Rom1 (rod outer segment membrane protein 1) - Rat Genome Database

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Gene: Rom1 (rod outer segment membrane protein 1) Mus musculus
Analyze
Symbol: Rom1
Name: rod outer segment membrane protein 1
RGD ID: 1314475
MGI Page MGI
Description: Enables protein homodimerization activity. Acts upstream of or within several processes, including detection of light stimulus involved in visual perception; protein complex oligomerization; and retina development in camera-type eye. Located in photoreceptor outer segment membrane. Is expressed in photoreceptor layer; photoreceptor layer outer segment; and retina. Human ortholog(s) of this gene implicated in retinitis pigmentosa 7. Orthologous to human ROM1 (retinal outer segment membrane protein 1).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: M101156; Rgsc11; Rgsc1156; Rom; Rom-1; Rosp1; Tsp; Tspan23
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39198,904,746 - 8,906,720 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl198,904,755 - 8,906,720 (-)EnsemblGRCm39 Ensembl
GRCm38198,927,382 - 8,929,356 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl198,927,391 - 8,929,356 (-)EnsemblGRCm38mm10GRCm38
MGSCv37199,001,872 - 9,003,846 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36198,994,443 - 8,996,401 (-)NCBIMGSCv36mm8
Celera198,688,158 - 8,690,132 (-)NCBICelera
Cytogenetic Map19ANCBI
cM Map196.03NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Rom-1 is required for rod photoreceptor viability and the regulation of disk morphogenesis. Clarke G, etal., Nat Genet. 2000 May;25(1):67-73.
2. MGDs mouse GO annotations MGD data from the GO Consortium
3. MGD IEA MGD IEA
4. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
5. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
6. Mouse MP Annotation Import Pipeline RGD automated import pipeline
7. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:1415249   PMID:7835908   PMID:8504299   PMID:8603840   PMID:8630490   PMID:9730611   PMID:9886097   PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:11427722  
PMID:12477932   PMID:15163632   PMID:15489334   PMID:15539463   PMID:16000322   PMID:16141072   PMID:16141073   PMID:16267237   PMID:18171083   PMID:18654668   PMID:19805139   PMID:20055437  
PMID:20300562   PMID:20592197   PMID:21148103   PMID:21873635   PMID:22183387   PMID:22183407   PMID:25757744   PMID:26406599   PMID:26420485   PMID:28053051   PMID:29922981   PMID:30048641  
PMID:30307502   PMID:31696965   PMID:32071204   PMID:32290105   PMID:32716032   PMID:33500475   PMID:36070393   PMID:36293380   PMID:37991486  


Genomics

Comparative Map Data
Rom1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39198,904,746 - 8,906,720 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl198,904,755 - 8,906,720 (-)EnsemblGRCm39 Ensembl
GRCm38198,927,382 - 8,929,356 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl198,927,391 - 8,929,356 (-)EnsemblGRCm38mm10GRCm38
MGSCv37199,001,872 - 9,003,846 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36198,994,443 - 8,996,401 (-)NCBIMGSCv36mm8
Celera198,688,158 - 8,690,132 (-)NCBICelera
Cytogenetic Map19ANCBI
cM Map196.03NCBI
ROM1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381162,613,257 - 62,615,116 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1162,611,722 - 62,615,116 (+)EnsemblGRCh38hg38GRCh38
GRCh371162,380,729 - 62,382,588 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361162,137,199 - 62,139,164 (+)NCBINCBI36Build 36hg18NCBI36
Build 341162,137,198 - 62,139,162NCBI
Celera1159,709,778 - 59,712,156 (+)NCBICelera
Cytogenetic Map11q12.3NCBI
HuRef1158,709,131 - 58,711,511 (+)NCBIHuRef
CHM1_11162,263,259 - 62,265,638 (+)NCBICHM1_1
T2T-CHM13v2.01162,602,705 - 62,604,564 (+)NCBIT2T-CHM13v2.0
Rom1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81215,253,155 - 215,255,163 (-)NCBIGRCr8
mRatBN7.21205,824,050 - 205,826,058 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1205,824,052 - 205,826,175 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1214,232,482 - 214,234,490 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01221,267,416 - 221,269,424 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01213,960,273 - 213,962,281 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01225,126,732 - 225,128,740 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1225,126,734 - 225,128,740 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01232,064,352 - 232,066,360 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41211,604,295 - 211,606,303 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11211,762,725 - 211,764,733 (-)NCBI
Celera1203,336,848 - 203,338,856 (-)NCBICelera
Cytogenetic Map1q43NCBI
Rom1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955599573,426 - 579,812 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955599578,165 - 580,055 (-)NCBIChiLan1.0ChiLan1.0
ROM1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2963,840,032 - 63,842,342 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11164,882,740 - 64,884,782 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01157,970,290 - 57,972,658 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11161,324,900 - 61,327,278 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1161,324,900 - 61,327,278 (+)Ensemblpanpan1.1panPan2
ROM1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11854,025,603 - 54,027,803 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1854,025,606 - 54,027,375 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1852,630,636 - 52,632,899 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01855,078,090 - 55,080,354 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1855,078,093 - 55,079,861 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11854,174,207 - 54,176,469 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01853,749,070 - 53,751,332 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01854,544,718 - 54,546,985 (-)NCBIUU_Cfam_GSD_1.0
Rom1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494710,528,500 - 10,530,789 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936581641,753 - 644,637 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936581642,322 - 644,286 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ROM1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl29,125,381 - 9,127,615 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.129,125,377 - 9,127,615 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.228,471,019 - 8,472,866 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ROM1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1111,289,819 - 11,292,200 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl111,289,818 - 11,291,890 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666038108,625,071 - 108,627,450 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rom1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046249261,140,793 - 1,142,253 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046249261,140,082 - 1,142,434 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rom1
48 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:158
Count of miRNA genes:126
Interacting mature miRNAs:144
Transcripts:ENSMUST00000096242
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.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
4142302Nstr1_mnerve sheath tumor resistance QTL 1 (mouse)Not determined19122371338Mouse
1301271Datd_mdopamine transporter density (mouse)Not determined19132340234Mouse
1300923Bits4_mbitterness sensitivity 4 (mouse)Not determined19332321637323348Mouse
11039522Tbbr4_mTrypanosoma brucei brucei response 4 (mouse)19531332639313470Mouse
25394536Skmw86_mskeletal muscle weight 86, TA (mouse)1950648178957825Mouse
4142161Drinksac2_mdrink saccharin 2 (mouse)Not determined120695286Mouse
1357819Tgct2_mtesticular germ cell tumor 2 (mouse)Not determined19332855120539663Mouse
4142406Pbctlp1_mperipheral blood cytotoxic T lymphocyte percentage 1 (mouse)Not determined132875174Mouse
1300776Lfp3_mlong free running period 3 (mouse)Not determined19120328703Mouse
1300904Chab5_mcholesterol absorption 5 (mouse)Not determined19165376435653927Mouse
26884385Skwq14_mskull length QTL 14, 16 week (mouse)19325000035877400Mouse
1301800Faq10_mfluctuating asymmetry QTL 10 (mouse)Not determined19332321637323348Mouse
1300591Pas3_mpulmonary adenoma susceptibility 3 (mouse)Not determined19332321637323348Mouse
1302126Skull26_mskull morphology 26 (mouse)Not determined19332321637323348Mouse

