SCO1 (synthesis of cytochrome C oxidase 1) - Rat Genome Database

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Gene: SCO1 (synthesis of cytochrome C oxidase 1) Sus scrofa
Analyze
Symbol: SCO1
Name: synthesis of cytochrome C oxidase 1
RGD ID: 14118370
Description: ENCODES a protein that exhibits metal ion binding (inferred); INVOLVED IN cyclooxygenase pathway (ortholog); intracellular copper ion homeostasis (ortholog); mitochondrial cytochrome c oxidase assembly (ortholog); ASSOCIATED WITH Acute Liver Failure (ortholog); brain disease (ortholog); congenital myopathy 6 (ortholog); FOUND IN mitochondrial inner membrane (inferred); mitochondrion (inferred); myofibril (inferred)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: LOC100517855
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1255,405,483 - 55,424,118 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11255,406,730 - 55,424,120 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21258,039,030 - 58,056,122 (-)NCBISscrofa10.2Sscrofa10.2susScr3
JBrowse: View Region in Genome Browser (JBrowse)
Model


References
Additional References at PubMed
PMID:14681463   PMID:17145712   PMID:30032202  


Genomics

Comparative Map Data
SCO1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1255,405,483 - 55,424,118 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11255,406,730 - 55,424,120 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21258,039,030 - 58,056,122 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SCO1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381710,672,474 - 10,697,533 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1710,672,474 - 10,698,375 (-)EnsemblGRCh38hg38GRCh38
GRCh371710,575,791 - 10,600,850 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361710,524,379 - 10,541,562 (-)NCBINCBI36Build 36hg18NCBI36
Build 341710,524,379 - 10,541,562NCBI
Celera1710,614,503 - 10,631,739 (-)NCBICelera
Cytogenetic Map17p13.1NCBI
HuRef1710,483,694 - 10,500,930 (-)NCBIHuRef
CHM1_11710,593,847 - 10,611,094 (-)NCBICHM1_1
T2T-CHM13v2.01710,580,025 - 10,605,085 (-)NCBIT2T-CHM13v2.0
Sco1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391166,943,473 - 66,958,270 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1166,943,496 - 66,957,896 (+)EnsemblGRCm39 Ensembl
GRCm381167,052,600 - 67,067,444 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1167,052,670 - 67,067,070 (+)EnsemblGRCm38mm10GRCm38
MGSCv371166,866,172 - 66,880,942 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361166,868,834 - 66,883,637 (+)NCBIMGSCv36mm8
Celera1173,992,022 - 74,006,793 (+)NCBICelera
Cytogenetic Map11B3NCBI
cM Map1140.59NCBI
Sco1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81052,243,664 - 52,256,250 (+)NCBIGRCr8
mRatBN7.21051,744,656 - 51,757,246 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1051,744,656 - 51,757,237 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1056,400,719 - 56,413,172 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01055,890,679 - 55,903,132 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01051,401,050 - 51,413,510 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01053,595,854 - 53,608,437 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1053,595,854 - 53,608,435 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01053,346,887 - 53,359,470 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41053,751,335 - 53,763,923 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1050,927,764 - 50,940,347 (+)NCBICelera
Cytogenetic Map10q24NCBI
LOC102030058
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554676,519,873 - 6,537,753 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554676,519,873 - 6,535,321 (+)NCBIChiLan1.0ChiLan1.0
LOC100988585
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21963,020,386 - 63,070,290 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11767,830,389 - 67,881,266 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01740,923,397 - 40,973,382 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11745,703,642 - 45,720,520 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1745,703,642 - 45,720,520 (+)Ensemblpanpan1.1panPan2
PanPan1.1 Ensembl1745,670,405 - 45,685,641 (+)Ensemblpanpan1.1panPan2
SCO1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1534,957,358 - 34,971,684 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl534,957,785 - 34,971,661 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha535,091,457 - 35,108,332 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0535,059,898 - 35,076,769 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl535,062,467 - 35,076,795 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1535,025,378 - 35,042,230 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0534,982,468 - 34,999,354 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0535,163,599 - 35,180,758 (-)NCBIUU_Cfam_GSD_1.0
LOC101974307
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440560250,049,595 - 50,063,755 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365953,523,779 - 3,538,150 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365953,523,789 - 3,537,933 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SCO1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11610,021,480 - 10,036,920 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605911,307,499 - 11,322,823 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
LOC101701770
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462478613,036,426 - 13,053,210 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462478613,038,384 - 13,053,250 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in SCO1
847 total Variants

