Kidney mass QTL 13.2kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1223134011262090599Rat
2293655Bss36Bone structure and strength QTL 3610.660.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)1210980612255980612Rat
1298084Thym4Thymus enlargement QTL 410.68thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)1207243873252243873Rat
724531Uae5Urinary albumin excretion QTL 54urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)1160111426262090599Rat
2314011Gluco56Glucose level QTL 56blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1209203273254203273Rat
8552891Epfw5Epididymal fat weight QTL 54.4epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)1202543537247543537Rat
734769Niddm58Non-insulin dependent diabetes mellitus QTL 58body mass (VT:0001259)body weight (CMO:0000012)1225108840270108840Rat
724533Rf51Renal function QTL 515.30.0002kidney plasma flow trait (VT:0005524)renal plasma flow (CMO:0001914)1228180370266453608Rat
1354580Scort1Serum corticosterone level QTL 13.4blood corticosterone amount (VT:0005345)blood corticosterone level (CMO:0001172)1154961463266453731Rat
1358292Cm37Cardiac mass QTL 376.28e-07heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)1205674651250674651Rat
61376Bp42Blood pressure QTL 4223.4arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1207243873252243873Rat
634313Niddm43Non-insulin dependent diabetes mellitus QTL 43blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1208479811269633915Rat
70211Niddm24Non-insulin dependent diabetes mellitus QTL 243.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1224633915269633915Rat
724552Glom2Glomerulus QTL 23.30.0001kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)1232312773270518180Rat
1358916Kidm22Kidney mass QTL 223.32kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1212738576257738576Rat
2312564Glom18Glomerulus QTL 182.40.003kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)1194786607262083703Rat
634321Hc1Hypercalciuria QTL 12.91urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1188241285250779312Rat
2292218Kidm35Kidney mass QTL 35kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1208798288253798288Rat
61400Niddm1Non-insulin dependent diabetes mellitus QTL 111blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1228180243255849249Rat
1300168Bp170Blood pressure QTL 1702.76arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1192995199237995199Rat
61403Niddm4Non-insulin dependent diabetes mellitus QTL 4blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1201464383246464383Rat
1641926Teswt2Testicular weight QTL 22.82testis mass (VT:1000644)both testes wet weight (CMO:0000175)1203675682248675682Rat
631658Cm7Cardiac mass QTL 75.320.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)1205674651250674651Rat
1354610Bw34Body weight QTL 344.1body mass (VT:0001259)body weight (CMO:0000012)1160573753266453731Rat
2293700Bmd27Bone mineral density QTL 276.60.0001femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)1210980612255980612Rat
2293701Bmd34Bone mineral density QTL 348.30.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)1210980612255980612Rat
7387289Uae45Urinary albumin excretion QTL 452.860.0021urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1233204160270518180Rat
8655855Arrd3Age-related retinal degeneration QTL 33.07lens clarity trait (VT:0001304)cataract incidence/prevalence measurement (CMO:0001585)1193400541238400541Rat
1600374Mcs17Mammary carcinoma susceptibility QTL 173mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1207099883252099883Rat
6480786Bw97Body weight QTL 975.03body mass (VT:0001259)body weight (CMO:0000012)1234540191237018045Rat
1600363Hc6Hypercalciuria QTL 62.7urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)1210980612255980612Rat
8693618Alc25Alcohol consumption QTL 2530.28drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)1217412367238041033Rat
2293083Iddm25Insulin dependent diabetes mellitus QTL 254.18blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1191260175236260175Rat
738032Hcas5Hepatocarcinoma susceptibility QTL 53.12liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1185857683270518180Rat
2302040Pia35Pristane induced arthritis QTL 353.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)1226175591270518180Rat
631669Iddm9Insulin dependent diabetes mellitus QTL 92.80.039blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1233349180270518180Rat
7394701Uae46Urinary albumin excretion QTL 463.60.0056urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1210980612255980612Rat
1598821Rf55Renal function QTL 556.3renal blood flow trait (VT:2000006)ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)1228174566270518180Rat

Markers in Region
RH133844  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21226,868,658 - 226,868,875 (+)MAPPERmRatBN7.2
Rnor_6.01247,272,011 - 247,272,227NCBIRnor6.0
Rnor_5.01254,511,285 - 254,511,501UniSTSRnor5.0
RGSC_v3.41232,787,545 - 232,787,761UniSTSRGSC3.4
Celera1224,020,445 - 224,020,661UniSTS
RH 3.4 Map11614.5UniSTS
Cytogenetic Map1q52UniSTS


