Itm2c (integral membrane protein 2C) - Rat Genome Database

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Gene: Itm2c (integral membrane protein 2C) Rattus norvegicus
Analyze
Symbol: Itm2c
Name: integral membrane protein 2C
RGD ID: 1309503
Description: Predicted to enable ATP binding activity and amyloid-beta binding activity. Predicted to be involved in several processes, including negative regulation of amyloid precursor protein biosynthetic process; negative regulation of neuron projection development; and positive regulation of extrinsic apoptotic signaling pathway. Predicted to be located in lysosome and perinuclear region of cytoplasm. Predicted to be active in Golgi apparatus and plasma membrane. Orthologous to human ITM2C (integral membrane protein 2C); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; all-trans-retinoic acid; amphetamine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: integral membrane protein 3; LOC301575; MGC94903
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
GRCr8993,993,922 - 94,007,737 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl993,993,895 - 94,007,704 (+)EnsemblGRCr8
mRatBN7.2986,545,927 - 86,559,745 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl986,545,921 - 86,559,742 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx994,963,890 - 94,977,710 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.09100,092,388 - 100,106,210 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0998,473,052 - 98,486,892 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0992,916,469 - 92,930,306 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl992,916,469 - 92,930,279 (+)Ensemblrn6Rnor6.0
Rnor_5.0992,645,770 - 92,659,607 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4984,611,756 - 84,625,391 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera983,967,245 - 83,980,873 (+)NCBICelera
RGSC_v3.1984,795,174 - 84,808,783 (+)NCBI
Cytogenetic Map9q35NCBI
JBrowse:




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

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10679242   PMID:12477932   PMID:14592447   PMID:15489334   PMID:18452648   PMID:19056867   PMID:19114711   PMID:19199708   PMID:19849849   PMID:22871113   PMID:23376485  


Genomics

Comparative Map Data
Itm2c
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8993,993,922 - 94,007,737 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl993,993,895 - 94,007,704 (+)EnsemblGRCr8
mRatBN7.2986,545,927 - 86,559,745 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl986,545,921 - 86,559,742 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx994,963,890 - 94,977,710 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.09100,092,388 - 100,106,210 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0998,473,052 - 98,486,892 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0992,916,469 - 92,930,306 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl992,916,469 - 92,930,279 (+)Ensemblrn6Rnor6.0
Rnor_5.0992,645,770 - 92,659,607 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4984,611,756 - 84,625,391 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera983,967,245 - 83,980,873 (+)NCBICelera
RGSC_v3.1984,795,174 - 84,808,783 (+)NCBI
Cytogenetic Map9q35NCBI
ITM2C
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382230,864,185 - 230,879,254 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2230,864,639 - 230,879,248 (+)Ensemblhg38GRCh38
GRCh372231,728,900 - 231,743,969 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362231,437,865 - 231,452,207 (+)NCBIBuild 36Build 36hg18NCBI36
Build 342231,555,125 - 231,569,467NCBI
Celera2225,506,038 - 225,520,369 (+)NCBICelera
Cytogenetic Map2q37.1NCBI
HuRef2223,571,781 - 223,586,111 (+)NCBIHuRef
CHM1_12231,735,449 - 231,749,771 (+)NCBICHM1_1
T2T-CHM13v2.02231,347,355 - 231,362,416 (+)NCBIT2T-CHM13v2.0
Itm2c
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39185,822,231 - 85,836,419 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl185,822,002 - 85,836,396 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38185,894,510 - 85,908,698 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl185,894,281 - 85,908,675 (+)Ensemblmm10GRCm38
MGSCv37187,791,085 - 87,805,273 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36187,725,736 - 87,739,863 (+)NCBIMGSCv36mm8
Celera188,859,731 - 88,873,901 (+)NCBICelera
Cytogenetic Map1C5NCBI
cM Map143.94NCBI
Itm2c
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554534,543,476 - 4,557,757 (-)Ensembl
ChiLan1.0NW_0049554534,546,736 - 4,557,649 (-)NCBIChiLan1.0ChiLan1.0
ITM2C
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v213133,488,296 - 133,502,794 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12B133,503,291 - 133,517,765 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02B118,116,228 - 118,131,379 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12B236,921,544 - 236,927,392 (+)NCBIPanPan1.1PanPan1.1panPan2
ITM2C
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12542,829,825 - 42,842,737 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2542,829,608 - 42,883,055 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha2543,390,533 - 43,403,440 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.02543,087,071 - 43,099,974 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2543,086,948 - 43,101,722 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12543,015,981 - 43,028,888 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02542,858,683 - 42,871,592 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02543,014,005 - 43,026,924 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Itm2c
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303185,012,341 - 185,025,221 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365255,914,954 - 5,927,299 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365255,913,913 - 5,927,385 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ITM2C
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl15131,614,743 - 131,628,619 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.115131,614,887 - 131,627,428 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.215145,293,455 - 145,305,999 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ITM2C
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.110116,902,785 - 116,917,332 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl10116,903,113 - 116,917,549 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604082,544,392 - 82,559,437 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Itm2c
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248434,232,588 - 4,242,147 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248434,232,482 - 4,243,079 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Itm2c
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v14158,036,517 - 158,050,220 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Itm2c
82 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:130
Count of miRNA genes:97
Interacting mature miRNAs:107
Transcripts:ENSRNOT00000023535
Prediction methods:Miranda, 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
631656Bp108Blood pressure QTL 1085.970.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)956047863101047863Rat
1582203Gluco19Glucose level QTL 193.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)963376862108376862Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)94445825699506504Rat
724515Uae16Urinary albumin excretion QTL 168urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)965657365108376720Rat
724547Cm21Cardiac mass QTL 212.7heart mass (VT:0007028)calculated heart weight (CMO:0000073)986720043110356905Rat
2303178Bp334Blood pressure QTL 3343.70.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)986720043121768150Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)964220169109220169Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)944458256121768150Rat
1578760Cm53Cardiac mass QTL 533.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)964220169109220169Rat
1581580Uae34Urinary albumin excretion QTL 34urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)964220169109220169Rat
1300134Bp185Blood pressure QTL 1853.73arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)968875497121768150Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)983161999118999486Rat
4889852Pur26Proteinuria QTL 26150.001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)985262459109044727Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)985262459118999486Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)948718864108376862Rat
4889943Bss90Bone structure and strength QTL 904.1tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)95450650499506504Rat
1578757Pur6Proteinuria QTL 63.30.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)964220169109220169Rat