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 hemolymphoid system musculoskeletal system nervous system renal system reproductive system respiratory system
High
Medium 7 2 1 5 4 2 3 1
Low 3 2 2 2 19 2
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSSSCT00000019602   ⟹   ENSSSCP00000019083
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1255,405,483 - 55,424,118 (-)Ensembl
RefSeq Acc Id: ENSSSCT00000055018   ⟹   ENSSSCP00000041516
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl1255,406,731 - 55,423,835 (-)Ensembl
RefSeq Acc Id: XM_003131996   ⟹   XP_003132044
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.11255,406,730 - 55,424,120 (-)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: XP_003132044   ⟸   XM_003131996
- UniProtKB: A0A287ACH8 (UniProtKB/TrEMBL),   A0A4X1SMK3 (UniProtKB/TrEMBL),   A0A8D1V0U8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSSCP00000019083   ⟸   ENSSSCT00000019602
RefSeq Acc Id: ENSSSCP00000041516   ⟸   ENSSSCT00000055018


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000018008 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00015024247 UniProtKB/TrEMBL
  ENSSSCG00025076296 UniProtKB/TrEMBL
  ENSSSCG00035050364 UniProtKB/TrEMBL
  ENSSSCG00045030194 UniProtKB/TrEMBL
  ENSSSCG00060029691 UniProtKB/TrEMBL
  ENSSSCG00065014551 UniProtKB/TrEMBL
  ENSSSCG00070002107 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000019602.5 UniProtKB/TrEMBL
  ENSSSCT00000055018 ENTREZGENE
  ENSSSCT00000055018.2 UniProtKB/TrEMBL
  ENSSSCT00015032261.1 UniProtKB/TrEMBL
  ENSSSCT00015032324.1 UniProtKB/TrEMBL
  ENSSSCT00025105627.1 UniProtKB/TrEMBL
  ENSSSCT00035067139.1 UniProtKB/TrEMBL
  ENSSSCT00045051585.1 UniProtKB/TrEMBL
  ENSSSCT00060040123.1 UniProtKB/TrEMBL
  ENSSSCT00065019393.1 UniProtKB/TrEMBL
  ENSSSCT00070003934.1 UniProtKB/TrEMBL
Gene3D-CATH Glutaredoxin UniProtKB/TrEMBL
InterPro SCO1/SenC UniProtKB/TrEMBL
  Thioredoxin-like_sf UniProtKB/TrEMBL
KEGG Report ssc:100517855 UniProtKB/TrEMBL
NCBI Gene LOC100517855 ENTREZGENE
PANTHER PROTEIN SCO1 HOMOLOG, MITOCHONDRIAL UniProtKB/TrEMBL
  PTHR12151 UniProtKB/TrEMBL
Pfam SCO1-SenC UniProtKB/TrEMBL
Superfamily-SCOP SSF52833 UniProtKB/TrEMBL
UniProt A0A287ACH8 ENTREZGENE, UniProtKB/TrEMBL
  A0A4X1SMK3 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1V0U8 ENTREZGENE, UniProtKB/TrEMBL
  F1SS60_PIG UniProtKB/TrEMBL
VGNC ID VGNC:92644 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-03-04 SCO1  synthesis of cytochrome C oxidase 1  LOC100517855  protein SCO1 homolog, mitochondrial  Symbol and/or name change 5135510 APPROVED