Surf1 (SURF1, cytochrome c oxidase assembly factor) - Rat Genome Database

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Gene: Surf1 (SURF1, cytochrome c oxidase assembly factor) Rattus norvegicus
Analyze
Symbol: Surf1
Name: SURF1, cytochrome c oxidase assembly factor
RGD ID: 620527
Description: Predicted to enable cytochrome-c oxidase activity. Predicted to be involved in mitochondrial cytochrome c oxidase assembly. Predicted to be located in mitochondrial inner membrane. Human ortholog(s) of this gene implicated in Charcot-Marie-Tooth disease type 4K; Leigh disease; and mitochondrial complex IV deficiency nuclear type 1. Orthologous to human SURF1 (SURF1 cytochrome c oxidase assembly factor); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; amitrole.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Ab1-205; LOC100912008; surfeit 1; surfeit locus protein 1; uncharacterized LOC100912008
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
GRCr8330,639,868 - 30,642,759 (-)NCBIGRCr8GRCr8GRCr8
mRatBN7.2310,241,793 - 10,244,686 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl310,241,837 - 10,263,315 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx313,301,794 - 13,304,626 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0321,887,195 - 21,890,027 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0320,142,496 - 20,145,328 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.035,461,717 - 5,464,560 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl34,869,795 - 4,872,632 (-)Ensemblrn6Rnor6.0
Rnor_5.0310,823,627 - 10,826,484 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.435,810,638 - 5,813,475 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera35,039,828 - 5,042,665 (-)NCBICelera
RGSC_v3.135,810,937 - 5,813,775 (-)NCBI
Cytogenetic Map3p13NCBI
JBrowse:




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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
4. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
5. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
6. Sequence conservation from human to prokaryotes of Surf1, a protein involved in cytochrome c oxidase assembly, deficient in Leigh syndrome. Poyau A, etal., FEBS Lett 1999 Dec 3;462(3):416-20.
7. Missense mutations in SURF1 associated with deficient cytochrome c oxidase assembly in Leigh syndrome patients. Poyau A, etal., Hum Genet 2000 Feb;106(2):194-205.
8. GOA pipeline RGD automated data pipeline
9. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
10. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
11. Comprehensive gene review and curation RGD comprehensive gene curation
12. SURF1, encoding a factor involved in the biogenesis of cytochrome c oxidase, is mutated in Leigh syndrome. Zhu Z, etal., Nat Genet. 1998 Dec;20(4):337-43.
Additional References at PubMed
PMID:12566387   PMID:20888800   PMID:23838831   PMID:24027061   PMID:34800366  


