Clptm1l (CLPTM1-like) - Rat Genome Database

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Gene: Clptm1l (CLPTM1-like) Rattus norvegicus
Analyze
Symbol: Clptm1l
Name: CLPTM1-like
RGD ID: 1307896
Description: Predicted to be integral component of membrane. Predicted to be active in membrane. Human ortholog(s) of this gene implicated in carcinoma (multiple) and lung disease (multiple). Orthologous to human CLPTM1L (CLPTM1 like); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 5-methoxy-2-\{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfinyl\}-1H-benzimidazole; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: cleft lip and palate transmembrane protein 1-like protein; LOC316916; RGD1307896; similar to cisplatin resistance related protein CRR9p
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
mRatBN7.2129,667,545 - 29,683,530 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl129,667,545 - 29,683,530 (-)Ensembl
Rnor_6.0132,281,207 - 32,297,196 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl132,281,207 - 32,297,190 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0133,706,075 - 33,722,058 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4130,474,672 - 30,490,655 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1130,477,611 - 30,493,598 (-)NCBI
Celera128,315,536 - 28,331,519 (-)NCBICelera
Cytogenetic Map1p11NCBI
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. A genetic sequence variant (GSV) at susceptibility loci of 5p15.33 (TERT-CLPTM1L) is associated with survival outcome in locally advanced and metastatic non-small-cell lung cancer (NSCLC). Azad AK, etal., Lung Cancer. 2014 Jun;84(3):289-94. doi: 10.1016/j.lungcan.2014.03.008. Epub 2014 Mar 13.
2. A GWAS Meta-analysis and Replication Study Identifies a Novel Locus within CLPTM1L/TERT Associated with Nasopharyngeal Carcinoma in Individuals of Chinese Ancestry. Bei JX, etal., Cancer Epidemiol Biomarkers Prev. 2016 Jan;25(1):188-92. doi: 10.1158/1055-9965.EPI-15-0144. Epub 2015 Nov 6.
3. The role of TERT-CLPTM1L SNPs, hTERT expression and telomere length in the pathogenesis of oral squamous cell carcinoma. Carkic J, etal., J Oral Sci. 2016;58(4):449-458. doi: 10.2334/josnusd.16-0108.
4. The associations of TERT-CLPTM1L variants and TERT mRNA expression with the prognosis of early stage non-small cell lung cancer. Chen Z, etal., Cancer Gene Ther. 2017 Jan;24(1):20-27. doi: 10.1038/cgt.2016.74. Epub 2016 Dec 16.
5. 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.
6. CRR9/CLPTM1L regulates cell survival signaling and is required for Ras transformation and lung tumorigenesis. James MA, etal., Cancer Res. 2014 Feb 15;74(4):1116-27. doi: 10.1158/0008-5472.CAN-13-1617. Epub 2013 Dec 23.
7. TERT-rs33963617 and CLPTM1L-rs77518573 reduce the risk of non-small cell lung cancer in Chinese population. Ji Z, etal., Gene. 2020 Mar 20;731:144357. doi: 10.1016/j.gene.2020.144357. Epub 2020 Jan 11.
8. Genetic variant rs401681 at 5p15.33 modifies susceptibility to lung cancer but not esophageal squamous cell carcinoma. Jiang M, etal., PLoS One. 2013 Dec 30;8(12):e84277. doi: 10.1371/journal.pone.0084277. eCollection 2013.
9. CLPTM1L polymorphism as a protective factor for lung cancer: a case-control study in southern Chinese population. Jin T, etal., Tumour Biol. 2016 Aug;37(8):10533-8. doi: 10.1007/s13277-016-4938-9. Epub 2016 Feb 6.
10. TERT-CLPTM1 locus polymorphism (rs401681) is associated with the prognosis of hepatocellular carcinoma. Lee HW, etal., Onco Targets Ther. 2017 Oct 3;10:4853-4858. doi: 10.2147/OTT.S138956. eCollection 2017.
11. Genetic variations in TERT-CLPTM1L genes and risk of lung cancer in Chinese women nonsmokers. Li C, etal., PLoS One. 2013 May 30;8(5):e64988. doi: 10.1371/journal.pone.0064988. Print 2013.