Markers in Region
RH137067  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2986,559,451 - 86,559,671 (+)MAPPERmRatBN7.2
Rnor_6.0992,930,013 - 92,930,232NCBIRnor6.0
Rnor_5.0992,659,314 - 92,659,533UniSTSRnor5.0
RGSC_v3.4984,625,098 - 84,625,317UniSTSRGSC3.4
Celera983,980,580 - 83,980,799UniSTS
Cytogenetic Map9q35UniSTS


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 67 162 91 90 59 92 59 6 356 192 11 141 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000023535   ⟹   ENSRNOP00000023535
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl993,993,895 - 94,007,704 (+)Ensembl
mRatBN7.2 Ensembl986,545,921 - 86,559,742 (+)Ensembl
Rnor_6.0 Ensembl992,916,469 - 92,930,279 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000103926   ⟹   ENSRNOP00000089071
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl993,993,910 - 94,007,704 (+)Ensembl
mRatBN7.2 Ensembl986,545,921 - 86,559,742 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000161256   ⟹   ENSRNOP00000108705
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl993,993,910 - 94,007,704 (+)Ensembl
RefSeq Acc Id: NM_001009674   ⟹   NP_001009674
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8993,993,922 - 94,007,737 (+)NCBI
mRatBN7.2986,545,927 - 86,559,745 (+)NCBI
Rnor_6.0992,916,469 - 92,930,306 (+)NCBI
Rnor_5.0992,645,770 - 92,659,607 (+)NCBI
RGSC_v3.4984,611,756 - 84,625,391 (+)RGD
Celera983,967,245 - 83,980,873 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001009674 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH87127 (Get FASTA)   NCBI Sequence Viewer  
  EDL75563 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000023535.4
  ENSRNOP00000108705
GenBank Protein Q5PQL7 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001009674   ⟸   NM_001009674
- UniProtKB: Q5PQL7 (UniProtKB/Swiss-Prot),   A6JWF5 (UniProtKB/TrEMBL),   A0A8I6AAT4 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000023535   ⟸   ENSRNOT00000023535
Ensembl Acc Id: ENSRNOP00000089071   ⟸   ENSRNOT00000103926
Ensembl Acc Id: ENSRNOP00000108705   ⟸   ENSRNOT00000161256
Protein Domains
BRICHOS

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5PQL7-F1-model_v2 AlphaFold Q5PQL7 1-269 view protein structure

Transcriptome

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

Promoters
RGD ID:13696817
Promoter ID:EPDNEW_R7342
Type:initiation region
Name:Itm2c_1
Description:integral membrane protein 2C
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_6.0992,916,446 - 92,916,506EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309503 AgrOrtholog
BioCyc Gene G2FUF-26922 BioCyc
Ensembl Genes ENSRNOG00000017359 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000023535.6 UniProtKB/Swiss-Prot
  ENSRNOT00000161256 ENTREZGENE
Gene3D-CATH 3.30.390.150 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7111761 IMAGE-MGC_LOAD
InterPro BRICHOS_dom UniProtKB/Swiss-Prot
  ITM2 UniProtKB/Swiss-Prot
KEGG Report rno:301575 UniProtKB/Swiss-Prot
MGC_CLONE MGC:94903 IMAGE-MGC_LOAD
NCBI Gene 301575 ENTREZGENE
PANTHER INTEGRAL MEMBRANE PROTEIN 2C UniProtKB/Swiss-Prot
  PTHR10962 UniProtKB/Swiss-Prot
Pfam BRICHOS UniProtKB/Swiss-Prot
PhenoGen Itm2c PhenoGen
PROSITE BRICHOS UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000017359 RatGTEx
SMART BRICHOS UniProtKB/Swiss-Prot
UniProt A0A8I6AAT4 ENTREZGENE, UniProtKB/TrEMBL
  A6JWF5 ENTREZGENE, UniProtKB/TrEMBL
  ITM2C_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-12-06 Itm2c  integral membrane protein 2C  Itm2c_predicted  integral membrane protein 2C (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Itm2c_predicted  integral membrane protein 2C (predicted)      Symbol and Name status set to approved 70820 APPROVED