Ofd1 (Ofd1 centriole and centriolar satellite protein) - Rat Genome Database

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Gene: Ofd1 (Ofd1 centriole and centriolar satellite protein) Rattus norvegicus
Analyze
Symbol: Ofd1
Name: Ofd1 centriole and centriolar satellite protein
RGD ID: 1562231
Description: Predicted to enable identical protein binding activity; molecular adaptor activity; and tubulin binding activity. Involved in cilium assembly. Predicted to be located in centriolar satellite; centriole; and cilium. Predicted to be active in centrosome; ciliary basal body; and motile cilium. Biomarker of retinal degeneration. Human ortholog(s) of this gene implicated in Joubert syndrome 10; Simpson-Golabi-Behmel syndrome type 2; orofaciodigital syndrome I; retinitis pigmentosa; and retinitis pigmentosa 23. Orthologous to human OFD1 (OFD1 centriole and centriolar satellite protein); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: centriole and centriolar satellite protein OFD1; LOC302661; OFD1, centriole and centriolar satellite protein; oral-facial-digital syndrome 1; oral-facial-digital syndrome 1 gene homolog; oral-facial-digital syndrome 1 gene homolog (human); RGD1562231; similar to Ofd1 protein
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X31,647,000 - 31,687,768 (+)NCBIGRCr8
mRatBN7.2X28,015,347 - 28,056,115 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX28,015,347 - 28,056,110 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX29,049,925 - 29,090,559 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X32,485,025 - 32,525,793 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X28,664,565 - 28,705,199 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X29,562,165 - 29,602,934 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX29,562,165 - 29,602,925 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X29,955,456 - 29,996,224 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X48,701,675 - 48,742,443 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX28,388,104 - 28,428,825 (+)NCBICelera
Cytogenetic MapXq13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Novel mutations including deletions of the entire OFD1 gene in 30 families with type 1 orofaciodigital syndrome: a study of the extensive clinical variability. Bisschoff IJ, etal., Hum Mutat. 2013 Jan;34(1):237-47. doi: 10.1002/humu.22224. Epub 2012 Oct 17.
2. A novel X-linked recessive mental retardation syndrome comprising macrocephaly and ciliary dysfunction is allelic to oral-facial-digital type I syndrome. Budny B, etal., Hum Genet. 2006 Sep;120(2):171-8. Epub 2006 Jun 17.
3. OFD1 is mutated in X-linked Joubert syndrome and interacts with LCA5-encoded lebercilin. Coene KL, etal., Am J Hum Genet. 2009 Oct;85(4):465-81. doi: 10.1016/j.ajhg.2009.09.002.
4. A novel mutation in the OFD1 (Cxorf5) gene may contribute to oral phenotype in patients with oral-facial-digital syndrome type 1. Diz P, etal., Oral Dis. 2011 Sep;17(6):610-4. doi: 10.1111/j.1601-0825.2011.01823.x. Epub 2011 Jul 6.
5. 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.
6. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
7. Four novel mutations in the OFD1 (Cxorf5) gene in Finnish patients with oral-facial-digital syndrome 1. Rakkolainen A, etal., J Med Genet. 2002 Apr;39(4):292-6.
8. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
9. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
10. Comprehensive gene review and curation RGD comprehensive gene curation
11. Buccal anomalies, cephalometric analysis and genetic study of two sisters with orofaciodigital syndrome type I. Romero M, etal., Cleft Palate Craniofac J. 2007 Nov;44(6):660-6. doi: 10.1597/06-225.1.
12. Clinical, molecular, and genotype-phenotype correlation studies from 25 cases of oral-facial-digital syndrome type 1: a French and Belgian collaborative study. Thauvin-Robinet C, etal., J Med Genet. 2006 Jan;43(1):54-61.
13. OFD1, as a Ciliary Protein, Exhibits Neuroprotective Function in Photoreceptor Degeneration Models. Wang J, etal., PLoS One. 2016 May 19;11(5):e0155860. doi: 10.1371/journal.pone.0155860. eCollection 2016.
14. Deep intronic mutation in OFD1, identified by targeted genomic next-generation sequencing, causes a severe form of X-linked retinitis pigmentosa (RP23). Webb TR, etal., Hum Mol Genet. 2012 Aug 15;21(16):3647-54. doi: 10.1093/hmg/dds194. Epub 2012 May 22.
Additional References at PubMed
PMID:16311594   PMID:17761535   PMID:19946888   PMID:20230748   PMID:21399614   PMID:23806618   PMID:24089205   PMID:24469809   PMID:29487109  