12. Evaluation of Rare and Common Variants from Suspected Familial or Sporadic Nasopharyngeal Carcinoma (NPC) Susceptibility Genes in Sporadic NPC. Liu Z, etal., Cancer Epidemiol Biomarkers Prev. 2019 Oct;28(10):1682-1686. doi: 10.1158/1055-9965.EPI-19-0007. Epub 2019 Jul 3.
13. Genetic variant in CLPTM1L confers reduced risk of lung cancer: a replication study in Chinese and a meta-analysis. Luo X, etal., Asian Pac J Cancer Prev. 2014;15(21):9241-7. doi: 10.7314/apjcp.2014.15.21.9241.
14. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
15. Novel genetic variants in the chromosome 5p15.33 region associate with lung cancer risk. Pande M, etal., Carcinogenesis. 2011 Oct;32(10):1493-9. doi: 10.1093/carcin/bgr136. Epub 2011 Jul 18.
16. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
17. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
18. Polymorphisms of TERT and CLPTM1L and the risk of hepatocellular carcinoma in Chinese males. Su LY, etal., Asian Pac J Cancer Prev. 2014;15(19):8197-201. doi: 10.7314/apjcp.2014.15.19.8197.
19. No association of XRCC1 and CLPTM1L polymorphisms with non-small cell lung cancer in a non-smoking Han Chinese population. Sun Y, etal., Asian Pac J Cancer Prev. 2013;14(9):5171-4. doi: 10.7314/apjcp.2013.14.9.5171.
20. Role of 5p15.33 (TERT-CLPTM1L), 6p21.33 and 15q25.1 (CHRNA5-CHRNA3) variation and lung cancer risk in never-smokers. Wang Y, etal., Carcinogenesis. 2010 Feb;31(2):234-8. doi: 10.1093/carcin/bgp287. Epub 2009 Dec 2.
21. The TERT-CLPTM1L locus for lung cancer predisposes to bronchial obstruction and emphysema. Wauters E, etal., Eur Respir J. 2011 Oct;38(4):924-31. doi: 10.1183/09031936.00187110. Epub 2011 May 26.
22. CLPTM1L genetic polymorphisms and interaction with smoking and alcohol drinking in lung cancer risk: a case-control study in the Han population from northwest China. Xun X, etal., Medicine (Baltimore). 2014 Dec;93(28):e289. doi: 10.1097/MD.0000000000000289.
23. Association of TERT-CLPTM1L and 8q24 Common Genetic Variants with Gallbladder Cancer Susceptibility and Prognosis in North Indian Population. Yadav S, etal., Biochem Genet. 2018 Aug;56(4):267-282. doi: 10.1007/s10528-018-9843-z. Epub 2018 Feb 15.
24. TERT-CLPTM1L Rs401681 C>T polymorphism was associated with a decreased risk of esophageal cancer in a Chinese population. Yin J, etal., PLoS One. 2014 Jul 9;9(7):e100667. doi: 10.1371/journal.pone.0100667. eCollection 2014.
25. Polymorphisms of the TERT-CLPTM1L Gene Are Associated with Pharynx-Larynx Cancer. Yu J, etal., DNA Cell Biol. 2019 Sep;38(9):915-921. doi: 10.1089/dna.2019.4744. Epub 2019 Aug 20.
26. Upregulation of miR-494 Inhibits Cell Growth and Invasion and Induces Cell Apoptosis by Targeting Cleft Lip and Palate Transmembrane 1-Like in Esophageal Squamous Cell Carcinoma. Zhang R, etal., Dig Dis Sci. 2015 May;60(5):1247-55. doi: 10.1007/s10620-014-3433-7. Epub 2014 Dec 6.
27. Genetic polymorphisms of TERT and CLPTM1L and risk of lung cancer: a case-control study in northeast Chinese male population. Zhang Y, etal., Med Oncol. 2014 Jul;31(7):18. doi: 10.1007/s12032-014-0018-4. Epub 2014 May 27.
28. Common variations in TERT-CLPTM1L locus are reproducibly associated with the risk of nasopharyngeal carcinoma in Chinese populations. Zhang Y, etal., Oncotarget. 2016 Jan 5;7(1):759-70. doi: 10.18632/oncotarget.6397.
29. Genetic variations in TERT-CLPTM1L locus are associated with risk of lung cancer in Chinese population. Zhong R, etal., Mol Carcinog. 2013 Nov;52 Suppl 1:E118-26. doi: 10.1002/mc.22043. Epub 2013 Jun 12.
30. The identification of two regulatory ESCC susceptibility genetic variants in the TERT-CLPTM1L loci. Zhou L, etal., Oncotarget. 2016 Feb 2;7(5):5495-506. doi: 10.18632/oncotarget.6747.
Additional References at PubMed
PMID:12477932   PMID:19946888  