Genomics

Comparative Map Data
Surf1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8330,639,868 - 30,642,759 (-)NCBIGRCr8GRCr8GRCr8
mRatBN7.2310,241,793 - 10,244,686 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl310,241,837 - 10,263,315 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx313,301,794 - 13,304,626 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0321,887,195 - 21,890,027 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0320,142,496 - 20,145,328 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.035,461,717 - 5,464,560 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl34,869,795 - 4,872,632 (-)Ensemblrn6Rnor6.0
Rnor_5.0310,823,627 - 10,826,484 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.435,810,638 - 5,813,475 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera35,039,828 - 5,042,665 (-)NCBICelera
RGSC_v3.135,810,937 - 5,813,775 (-)NCBI
Cytogenetic Map3p13NCBI
SURF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389133,351,758 - 133,356,487 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9133,351,758 - 133,356,676 (-)Ensemblhg38GRCh38
GRCh379136,218,613 - 136,223,363 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369135,208,487 - 135,213,182 (-)NCBIBuild 36Build 36hg18NCBI36
Build 349133,248,219 - 133,252,915NCBI
Celera9106,769,152 - 106,773,840 (-)NCBICelera
Cytogenetic Map9q34.2NCBI
HuRef9105,718,581 - 105,723,261 (-)NCBIHuRef
CHM1_19136,368,824 - 136,373,504 (-)NCBICHM1_1
T2T-CHM13v2.09145,565,698 - 145,570,441 (-)NCBIT2T-CHM13v2.0
Surf1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39226,803,390 - 26,806,667 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl226,803,393 - 26,806,542 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38226,913,378 - 26,916,610 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl226,913,381 - 26,916,530 (-)Ensemblmm10GRCm38
MGSCv37226,768,898 - 26,772,050 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36226,735,445 - 26,738,340 (-)NCBIMGSCv36mm8
Celera226,623,123 - 26,626,275 (-)NCBICelera
Cytogenetic Map2A3NCBI
cM Map219.1NCBI
Surf1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555132,707,951 - 2,711,566 (-)Ensembl
ChiLan1.0NW_0049555132,707,877 - 2,711,606 (-)NCBIChiLan1.0ChiLan1.0
LOC100983451
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2115,996,845 - 6,001,561 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan195,999,191 - 6,003,897 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v09104,475,018 - 104,479,714 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19133,085,739 - 133,088,911 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9133,085,739 - 133,088,904 (-)EnsemblpanPan2panpan1.1
SURF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1949,786,562 - 49,790,004 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl949,786,085 - 49,790,148 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha949,066,928 - 49,071,492 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0950,659,471 - 50,664,036 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl950,660,593 - 50,664,180 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1949,421,907 - 49,426,471 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0949,763,390 - 49,767,971 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0949,841,389 - 49,845,964 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
LOC101971854
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947199,842,971 - 199,847,440 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366693,527,761 - 3,534,586 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366693,527,741 - 3,532,087 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SURF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1272,965,643 - 272,970,483 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11272,965,637 - 272,970,516 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
SURF1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1124,780,415 - 4,785,538 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl124,780,568 - 4,785,385 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_023666058203,090 - 208,286 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
LOC101710326
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247601,815,224 - 1,818,991 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247601,815,215 - 1,819,014 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
LOC116901251
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v159,738,418 - 9,741,106 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Surf1
16 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:188
Count of miRNA genes:130
Interacting mature miRNAs:142
Transcripts:ENSRNOT00000061242, ENSRNOT00000071754
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1558647Cm46Cardiac mass QTL 465.40.0000055heart mass (VT:0007028)heart wet weight (CMO:0000069)32267715050766390Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)32905627547904329Rat
6893355Bw101Body weight QTL 1010.40.38body mass (VT:0001259)body weight (CMO:0000012)3576639050766390Rat
10450811Scl73Serum cholesterol level QTL 734.70.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)3290432947904329Rat
2292615Ept17Estrogen-induced pituitary tumorigenesis QTL 176.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3655634751556347Rat
10450808Scl72Serum cholesterol level QTL 724.40.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)3290432947904329Rat
10450806Scl71Serum cholesterol level QTL 715.80.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)3290432947904329Rat
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)3576639050766390Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)32862533967641995Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)3612543751125437Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3136721849Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)31141509147Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3655634751556347Rat
1558657Cm43Cardiac mass QTL 436.63e-08heart mass (VT:0007028)heart wet weight (CMO:0000069)32267715050766390Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)31527234860272348Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)3576639050766390Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)32905627547904329Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)35675975141509147Rat
1358185Ept6Estrogen-induced pituitary tumorigenesis QTL 66.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)3655634751556347Rat

Markers in Region
RH141176  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr8330,639,962 - 30,640,395 (+)Marker Load Pipeline
mRatBN7.2310,241,887 - 10,242,320 (+)MAPPERmRatBN7.2
Rnor_6.035,461,812 - 5,462,244NCBIRnor6.0
Rnor_6.034,869,885 - 4,870,317NCBIRnor6.0
Rnor_5.0310,225,082 - 10,225,514UniSTSRnor5.0
Rnor_5.0310,823,722 - 10,824,154UniSTSRnor5.0
RGSC_v3.435,810,728 - 5,811,160UniSTSRGSC3.4
Celera35,039,918 - 5,040,350UniSTS
RH 3.4 Map321.9UniSTS
Cytogenetic Map3p12UniSTS


