Ostm1 (osteoclastogenesis associated transmembrane protein 1) - Rat Genome Database

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Gene: Ostm1 (osteoclastogenesis associated transmembrane protein 1) Rattus norvegicus
Analyze
Symbol: Ostm1
Name: osteoclastogenesis associated transmembrane protein 1
RGD ID: 1564976
Description: Predicted to be involved in osteoclast differentiation and transepithelial chloride transport. Predicted to be located in lysosomal membrane. Predicted to be part of chloride channel complex. Predicted to be active in cytosol. Human ortholog(s) of this gene implicated in autosomal recessive osteopetrosis 5. Orthologous to human OSTM1 (osteoclastogenesis associated transmembrane protein 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acetamide; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: GAIP interacting protein N terminus; Gipn; LOC499474; MGC116111; osteopetrosis associated transmembrane protein 1; osteopetrosis associated transmembrane protein 1-like; osteopetrosis-associated transmembrane protein 1; similar to osteopetrosis associated transmembrane protein 1
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
mRatBN7.22046,071,657 - 46,187,049 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2046,153,075 - 46,187,023 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2047,870,532 - 47,904,458 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.02047,520,687 - 47,554,613 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.02048,212,885 - 48,246,518 (+)NCBIRnor_WKY
Rnor_6.02047,394,979 - 47,430,304 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2047,395,014 - 47,430,284 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02049,062,739 - 49,092,292 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera2053,793,629 - 53,820,512 (-)NCBICelera
Cytogenetic Map20q13NCBI
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

Biological Process

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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
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
6. 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:12627228   PMID:12826607   PMID:21527911  


Genomics

Comparative Map Data
Ostm1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22046,071,657 - 46,187,049 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2046,153,075 - 46,187,023 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2047,870,532 - 47,904,458 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.02047,520,687 - 47,554,613 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.02048,212,885 - 48,246,518 (+)NCBIRnor_WKY
Rnor_6.02047,394,979 - 47,430,304 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2047,395,014 - 47,430,284 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02049,062,739 - 49,092,292 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera2053,793,629 - 53,820,512 (-)NCBICelera
Cytogenetic Map20q13NCBI
OSTM1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386108,041,409 - 108,074,741 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl6108,029,245 - 108,165,854 (-)EnsemblGRCh38hg38GRCh38
GRCh376108,362,613 - 108,395,945 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 366108,469,306 - 108,502,634 (-)NCBINCBI36Build 36hg18NCBI36
Build 346108,469,305 - 108,502,634NCBI
Celera6109,109,095 - 109,142,438 (-)NCBICelera
Cytogenetic Map6q21NCBI
HuRef6105,930,856 - 105,964,198 (-)NCBIHuRef
CHM1_16108,625,219 - 108,658,570 (-)NCBICHM1_1
T2T-CHM13v2.06109,218,461 - 109,251,819 (-)NCBIT2T-CHM13v2.0
Ostm1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391042,554,912 - 42,578,458 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1042,459,818 - 42,578,455 (+)EnsemblGRCm39 Ensembl
GRCm381042,678,916 - 42,702,462 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1042,583,822 - 42,702,459 (+)EnsemblGRCm38mm10GRCm38
MGSCv371042,398,723 - 42,422,261 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361042,367,332 - 42,390,870 (+)NCBIMGSCv36mm8
Celera1043,546,113 - 43,569,890 (+)NCBICelera
Cytogenetic Map10B2NCBI
cM Map1022.89NCBI
Ostm1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541133,171,264 - 33,205,486 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541133,168,868 - 33,205,452 (-)NCBIChiLan1.0ChiLan1.0
OSTM1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan16125,938,015 - 125,970,220 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06105,842,261 - 105,874,429 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16109,705,522 - 109,738,691 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6109,705,519 - 109,738,691 (-)Ensemblpanpan1.1panPan2
OSTM1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11265,085,456 - 65,120,827 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1265,087,243 - 65,120,832 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1264,901,693 - 64,936,804 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01265,961,124 - 65,996,247 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1265,961,124 - 65,996,266 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11265,317,035 - 65,352,393 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01265,162,813 - 65,198,133 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01265,436,313 - 65,471,416 (-)NCBIUU_Cfam_GSD_1.0
Ostm1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946100,026,706 - 100,057,222 (-)NCBIHiC_Itri_2
SpeTri2.0NW_0049365644,301,569 - 4,332,070 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
OSTM1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl174,139,330 - 74,181,084 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1174,139,326 - 74,181,165 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2183,410,028 - 83,451,815 (-)NCBISscrofa10.2Sscrofa10.2susScr3
OSTM1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11365,774,825 - 65,812,606 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1365,774,844 - 65,809,272 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604038,103,051 - 38,151,291 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ostm1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462478014,212,762 - 14,247,994 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462478014,212,803 - 14,247,818 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ostm1
708 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:203
Count of miRNA genes:150
Interacting mature miRNAs:169
Transcripts:ENSRNOT00000057116
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201761783247606836Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201769755054435887Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)201919072154435887Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202510672254435887Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202510672254435887Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202510672254435887Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202520973454435887Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)202924438854435887Rat


