Cltrn (collectrin, amino acid transport regulator) - Rat Genome Database

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Gene: Cltrn (collectrin, amino acid transport regulator) Rattus norvegicus
Analyze
Symbol: Cltrn
Name: collectrin, amino acid transport regulator
RGD ID: 708489
Description: Predicted to enable protein homodimerization activity and transporter activator activity. Predicted to be involved in SNARE complex assembly and positive regulation of L-proline import across plasma membrane. Predicted to act upstream of with a positive effect on calcium-ion regulated exocytosis and insulin secretion involved in cellular response to glucose stimulus. Predicted to be located in brush border membrane and cytoplasm. Predicted to be active in plasma membrane. Orthologous to human CLTRN (collectrin, amino acid transport regulator); INTERACTS WITH 1-naphthyl isothiocyanate; 17beta-estradiol 3-benzoate; ammonium chloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: collectrin; kidney-specific membrane protein; MGC93468; NX-17; Nx17; Tmem27; transmembrane protein 27
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
GRCr8X33,993,825 - 34,027,124 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX33,993,825 - 34,027,181 (-)EnsemblGRCr8
mRatBN7.2X30,361,967 - 30,395,264 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX30,361,967 - 30,395,349 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX31,394,873 - 31,428,148 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X34,831,861 - 34,865,158 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X31,019,084 - 31,052,359 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X32,118,082 - 32,153,687 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX32,118,054 - 32,153,794 (-)Ensemblrn6Rnor6.0
Rnor_5.0X32,490,603 - 32,522,780 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X51,118,665 - 51,149,768 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX30,705,756 - 30,738,867 (-)NCBICelera
RGSC_v3.1X51,172,133 - 51,203,237 (-)NCBI
Cytogenetic MapXq14NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
brush border membrane  (IEA,ISO)
cytoplasm  (IEA,ISO)
plasma membrane  (IBA,IEA,ISO,ISS)

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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. 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.
5. Collectrin, a collecting duct-specific transmembrane glycoprotein, is a novel homolog of ACE2 and is developmentally regulated in embryonic kidneys. Zhang H, etal., J Biol Chem 2001 May 18;276(20):17132-9. Epub 2001 Jan 31.
6. Screening for genes up-regulated in 5/6 nephrectomized mouse kidney. Zhang H, etal., Kidney Int 1999 Aug;56(2):549-58.
Additional References at PubMed
PMID:15489334   PMID:16330323   PMID:16330324   PMID:17167413   PMID:18981302   PMID:19056867   PMID:21907142   PMID:22628310   PMID:22701690   PMID:23376485  


Genomics

Comparative Map Data
Cltrn
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X33,993,825 - 34,027,124 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX33,993,825 - 34,027,181 (-)EnsemblGRCr8
mRatBN7.2X30,361,967 - 30,395,264 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX30,361,967 - 30,395,349 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX31,394,873 - 31,428,148 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X34,831,861 - 34,865,158 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X31,019,084 - 31,052,359 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X32,118,082 - 32,153,687 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX32,118,054 - 32,153,794 (-)Ensemblrn6Rnor6.0
Rnor_5.0X32,490,603 - 32,522,780 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X51,118,665 - 51,149,768 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX30,705,756 - 30,738,867 (-)NCBICelera
RGSC_v3.1X51,172,133 - 51,203,237 (-)NCBI
Cytogenetic MapXq14NCBI
CLTRN
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X15,627,318 - 15,675,644 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX15,627,085 - 15,675,377 (-)Ensemblhg38GRCh38
GRCh37X15,645,441 - 15,682,928 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X15,555,372 - 15,593,075 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34X15,405,107 - 15,442,811NCBI
CeleraX19,760,931 - 19,798,641 (-)NCBICelera
Cytogenetic MapXp22.2NCBI
HuRefX13,399,991 - 13,438,249 (-)NCBIHuRef
CHM1_1X15,676,401 - 15,714,121 (-)NCBICHM1_1
T2T-CHM13v2.0X15,210,303 - 15,247,770 (-)NCBIT2T-CHM13v2.0
Cltrn
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X162,873,183 - 162,901,855 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX162,871,826 - 162,901,856 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38X164,090,187 - 164,118,859 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX164,088,830 - 164,118,860 (+)Ensemblmm10GRCm38
MGSCv37X160,528,119 - 160,556,791 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36X159,434,292 - 159,462,964 (+)NCBIMGSCv36mm8
CeleraX147,304,655 - 147,333,264 (+)NCBICelera
Cytogenetic MapXF5NCBI
cM MapX76.12NCBI
Cltrn
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555192,522,155 - 2,570,972 (+)Ensembl
ChiLan1.0NW_0049555192,522,154 - 2,569,722 (+)NCBIChiLan1.0ChiLan1.0
CLTRN
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X17,428,298 - 17,465,905 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X17,431,727 - 17,469,290 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X8,255,666 - 8,293,354 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X15,537,112 - 15,574,842 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX15,535,069 - 15,575,268 (-)EnsemblpanPan2panpan1.1
CLTRN
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X11,863,479 - 11,908,361 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX11,798,839 - 11,900,594 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_TashaX11,770,083 - 11,786,549 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0X11,824,506 - 11,859,272 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX11,825,149 - 11,861,692 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X11,887,674 - 11,922,326 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X11,881,588 - 11,916,356 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X11,907,346 - 11,941,809 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Cltrn
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X5,040,429 - 5,129,055 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364705,040,795 - 5,124,192 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049364705,040,831 - 5,124,611 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CLTRN
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX12,183,796 - 12,224,964 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1X12,183,793 - 12,215,474 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X13,279,802 - 13,292,665 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CLTRN
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X14,103,046 - 14,154,936 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX14,102,497 - 14,154,123 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366605615,936,757 - 15,975,408 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cltrn
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624829412,532 - 446,938 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_004624829412,797 - 447,076 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Cltrn
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1X24,686,036 - 24,711,972 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Cltrn
536 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:270
Count of miRNA genes:185
Interacting mature miRNAs:206
Transcripts:ENSRNOT00000005348
Prediction methods:Microtar, Miranda, Pita, Rnahybrid
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
1598873Memor2Memory QTL 22.5exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)X2447036044931007Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X400149344939387Rat
2290375Gluco34Glucose level QTL 342.75blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X2447036045082063Rat
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X197044046970440Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X811148653111486Rat