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 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000061242   ⟹   ENSRNOP00000057954
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl310,241,837 - 10,263,315 (-)Ensembl
Rnor_6.0 Ensembl34,869,795 - 4,872,632 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000118510   ⟹   ENSRNOP00000092828
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl310,241,842 - 10,263,315 (-)Ensembl
RefSeq Acc Id: NM_172068   ⟹   NP_742065
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8330,639,873 - 30,642,710 (-)NCBI
mRatBN7.2310,241,798 - 10,244,635 (-)NCBI
Rnor_6.035,461,722 - 5,464,559 (-)NCBI
Rnor_5.0310,823,627 - 10,826,484 (-)NCBI
RGSC_v3.435,810,638 - 5,813,475 (-)RGD
Celera35,039,828 - 5,042,665 (-)RGD
Sequence:
RefSeq Acc Id: XM_017592099   ⟹   XP_017447588
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8330,639,868 - 30,642,759 (-)NCBI
mRatBN7.2310,241,793 - 10,244,686 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_742065 (Get FASTA)   NCBI Sequence Viewer  
  XP_017447588 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAF19608 (Get FASTA)   NCBI Sequence Viewer  
  EDL93455 (Get FASTA)   NCBI Sequence Viewer  
  EDL93456 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000065447.3
  ENSRNOP00000092828.1
GenBank Protein Q9QXU2 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_742065   ⟸   NM_172068
- UniProtKB: Q9QXU2 (UniProtKB/Swiss-Prot),   A6JTJ1 (UniProtKB/TrEMBL),   A6JTJ2 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000057954   ⟸   ENSRNOT00000061242
RefSeq Acc Id: XP_017447588   ⟸   XM_017592099
- Peptide Label: isoform X1
- UniProtKB: A6JTJ2 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000092828   ⟸   ENSRNOT00000118510

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9QXU2-F1-model_v2 AlphaFold Q9QXU2 1-306 view protein structure
AF-Q7TP91-F1-model_v2 AlphaFold Q7TP91 1-733 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620527 AgrOrtholog
BioCyc Gene G2FUF-50320 BioCyc
Ensembl Genes ENSRNOG00000005247 Ensembl, UniProtKB/Swiss-Prot
  ENSRNOG00000060005 Ensembl, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000071754.3 UniProtKB/Swiss-Prot
  ENSRNOT00000118510.1 UniProtKB/Swiss-Prot
InterPro Surf1/Shy1 UniProtKB/Swiss-Prot
  Surf1/Surf4 UniProtKB/Swiss-Prot
KEGG Report rno:64463 UniProtKB/Swiss-Prot
NCBI Gene 64463 ENTREZGENE
PANTHER PTHR23427 UniProtKB/Swiss-Prot
  SURFEIT LOCUS PROTEIN 1 UniProtKB/Swiss-Prot
Pfam SURF1 UniProtKB/Swiss-Prot
PhenoGen Surf1 PhenoGen
PROSITE SURF1 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000005247 RatGTEx
  ENSRNOG00000060005 RatGTEx
UniProt A0A8I5ZX53_RAT UniProtKB/TrEMBL
  A0A8L2UMZ7_RAT UniProtKB/TrEMBL
  A6JTJ1 ENTREZGENE, UniProtKB/TrEMBL
  A6JTJ2 ENTREZGENE, UniProtKB/TrEMBL
  Q9QXU2 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Surf1  SURF1, cytochrome c oxidase assembly factor  LOC100912008  uncharacterized LOC100912008  Data merged from RGD:6489329 737654 PROVISIONAL
2018-04-19 Surf1  SURF1, cytochrome c oxidase assembly factor  Surf1  surfeit 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-07-05 LOC100912008  uncharacterized LOC100912008      Symbol and Name status set to provisional 70820 PROVISIONAL
2004-12-14 Surf1  surfeit 1    Surfeit 1  Name updated 1299863 APPROVED
2002-08-07 Surf1  Surfeit 1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_disease human homolog is mutated in patients with Leigh syndrome associated with cytochrome c oxidase deficiency 634132