Genomics

Comparative Map Data
Ofd1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X31,647,000 - 31,687,768 (+)NCBIGRCr8
mRatBN7.2X28,015,347 - 28,056,115 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX28,015,347 - 28,056,110 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX29,049,925 - 29,090,559 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X32,485,025 - 32,525,793 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X28,664,565 - 28,705,199 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X29,562,165 - 29,602,934 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX29,562,165 - 29,602,925 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X29,955,456 - 29,996,224 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X48,701,675 - 48,742,443 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX28,388,104 - 28,428,825 (+)NCBICelera
Cytogenetic MapXq13NCBI
OFD1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X13,714,505 - 13,773,738 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX13,734,743 - 13,777,955 (+)EnsemblGRCh38hg38GRCh38
GRCh37X13,752,867 - 13,787,476 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X13,662,801 - 13,697,393 (+)NCBINCBI36Build 36hg18NCBI36
Build 34X13,512,536 - 13,547,127NCBI
CeleraX17,869,913 - 17,904,562 (+)NCBICelera
Cytogenetic MapXp22.2NCBI
HuRefX11,510,937 - 11,544,940 (+)NCBIHuRef
CHM1_1X13,783,650 - 13,818,298 (+)NCBICHM1_1
T2T-CHM13v2.0X13,295,911 - 13,355,418 (+)NCBIT2T-CHM13v2.0
Ofd1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X165,171,503 - 165,223,704 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX165,173,029 - 165,223,700 (-)EnsemblGRCm39 Ensembl
GRCm38X166,386,573 - 166,440,704 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX166,390,033 - 166,440,704 (-)EnsemblGRCm38mm10GRCm38
MGSCv37X162,827,965 - 162,878,636 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X161,735,041 - 161,784,660 (-)NCBIMGSCv36mm8
CeleraX149,569,705 - 149,620,495 (-)NCBICelera
Cytogenetic MapXF5NCBI
cM MapX72.0NCBI
Ofd1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555194,433,855 - 4,471,070 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555194,433,747 - 4,470,842 (-)NCBIChiLan1.0ChiLan1.0
OFD1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X15,468,675 - 15,552,455 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X15,472,486 - 15,552,078 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X6,296,597 - 6,376,197 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X13,630,006 - 13,669,285 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX13,611,304 - 13,664,512 (+)Ensemblpanpan1.1panPan2
OFD1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X10,140,439 - 10,194,478 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX10,140,067 - 10,194,472 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX10,114,679 - 10,168,786 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0X10,098,262 - 10,152,653 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX10,092,106 - 10,152,605 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X10,166,885 - 10,220,990 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X10,158,225 - 10,212,581 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X10,184,578 - 10,238,702 (+)NCBIUU_Cfam_GSD_1.0
Ofd1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X3,292,935 - 3,331,915 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364703,292,249 - 3,331,800 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049364703,292,961 - 3,331,915 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
OFD1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1X10,361,403 - 10,415,502 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X11,314,606 - 11,369,244 (+)NCBISscrofa10.2Sscrofa10.2susScr3
OFD1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X12,222,396 - 12,256,802 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX12,222,760 - 12,256,557 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605614,039,780 - 14,076,648 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ofd1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624882376,556 - 416,509 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624882376,447 - 417,066 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ofd1
73 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:71
Count of miRNA genes:69
Interacting mature miRNAs:69
Transcripts:ENSRNOT00000006074
Prediction methods:Microtar, 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 (mRatBN7.2)
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)X2099094741052531Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X144812931706553Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X292789847927898Rat
2290375Gluco34Glucose level QTL 342.75blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X2099094741203591Rat
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X143491017Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7440600049406000Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X449454949494549Rat
71116Niddm16Non-insulin dependent diabetes mellitus QTL 167.81blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X1529780260297802Rat


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 6 18 59 18 61 18 207 72 105 37
Low 15 123 168 129 129 36 45 43 43 40 24
Below cutoff