Markers in Region
M96760  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38198,927,444 - 8,927,585UniSTSGRCm38
MGSCv37199,001,934 - 9,002,075UniSTSGRCm37
Celera198,688,220 - 8,688,361UniSTS
Cytogenetic Map19AUniSTS
cM Map198.0UniSTS
Whitehead/MRC_RH1981.95UniSTS


Expression

RNA-SEQ Expression


Sequence


Ensembl Acc Id: ENSMUST00000096242   ⟹   ENSMUSP00000093961
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl198,904,755 - 8,906,720 (-)Ensembl
GRCm38.p6 Ensembl198,927,391 - 8,929,356 (-)Ensembl
RefSeq Acc Id: NM_009073   ⟹   NP_033099
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39198,904,746 - 8,906,720 (-)NCBI
GRCm38198,927,382 - 8,929,356 (-)ENTREZGENE
MGSCv37199,001,872 - 9,003,846 (-)RGD
Celera198,688,158 - 8,690,132 (-)RGD
cM Map19 ENTREZGENE
Sequence:
Protein Sequences
Protein RefSeqs NP_033099 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA40063 (Get FASTA)   NCBI Sequence Viewer  
  AAH14827 (Get FASTA)   NCBI Sequence Viewer  
  BAE21708 (Get FASTA)   NCBI Sequence Viewer  
  EDL33403 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSMUSP00000093961
  ENSMUSP00000093961.4
GenBank Protein P32958 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_033099   ⟸   NM_009073
- UniProtKB: P32958 (UniProtKB/Swiss-Prot),   Q3UZZ7 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSMUSP00000093961   ⟸   ENSMUST00000096242

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P32958-F1-model_v2 AlphaFold P32958 1-351 view protein structure

Promoters
RGD ID:13678848
Promoter ID:EPDNEW_M23573
Type:multiple initiation site
Name:Rom1_2
Description:Mus musculus rod outer segment membrane protein 1 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M23574  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38198,929,196 - 8,929,256EPDNEW
RGD ID:13678850
Promoter ID:EPDNEW_M23574
Type:multiple initiation site
Name:Rom1_1
Description:Mus musculus rod outer segment membrane protein 1 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_M23573  
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38198,929,330 - 8,929,390EPDNEW
RGD ID:6829991
Promoter ID:MM_KWN:26323
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:NM_009073,   NM_144872,   UC008GOE.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36199,002,471 - 9,004,462 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:97998 AgrOrtholog
Ensembl Genes ENSMUSG00000003675
  ENSMUSG00000071648 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000096242 ENTREZGENE
  ENSMUST00000096242.5 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.1450.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Peripherin/rom-1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peripherin/rom-1_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Peripherin_LEL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tetraspanin/Peripherin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Tetraspanin_EC2_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:19881 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGD MGI:97998 ENTREZGENE
NCBI Gene 19881 ENTREZGENE
PANTHER ROD OUTER SEGMENT MEMBRANE PROTEIN 1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TETRASPANIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Tetraspanin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Rom1 PhenoGen
PRINTS PERIPHERNRDS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE RDS_ROM1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48652 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt P32958 ENTREZGENE
  Q3UZZ7 ENTREZGENE, UniProtKB/TrEMBL
  ROM1_MOUSE UniProtKB/Swiss-Prot