Human Gene ROM1 (uc001ntv.3) Description and Page Index
  Description: Homo sapiens retinal outer segment membrane protein 1 (ROM1), mRNA.
RefSeq Summary (NM_000327): This gene is a member of a photoreceptor-specific gene family and encodes an integral membrane protein found in the photoreceptor disk rim of the eye. This protein can form homodimers or can heterodimerize with another photoreceptor, retinal degeneration slow (RDS). It is essential for disk morphogenesis, and may also function as an adhesion molecule involved in the stabilization and compaction of outer segment disks or in the maintenance of the curvature of the rim. Certain defects in this gene have been associated with the degenerative eye disease retinitis pigmentosa. [provided by RefSeq, Jul 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: AK313674.1, BC008100.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr11:62,380,213-62,382,592 Size: 2,380 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg19 chr11:62,380,754-62,382,311 Size: 1,558 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsOther NamesGeneReviewsModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:62,380,213-62,382,592)mRNA (may differ from genome)Protein (351 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedStanford SOURCETreefamUniProtKB
Wikipedia

-  Comments and Description Text from UniProtKB
  ID: ROM1_HUMAN
DESCRIPTION: RecName: Full=Rod outer segment membrane protein 1; Short=ROSP1; AltName: Full=Tetraspanin-23; Short=Tspan-23;
FUNCTION: May function as an adhesion molecule involved in stabilization and compaction of outer segment disks or in the maintenance of the curvature of the rim. It is essential for disk morphogenesis.
SUBUNIT: Homodimer; disulfide-linked. Probably forms a complex with a PRPH2 homodimer. Other proteins could associate with this complex in rods.
SUBCELLULAR LOCATION: Membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Retina (photoreceptor). In rim region of ROS (rod outer segment) disks.
DISEASE: Defects in ROM1 may cause retinitis pigmentosa (RP) [MIM:268000]; when associated with defects in PRPH2.
SIMILARITY: Belongs to the PRPH2/ROM1 family.
WEB RESOURCE: Name=Mutations of the ROM1 gene; Note=Retina International's Scientific Newsletter; URL="http://www.retina-international.org/files/sci-news/rommut.htm";

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): ROM1
CDC HuGE Published Literature: ROM1
Positive Disease Associations: retinitis pigmentosa.
Related Studies:
  1. retinitis pigmentosa.
    Martinez-Mir A et al. 1997, Putative association of a mutant ROM1 allele with retinitis pigmentosa., Human genetics. 1997 Jun;99(6):827-30. [PubMed 9187681]

-  MalaCards Disease Associations
  MalaCards Gene Search: ROM1
Diseases sorted by gene-association score: retinitis pigmentosa 7 and digenic* (636), rhyns syndrome* (283), retinitis pigmentosa* (178), rom1-related retinitis pigmentosa* (100), vitelliform macular dystrophy (16), best vitelliform macular dystrophy (13), neisseria meningitidis infection (11), peripheral retinal degeneration (9), stargardt disease 1 (9), butterfly-shaped pigment dystrophy (8), meningococcal infection (7), gyrate atrophy of choroid and retina with or without ornithinemia (6), eye disease (6), retinal degeneration (5), retinal disease (3), fundus dystrophy (1)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 37.41 RPKM in Brain - Spinal cord (cervical c-1)
Total median expression: 495.46 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -294.60541-0.545 Picture PostScript Text
3' UTR -97.00281-0.345 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR000830 - Peripherin/rom-1
IPR018498 - Peripherin/rom-1_CS
IPR018499 - Tetraspanin/Peripherin
IPR008952 - Tetraspanin_EC2

Pfam Domains:
PF00335 - Tetraspanin family

SCOP Domains:
48652 - Tetraspanin

ModBase Predicted Comparative 3D Structure on Q03395
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologGenome BrowserNo orthologNo ortholog
Gene DetailsGene Details Gene Details  
Gene SorterGene Sorter Gene Sorter  
 RGD FlyBase  
 Protein Sequence Protein Sequence  
 Alignment Alignment  

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Biological Process:
GO:0007155 cell adhesion
GO:0007166 cell surface receptor signaling pathway
GO:0007601 visual perception
GO:0010468 regulation of gene expression
GO:0060042 retina morphogenesis in camera-type eye
GO:0060219 camera-type eye photoreceptor cell differentiation
GO:0061298 retina vasculature development in camera-type eye

Cellular Component:
GO:0001750 photoreceptor outer segment
GO:0005887 integral component of plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0042622 photoreceptor outer segment membrane


-  Descriptions from all associated GenBank mRNAs
  AK313674 - Homo sapiens cDNA, FLJ94260, Homo sapiens retinal outer segment membrane protein 1 (ROM1), mRNA.
DQ426890 - Homo sapiens retinal outer segment membrane protein 1 (ROM1) mRNA, 5' UTR.
BC036268 - Homo sapiens retinal outer segment membrane protein 1, mRNA (cDNA clone IMAGE:4179213).
BC008100 - Homo sapiens retinal outer segment membrane protein 1, mRNA (cDNA clone MGC:17106 IMAGE:4177529), complete cds.
JD486042 - Sequence 467066 from Patent EP1572962.
JD333792 - Sequence 314816 from Patent EP1572962.
JD072869 - Sequence 53893 from Patent EP1572962.
JD519590 - Sequence 500614 from Patent EP1572962.
JD392416 - Sequence 373440 from Patent EP1572962.
JD133805 - Sequence 114829 from Patent EP1572962.
JD531309 - Sequence 512333 from Patent EP1572962.
JD437776 - Sequence 418800 from Patent EP1572962.
JD051183 - Sequence 32207 from Patent EP1572962.
L07894 - Human rod outer segment membrane protein 1 (ROM1) mRNA, complete cds.
CU675931 - Synthetic construct Homo sapiens gateway clone IMAGE:100017073 5' read ROM1 mRNA.
AB464146 - Synthetic construct DNA, clone: pF1KB8205, Homo sapiens ROM1 gene for retinal outer segment membrane protein 1, without stop codon, in Flexi system.
HQ448285 - Synthetic construct Homo sapiens clone IMAGE:100071688; CCSB002804_01 retinal outer segment membrane protein 1 (ROM1) gene, encodes complete protein.
KJ897478 - Synthetic construct Homo sapiens clone ccsbBroadEn_06872 ROM1 gene, encodes complete protein.
KR709652 - Synthetic construct Homo sapiens clone CCSBHm_00004926 ROM1 (ROM1) mRNA, encodes complete protein.
KR709653 - Synthetic construct Homo sapiens clone CCSBHm_00004929 ROM1 (ROM1) mRNA, encodes complete protein.
JD076100 - Sequence 57124 from Patent EP1572962.
JD073143 - Sequence 54167 from Patent EP1572962.
JD294672 - Sequence 275696 from Patent EP1572962.
JD495996 - Sequence 477020 from Patent EP1572962.
JD476494 - Sequence 457518 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B2R978, NM_000327, NP_000318, Q03395, ROM1_HUMAN, TSPAN23
UCSC ID: uc001ntv.3
RefSeq Accession: NM_000327
Protein: Q03395 (aka ROM1_HUMAN)
CCDS: CCDS8024.1

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene ROM1:
rp-overview (Nonsyndromic Retinitis Pigmentosa Overview)

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_000327.3
exon count: 3CDS single in 3' UTR: no RNA size: 1894
ORF size: 1056CDS single in intron: no Alignment % ID: 99.89
txCdsPredict score: 2227.00frame shift in genome: no % Coverage: 99.16
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.