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 8 31 17 18 17 2 74 25 20 11
Low 35 26 24 1 24 8 9 10 21 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000057116   ⟹   ENSRNOP00000053945
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2046,153,075 - 46,186,062 (+)Ensembl
Rnor_6.0 Ensembl2047,395,014 - 47,430,284 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000114998   ⟹   ENSRNOP00000091994
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2046,153,148 - 46,187,023 (+)Ensembl
RefSeq Acc Id: NM_001029925   ⟹   NP_001025096
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22046,153,162 - 46,185,379 (+)NCBI
Rnor_6.02047,395,014 - 47,430,284 (+)NCBI
Rnor_5.02049,062,739 - 49,092,292 (+)NCBI
Celera2053,793,629 - 53,820,512 (-)RGD
Sequence:
RefSeq Acc Id: XM_006256577   ⟹   XP_006256639
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22046,153,110 - 46,187,049 (+)NCBI
Rnor_6.02047,394,979 - 47,430,304 (+)NCBI
Rnor_5.02049,062,739 - 49,092,292 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039099031   ⟹   XP_038954959
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22046,071,657 - 46,187,049 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001025096 (Get FASTA)   NCBI Sequence Viewer  
  XP_006256639 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954959 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH97978 (Get FASTA)   NCBI Sequence Viewer  
  EDL99701 (Get FASTA)   NCBI Sequence Viewer  
  EDL99702 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001025096   ⟸   NM_001029925
- Peptide Label: precursor
- UniProtKB: Q4QQU9 (UniProtKB/TrEMBL),   F1LP89 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256639   ⟸   XM_006256577
- Peptide Label: isoform X1
- UniProtKB: A0A8J8Y8J8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000053945   ⟸   ENSRNOT00000057116
RefSeq Acc Id: XP_038954959   ⟸   XM_039099031
- Peptide Label: isoform X2
RefSeq Acc Id: ENSRNOP00000091994   ⟸   ENSRNOT00000114998

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q4QQU9-F1-model_v2 AlphaFold Q4QQU9 1-338 view protein structure

Transcriptome

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

Promoters
RGD ID:13701670
Promoter ID:EPDNEW_R12194
Type:multiple initiation site
Name:Ostm1_1
Description:osteopetrosis associated transmembrane protein 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_6.02047,394,995 - 47,395,055EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1564976 AgrOrtholog
BioCyc Gene G2FUF-3357 BioCyc
Ensembl Genes ENSRNOG00000037647 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000053945 ENTREZGENE
  ENSRNOP00000053945.4 UniProtKB/TrEMBL
  ENSRNOP00000091994 ENTREZGENE
  ENSRNOP00000091994.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000057116 ENTREZGENE
  ENSRNOT00000057116.4 UniProtKB/TrEMBL
  ENSRNOT00000114998 ENTREZGENE
  ENSRNOT00000114998.1 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7442765 IMAGE-MGC_LOAD
InterPro Osteopetrosis-assoc_TM_1 UniProtKB/TrEMBL
KEGG Report rno:499474 UniProtKB/TrEMBL
MGC_CLONE MGC:116111 IMAGE-MGC_LOAD
NCBI Gene 499474 ENTREZGENE
PANTHER OSTEOPETROSIS-ASSOCIATED TRANSMEMBRANE PROTEIN 1 UniProtKB/TrEMBL
  PTHR15644 UniProtKB/TrEMBL
Pfam OSTMP1 UniProtKB/TrEMBL
PhenoGen Ostm1 PhenoGen
UniProt A0A8J8Y8J8 ENTREZGENE, UniProtKB/TrEMBL
  F1LP89 ENTREZGENE
  Q4QQU9 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary F1LP89 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2018-08-21 Ostm1  osteoclastogenesis associated transmembrane protein 1  Ostm1  osteopetrosis associated transmembrane protein 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-05 Ostm1  osteopetrosis associated transmembrane protein 1  LOC499474  similar to osteopetrosis associated transmembrane protein 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 LOC499474  similar to osteopetrosis associated transmembrane protein 1      Symbol and Name status set to provisional 70820 PROVISIONAL