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 67 163 91 90 59 92 59 6 356 192 11 142 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000020809   ⟹   ENSRNOP00000020809
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1236,238,031 - 236,282,563 (+)Ensembl
mRatBN7.2 Ensembl1226,824,534 - 226,869,012 (+)Ensembl
Rnor_6.0 Ensembl1247,228,061 - 247,272,345 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000048910   ⟹   ENSRNOP00000044460
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1236,241,795 - 236,315,894 (+)Ensembl
mRatBN7.2 Ensembl1226,828,241 - 226,902,315 (+)Ensembl
Rnor_6.0 Ensembl1247,231,723 - 247,305,693 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000083511   ⟹   ENSRNOP00000073254
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1247,238,798 - 247,296,076 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000164559   ⟹   ENSRNOP00000099921
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1236,238,031 - 236,282,563 (+)Ensembl
RefSeq Acc Id: NM_001399456   ⟹   NP_001386385
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81236,238,115 - 236,282,597 (+)NCBI
mRatBN7.21226,824,561 - 226,869,046 (+)NCBI
RefSeq Acc Id: NM_001399457   ⟹   NP_001386386
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81236,266,754 - 236,282,597 (+)NCBI
mRatBN7.21226,853,203 - 226,869,046 (+)NCBI
RefSeq Acc Id: XM_063264530   ⟹   XP_063120600
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81236,238,078 - 236,275,974 (+)NCBI
Ensembl Acc Id: ENSRNOP00000020809   ⟸   ENSRNOT00000020809
Ensembl Acc Id: ENSRNOP00000044460   ⟸   ENSRNOT00000048910
Ensembl Acc Id: ENSRNOP00000073254   ⟸   ENSRNOT00000083511
RefSeq Acc Id: NP_001386385   ⟸   NM_001399456
- Peptide Label: isoform 1
- UniProtKB: Q5BJN0 (UniProtKB/TrEMBL),   A6I0V4 (UniProtKB/TrEMBL),   G3V7Z1 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001386386   ⟸   NM_001399457
- Peptide Label: isoform 2
RefSeq Acc Id: XP_063120600   ⟸   XM_063264530
- Peptide Label: isoform X1
Ensembl Acc Id: ENSRNOP00000099921   ⟸   ENSRNOT00000164559
Protein Domains
RNA 3'-terminal phosphate cyclase   RNA 3'-terminal phosphate cyclase insert

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q7TQ76-F1-model_v2 AlphaFold Q7TQ76 1-447 view protein structure

Transcriptome

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

Promoters
RGD ID:13690853
Promoter ID:EPDNEW_R1368
Type:initiation region
Name:Rcl1_1
Description:RNA terminal phosphate cyclase-like 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_6.01247,228,045 - 247,228,105EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305320 AgrOrtholog
BioCyc Gene G2FUF-55977 BioCyc
Ensembl Genes ENSRNOG00000015491 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000020809 ENTREZGENE
  ENSRNOT00000020809.8 UniProtKB/TrEMBL
  ENSRNOT00000048910.7 UniProtKB/TrEMBL
  ENSRNOT00000164559.1 UniProtKB/TrEMBL
Gene3D-CATH 3.30.360.20 UniProtKB/TrEMBL
  3.65.10.20 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7326310 IMAGE-MGC_LOAD
InterPro RNA3'-term_phos_cycl_insert UniProtKB/TrEMBL
  RNA3'_phos_cyclase_dom UniProtKB/TrEMBL
  RNA3'_phos_cyclase_dom_sf UniProtKB/TrEMBL
  RNA3'_term_phos_cyc_type_2 UniProtKB/TrEMBL
  RNA3'_term_phos_cycl-like UniProtKB/TrEMBL
  RNA3'_term_phos_cycl-like_CS UniProtKB/TrEMBL
  RNA3'P_cycl/enolpyr_Trfase_a/b UniProtKB/TrEMBL
  RPTC_insert UniProtKB/TrEMBL
MGC_CLONE MGC:109565 IMAGE-MGC_LOAD
NCBI Gene 309301 ENTREZGENE
PANTHER PTHR11096:SF1 UniProtKB/TrEMBL
  RNA3'_term_phos_cycl UniProtKB/TrEMBL
Pfam RTC UniProtKB/TrEMBL
  RTC_insert UniProtKB/TrEMBL
PhenoGen Rcl1 PhenoGen
PIRSF RNA3'_term_phos_cycl_euk UniProtKB/TrEMBL
PROSITE RTC UniProtKB/TrEMBL
RatGTEx ENSRNOG00000015491 RatGTEx
Superfamily-SCOP RNA3'_cycl/enolpyr_transf_A/B UniProtKB/TrEMBL
UniProt A0A0G2QBZ9_RAT UniProtKB/TrEMBL
  A0ABK0KY87_RAT UniProtKB/TrEMBL
  A6I0V4 ENTREZGENE, UniProtKB/TrEMBL
  G3V7Z1 ENTREZGENE, UniProtKB/TrEMBL
  Q5BJN0 ENTREZGENE
  Q7TQ76_RAT UniProtKB/TrEMBL
UniProt Secondary F1LRB6 UniProtKB/TrEMBL
  Q5BJN0 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-12-06 Rcl1  RNA terminal phosphate cyclase-like 1  Rcl1_predicted  RNA terminal phosphate cyclase-like 1 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Rcl1_predicted  RNA terminal phosphate cyclase-like 1 (predicted)      Symbol and Name status set to approved 70820 APPROVED