Genomics

Comparative Map Data
Clptm1l
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2129,667,545 - 29,683,530 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl129,667,545 - 29,683,530 (-)Ensembl
Rnor_6.0132,281,207 - 32,297,196 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl132,281,207 - 32,297,190 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0133,706,075 - 33,722,058 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4130,474,672 - 30,490,655 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1130,477,611 - 30,493,598 (-)NCBI
Celera128,315,536 - 28,331,519 (-)NCBICelera
Cytogenetic Map1p11NCBI
CLPTM1L
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3851,317,752 - 1,345,099 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl51,317,752 - 1,345,099 (-)EnsemblGRCh38hg38GRCh38
GRCh3751,317,867 - 1,345,214 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3651,370,999 - 1,398,002 (-)NCBINCBI36hg18NCBI36
Celera51,354,853 - 1,381,719 (-)NCBI
Cytogenetic Map5p15.33NCBI
HuRef51,298,289 - 1,325,657 (-)NCBIHuRef
CHM1_151,317,036 - 1,344,039 (-)NCBICHM1_1
T2T-CHM13v2.051,225,592 - 1,255,482 (-)NCBI
Clptm1l
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391373,752,121 - 73,768,758 (+)NCBIGRCm39mm39
GRCm39 Ensembl1373,752,125 - 73,768,724 (+)Ensembl
GRCm381373,604,002 - 73,620,639 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1373,604,006 - 73,620,605 (+)EnsemblGRCm38mm10GRCm38
MGSCv371373,741,749 - 73,758,053 (+)NCBIGRCm37mm9NCBIm37
MGSCv361374,070,303 - 74,086,607 (+)NCBImm8
Celera1375,933,177 - 75,949,481 (+)NCBICelera
Cytogenetic Map13C1NCBI
Clptm1l
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955504677,772 - 695,660 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955504677,824 - 695,660 (-)NCBIChiLan1.0ChiLan1.0
CLPTM1L
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.151,361,571 - 1,388,409 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl51,361,571 - 1,388,415 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v051,609,455 - 1,638,325 (-)NCBIMhudiblu_PPA_v0panPan3
CLPTM1L
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13411,263,274 - 11,277,666 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3411,263,162 - 11,277,436 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3415,773,118 - 15,787,519 (+)NCBI
ROS_Cfam_1.03411,163,710 - 11,178,126 (+)NCBI
ROS_Cfam_1.0 Ensembl3411,163,165 - 11,178,119 (+)Ensembl
UMICH_Zoey_3.13411,214,779 - 11,229,180 (+)NCBI
UNSW_CanFamBas_1.03411,193,877 - 11,208,264 (+)NCBI
UU_Cfam_GSD_1.03411,404,868 - 11,419,269 (+)NCBI
Clptm1l
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024407213244,260,711 - 244,284,271 (+)NCBI
SpeTri2.0NW_004936815421,996 - 445,577 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLPTM1L
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1679,236,986 - 79,248,500 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11679,237,000 - 79,248,503 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21685,904,744 - 85,907,064 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CLPTM1L
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.141,140,272 - 1,162,663 (-)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl41,140,132 - 1,162,898 (-)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605435,707,543 - 35,730,125 (-)NCBIVero_WHO_p1.0
Clptm1l
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624751652,767 - 669,587 (-)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_004624751652,857 - 669,400 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH128537  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2129,667,652 - 29,667,849 (+)MAPPERmRatBN7.2
Rnor_6.0132,281,315 - 32,281,511NCBIRnor6.0
Rnor_5.0133,706,183 - 33,706,379UniSTSRnor5.0
RGSC_v3.4130,474,780 - 30,474,976UniSTSRGSC3.4
Celera128,315,644 - 28,315,840UniSTS
Cytogenetic Map1p11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2313053Bss51Bone structure and strength QTL 513.80.0001tibia length (VT:0004357)tibia length (CMO:0000450)1132356093Rat
2313070Bss52Bone structure and strength QTL 524.40.0001body length (VT:0001256)body length (CMO:0000013)1132356093Rat
2313090Bmd69Bone mineral density QTL 694.40.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)1132356093Rat
738020Pia8Pristane induced arthritis QTL 84.7joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1165833076Rat
1578650Bmd6Bone mineral density QTL 612.2femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)150910843284926Rat
1578651Bmd7Bone mineral density QTL 714.2femur mineral mass (VT:0010011)cortical volumetric bone mineral density (CMO:0001730)150910843284926Rat
1578669Bss9Bone structure and strength QTL 96.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)150910843284926Rat
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)150910886060548Rat
1600360Mcs16Mammary carcinoma susceptibility QTL 162.4mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1224439043433040Rat
7421626Bp360Blood pressure QTL 3600.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1439328949393289Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15925874115540829Rat
631508Sald1Serum aldosterone level QTL 13.7blood aldosterone amount (VT:0005346)serum aldosterone level (CMO:0000487)1985600154856001Rat
2302038Pia31Pristane induced arthritis QTL 315.50.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)11099206555992065Rat
1300167Hrtrt2Heart rate QTL 24.35heart pumping trait (VT:2000009)heart rate (CMO:0000002)11148131275088344Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)11148131282174945Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)11148131282174945Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)11148131282174945Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)11148131282174945Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2317755Glom22Glomerulus QTL 223.8urine protein amount (VT:0005160)urine protein level (CMO:0000591)11148148232355910Rat
1578756Iddm22Insulin dependent diabetes mellitus QTL 222.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)11183518156835181Rat
5684998Bss101Bone structure and strength QTL 1013.6tibia strength trait (VT:1000284)tibia ultimate force (CMO:0001734)11543162149361612Rat
5684999Bss102Bone structure and strength QTL 1025.50.00000072tibia strength trait (VT:1000284)tibia stiffness (CMO:0001735)11543162149361612Rat
631494Bp95Blood pressure QTL 95400.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)11620621049268520Rat
634353Rends2Renal damage susceptibility QTL 20.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)11933357156983283Rat
1558642Prcr2Prostate cancer resistance QTL 24.3prostate integrity trait (VT:0010571)area of ventral prostate occupied by tumorous lesions to total ventral prostate area ratio (CMO:0000899)12076315844095856Rat
724520Bp145Blood pressure QTL 1452.10.0024arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)12078482865784828Rat
1357397Bw41Body weight QTL 414.190.0001body mass (VT:0001259)body weight (CMO:0000012)12234064749361612Rat
1357401Bw43Body weight QTL 433.75body mass (VT:0001259)body weight (CMO:0000012)12234064749361612Rat
1357400Bw62Body weight QTL624.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)12234064767340647Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)122340647102268831Rat
1331785Rf27Renal function QTL 274.643urine sodium amount (VT:0006274)urine sodium level (CMO:0000129)12887978078430678Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:69
Count of miRNA genes:52
Interacting mature miRNAs:61
Transcripts:ENSRNOT00000023211
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 37 57 41 19 41 1 4 74 35 41 11 1
Low 6 7 7 7
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000023211   ⟹   ENSRNOP00000023211
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl129,667,545 - 29,683,530 (-)Ensembl
Rnor_6.0 Ensembl132,281,207 - 32,297,190 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000099695   ⟹   ENSRNOP00000097926
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl129,667,545 - 29,683,098 (-)Ensembl
RefSeq Acc Id: NM_001108240   ⟹   NP_001101710
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2129,667,545 - 29,683,530 (-)NCBI
Rnor_6.0132,281,207 - 32,297,190 (-)NCBI
Rnor_5.0133,706,075 - 33,722,058 (-)NCBI
RGSC_v3.4130,474,672 - 30,490,655 (-)RGD
Celera128,315,536 - 28,331,519 (-)RGD
Sequence:
RefSeq Acc Id: XM_006227791   ⟹   XP_006227853
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2129,667,573 - 29,683,523 (-)NCBI
Rnor_6.0132,281,235 - 32,297,196 (-)NCBI
Rnor_5.0133,706,075 - 33,722,058 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001101710 (Get FASTA)   NCBI Sequence Viewer  
  XP_006227853 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL87654 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001101710   ⟸   NM_001108240
- UniProtKB: D4A416 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006227853   ⟸   XM_006227791
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000023211   ⟸   ENSRNOT00000023211
RefSeq Acc Id: ENSRNOP00000097926   ⟸   ENSRNOT00000099695