Markers in Region
RH131137  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X30,362,011 - 30,362,230 (+)MAPPERmRatBN7.2
Rnor_6.0X32,118,127 - 32,118,345NCBIRnor6.0
Rnor_5.0X32,490,648 - 32,490,866UniSTSRnor5.0
RGSC_v3.4X51,118,710 - 51,118,928UniSTSRGSC3.4
CeleraX30,705,801 - 30,706,019UniSTS
RH 3.4 MapX423.92UniSTS
Cytogenetic MapXq21UniSTS


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
1 10 18 108 76 73 51 20 51 4 198 57 2 93 81 44 22 10 10

Sequence


Ensembl Acc Id: ENSRNOT00000005348   ⟹   ENSRNOP00000005348
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX33,993,825 - 34,027,181 (-)Ensembl
mRatBN7.2 EnsemblX30,361,967 - 30,395,349 (-)Ensembl
Rnor_6.0 EnsemblX32,118,054 - 32,153,794 (-)Ensembl
RefSeq Acc Id: NM_020976   ⟹   NP_066125
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X33,993,825 - 34,027,124 (-)NCBI
mRatBN7.2X30,361,967 - 30,395,264 (-)NCBI
Rnor_6.0X32,118,082 - 32,153,687 (-)NCBI
Rnor_5.0X32,490,603 - 32,522,780 (-)NCBI
RGSC_v3.4X51,118,665 - 51,149,768 (-)RGD
CeleraX30,705,756 - 30,738,867 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_066125 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAG09307 (Get FASTA)   NCBI Sequence Viewer  
  AAH78838 (Get FASTA)   NCBI Sequence Viewer  
  AAV80218 (Get FASTA)   NCBI Sequence Viewer  
  EDL90513 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000005348
GenBank Protein Q9ESG3 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_066125   ⟸   NM_020976
- Peptide Label: precursor
- UniProtKB: Q9ESG3 (UniProtKB/Swiss-Prot),   Q6AYY2 (UniProtKB/Swiss-Prot),   A6K2L7 (UniProtKB/TrEMBL),   A0A8L2Q282 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000005348   ⟸   ENSRNOT00000005348
Protein Domains
Collectrin-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9ESG3-F1-model_v2 AlphaFold Q9ESG3 1-222 view protein structure

Transcriptome

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

Promoters
RGD ID:13701798
Promoter ID:EPDNEW_R12322
Type:initiation region
Name:Tmem27_1
Description:transmembrane protein 27
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_6.0X32,153,707 - 32,153,767EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:708489 AgrOrtholog
BioCyc Gene G2FUF-2581 BioCyc
Ensembl Genes ENSRNOG00000003960 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000005348 ENTREZGENE
IMAGE_CLONE IMAGE:7129929 IMAGE-MGC_LOAD
InterPro Collectrin UniProtKB/Swiss-Prot
  Collectrin_dom UniProtKB/Swiss-Prot
KEGG Report rno:57395 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93468 IMAGE-MGC_LOAD
NCBI Gene 57395 ENTREZGENE
PANTHER COLLECTRIN UniProtKB/Swiss-Prot
  PTHR46884 UniProtKB/Swiss-Prot
Pfam Collectrin UniProtKB/Swiss-Prot
PhenoGen Cltrn PhenoGen
PROSITE COLLECTRIN_LIKE UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000003960 RatGTEx
UniProt A0A8L2Q282 ENTREZGENE, UniProtKB/TrEMBL
  A6K2L7 ENTREZGENE, UniProtKB/TrEMBL
  CLTRN_RAT UniProtKB/Swiss-Prot
  Q6AYY2 ENTREZGENE
  Q9ESG3 ENTREZGENE
UniProt Secondary Q6AYY2 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-01-18 Cltrn  collectrin, amino acid transport regulator  Tmem27  transmembrane protein 27  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Tmem27  transmembrane protein 27    kidney-specific membrane protein  Name updated 1299863 APPROVED
2004-09-10 Tmem27  kidney-specific membrane protein  Nx17    Symbol and Name updated 1299863 APPROVED