Sequence


Ensembl Acc Id: ENSRNOT00000006074   ⟹   ENSRNOP00000006074
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX28,015,347 - 28,056,110 (+)Ensembl
Rnor_6.0 EnsemblX29,562,165 - 29,602,925 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000120152   ⟹   ENSRNOP00000088636
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX28,015,347 - 28,055,951 (+)Ensembl
RefSeq Acc Id: NM_001106961   ⟹   NP_001100431
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X31,647,000 - 31,687,768 (+)NCBI
mRatBN7.2X28,015,347 - 28,056,115 (+)NCBI
Rnor_6.0X29,562,165 - 29,602,934 (+)NCBI
Rnor_5.0X29,955,456 - 29,996,224 (+)NCBI
RGSC_v3.4X48,701,675 - 48,742,443 (+)RGD
CeleraX28,388,104 - 28,428,825 (+)RGD
Sequence:
RefSeq Acc Id: XM_008773164   ⟹   XP_008771386
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X31,647,584 - 31,687,768 (+)NCBI
mRatBN7.2X28,015,921 - 28,055,945 (+)NCBI
Rnor_6.0X29,562,766 - 29,602,706 (+)NCBI
Sequence:
RefSeq Acc Id: XM_063279934   ⟹   XP_063136004
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X31,647,271 - 31,687,768 (+)NCBI
RefSeq Acc Id: XR_010061184
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X31,647,271 - 31,676,370 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001100431 (Get FASTA)   NCBI Sequence Viewer  
  XP_008771386 (Get FASTA)   NCBI Sequence Viewer  
  XP_063136004 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL90547 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000006074.6
  ENSRNOP00000088636.1
RefSeq Acc Id: NP_001100431   ⟸   NM_001106961
- UniProtKB: D3ZUD5 (UniProtKB/TrEMBL),   A6K2I3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008771386   ⟸   XM_008773164
- Peptide Label: isoform X1
- UniProtKB: D3ZUD5 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000006074   ⟸   ENSRNOT00000006074
Ensembl Acc Id: ENSRNOP00000088636   ⟸   ENSRNOT00000120152
RefSeq Acc Id: XP_063136004   ⟸   XM_063279934
- Peptide Label: isoform X2
- UniProtKB: D3ZUD5 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZUD5-F1-model_v2 AlphaFold D3ZUD5 1-1025 view protein structure

Transcriptome

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

Promoters
RGD ID:13701789
Promoter ID:EPDNEW_R12313
Type:initiation region
Name:Ofd1_1
Description:OFD1, centriole and centriolar satellite protein
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_6.0X29,562,185 - 29,562,245EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1562231 AgrOrtholog
BioCyc Gene G2FUF-2608 BioCyc
Ensembl Genes ENSRNOG00000004574 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000006074.7 UniProtKB/TrEMBL
  ENSRNOT00000120152.1 UniProtKB/TrEMBL
InterPro LisH_dimerisation UniProtKB/TrEMBL
KEGG Report rno:302661 UniProtKB/TrEMBL
NCBI Gene 302661 ENTREZGENE
PANTHER LISH DOMAIN-CONTAINING PROTEIN UniProtKB/TrEMBL
  ORAL-FACIAL-DIGITAL SYNDROME 1 PROTEIN HOMOLOG UniProtKB/TrEMBL
Pfam LisH_2 UniProtKB/TrEMBL
PhenoGen Ofd1 PhenoGen
PROSITE LISH UniProtKB/TrEMBL
RatGTEx ENSRNOG00000004574 RatGTEx
SMART LisH UniProtKB/TrEMBL
UniProt A0A8I6AA62_RAT UniProtKB/TrEMBL
  A6K2I3 ENTREZGENE, UniProtKB/TrEMBL
  D3ZUD5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-04-29 Ofd1  Ofd1 centriole and centriolar satellite protein  Ofd1  OFD1, centriole and centriolar satellite protein  Name changed 629549 APPROVED
2016-06-02 Ofd1  OFD1, centriole and centriolar satellite protein  Ofd1  oral-facial-digital syndrome 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-01-22 Ofd1  oral-facial-digital syndrome 1  Ofd1  oral-facial-digital syndrome 1 gene homolog (human)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-29 Ofd1  oral-facial-digital syndrome 1 gene homolog (human)  RGD1562231_predicted  similar to Ofd1 protein (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1562231_predicted  similar to Ofd1 protein (predicted)  LOC302661  similar to Ofd1 protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC302661  similar to Ofd1 protein      Symbol and Name status set to provisional 70820 PROVISIONAL