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A416-F1-model_v2 AlphaFold D4A416 1-539 view protein structure

Transcriptome

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

Promoters
RGD ID:13689568
Promoter ID:EPDNEW_R93
Type:initiation region
Name:Clptm1l_1
Description:CLPTM1-like
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_6.0132,297,198 - 32,297,258EPDNEW

Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 30477488 30477489 G T snv LCR/2Mco (UMich)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307896 AgrOrtholog
BioCyc Gene G2FUF-61925 BioCyc
Ensembl Genes ENSRNOG00000016923 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000023211 ENTREZGENE
  ENSRNOP00000023211.5 UniProtKB/TrEMBL
  ENSRNOP00000097926.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000023211 ENTREZGENE
  ENSRNOT00000023211.6 UniProtKB/TrEMBL
  ENSRNOT00000099695.1 UniProtKB/TrEMBL
InterPro CLPTM1 UniProtKB/TrEMBL
  CLPTM1L UniProtKB/TrEMBL
KEGG Report rno:316916 UniProtKB/TrEMBL
NCBI Gene 316916 ENTREZGENE
PANTHER CLPTM1 UniProtKB/TrEMBL
  PTHR21347:SF12 UniProtKB/TrEMBL
Pfam CLPTM1 UniProtKB/TrEMBL
PhenoGen Clptm1l PhenoGen
UniProt A0A8I6AWZ9_RAT UniProtKB/TrEMBL
  D4A416 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-07 Clptm1l  CLPTM1-like  RGD1307896_predicted  similar to cisplatin resistance related protein CRR9p (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 RGD1307896_predicted  similar to cisplatin resistance related protein CRR9p (predicted)  LOC316916_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC316916_predicted  similar to cisplatin resistance related protein CRR9p (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL