Hccs (holocytochrome c synthase) - Rat Genome Database

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Gene: Hccs (holocytochrome c synthase) Rattus norvegicus
Analyze
Symbol: Hccs
Name: holocytochrome c synthase
RGD ID: 1563855
Description: Predicted to enable heme binding activity and holocytochrome-c synthase activity. Predicted to be located in membrane. Predicted to be active in cytosol and mitochondrion. Human ortholog(s) of this gene implicated in linear skin defects with multiple congenital anomalies 1 and microphthalmia. Orthologous to human HCCS (holocytochrome c synthase); PARTICIPATES IN porphyrin and chlorophyll metabolic pathway; INTERACTS WITH (+)-schisandrin B; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: holocytochrome c synthetase; holocytochrome c-type synthase; LOC317444; RGD1563855; similar to Hccs protein
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
GRCr8X28,505,370 - 28,514,812 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX28,505,417 - 28,514,812 (+)EnsemblGRCr8
mRatBN7.2X24,932,943 - 24,942,376 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX24,933,002 - 24,942,366 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX25,930,434 - 25,939,829 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X29,351,506 - 29,360,901 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X25,591,735 - 25,601,130 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X26,294,028 - 26,303,461 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX26,294,066 - 26,303,461 (+)Ensemblrn6Rnor6.0
Rnor_5.0X26,698,830 - 26,708,253 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X45,617,395 - 45,626,790 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX25,352,867 - 25,362,262 (+)NCBICelera
Cytogenetic MapXq13NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytosol  (IEA,ISO)
membrane  (IEA,ISO)
mitochondrial inner membrane  (IEA)
mitochondrion  (IBA,IEA,ISO)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Comprehensive gene review and curation RGD comprehensive gene curation
7. Mutations of the mitochondrial holocytochrome c-type synthase in X-linked dominant microphthalmia with linear skin defects syndrome. Wimplinger I, etal., Am J Hum Genet. 2006 Nov;79(5):878-89. Epub 2006 Sep 6.
Additional References at PubMed
PMID:11827457   PMID:14651853   PMID:18614015  


Genomics

Comparative Map Data
Hccs
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X28,505,370 - 28,514,812 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX28,505,417 - 28,514,812 (+)EnsemblGRCr8
mRatBN7.2X24,932,943 - 24,942,376 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX24,933,002 - 24,942,366 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX25,930,434 - 25,939,829 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X29,351,506 - 29,360,901 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X25,591,735 - 25,601,130 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X26,294,028 - 26,303,461 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX26,294,066 - 26,303,461 (+)Ensemblrn6Rnor6.0
Rnor_5.0X26,698,830 - 26,708,253 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X45,617,395 - 45,626,790 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX25,352,867 - 25,362,262 (+)NCBICelera
Cytogenetic MapXq13NCBI
HCCS
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X11,111,332 - 11,123,086 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX11,111,299 - 11,123,086 (+)Ensemblhg38GRCh38
GRCh37X11,129,452 - 11,141,206 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X11,039,373 - 11,051,122 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34X10,889,137 - 10,899,655NCBI
CeleraX15,256,857 - 15,268,657 (+)NCBICelera
Cytogenetic MapXp22.2NCBI
HuRefX8,910,155 - 8,921,955 (+)NCBIHuRef
CHM1_1X11,159,827 - 11,171,630 (+)NCBICHM1_1
T2T-CHM13v2.0X10,693,810 - 10,705,564 (+)NCBIT2T-CHM13v2.0
Hccs
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X168,094,526 - 168,103,361 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX168,033,189 - 168,103,368 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38X169,311,530 - 169,320,374 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX169,250,193 - 169,320,372 (-)Ensemblmm10GRCm38
MGSCv37X165,749,462 - 165,758,275 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36X164,655,640 - 164,664,385 (-)NCBIMGSCv36mm8
CeleraX152,476,573 - 152,485,230 (-)NCBICelera
Cytogenetic MapXF5NCBI
cM MapX78.98NCBI
LOC102006165
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555442,103,815 - 2,117,838 (-)Ensembl
ChiLan1.0NW_0049555442,105,486 - 2,117,830 (-)NCBIChiLan1.0ChiLan1.0
LOC100982890
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X12,913,370 - 12,925,158 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X12,917,035 - 12,928,823 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X3,741,316 - 3,753,115 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X11,032,260 - 11,044,055 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX11,031,638 - 11,044,055 (+)EnsemblpanPan2panpan1.1
HCCS
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X7,686,007 - 7,697,244 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX7,686,035 - 7,699,811 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_TashaX7,642,846 - 7,654,033 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0X7,639,242 - 7,650,429 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 EnsemblX7,639,260 - 7,651,630 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1X7,622,544 - 7,633,731 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X7,658,794 - 7,669,977 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X7,653,282 - 7,664,531 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
LOC101978619
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X1,024,984 - 1,038,534 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049364701,025,017 - 1,038,534 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HCCS
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX7,882,723 - 7,894,481 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1X7,882,609 - 7,894,489 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X8,444,630 - 8,456,468 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HCCS
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X9,569,858 - 9,581,569 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX9,569,884 - 9,582,149 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366605611,281,626 - 11,293,323 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
LOC101700661
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248823,221,041 - 3,233,090 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248823,221,145 - 3,233,040 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
LOC116888784
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1X27,781,824 - 27,790,842 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Hccs
35 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:307
Count of miRNA genes:189
Interacting mature miRNAs:227
Transcripts:ENSRNOT00000037862
Prediction methods:Miranda, Pita, 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 (GRCr8)
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)X2447036044931007Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X400149344939387Rat
2290375Gluco34Glucose level QTL 342.75blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X2447036045082063Rat
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X197044046970440Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X811148653111486Rat

Markers in Region
RH128400  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X24,941,921 - 24,942,106 (+)MAPPERmRatBN7.2
Rnor_6.0X26,303,007 - 26,303,191NCBIRnor6.0
Rnor_5.0X26,707,799 - 26,707,983UniSTSRnor5.0
RGSC_v3.4X45,626,336 - 45,626,520UniSTSRGSC3.4
CeleraX25,361,808 - 25,361,992UniSTS
Cytogenetic MapXq21UniSTS
RH129654  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X24,942,084 - 24,942,270 (+)MAPPERmRatBN7.2
Rnor_6.0X26,303,170 - 26,303,355NCBIRnor6.0
Rnor_5.0X26,707,962 - 26,708,147UniSTSRnor5.0
RGSC_v3.4X45,626,499 - 45,626,684UniSTSRGSC3.4
CeleraX25,361,971 - 25,362,156UniSTS
Cytogenetic MapXq21UniSTS


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: ENSRNOT00000037862   ⟹   ENSRNOP00000034552
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX28,505,417 - 28,514,812 (+)Ensembl
mRatBN7.2 EnsemblX24,933,002 - 24,942,366 (+)Ensembl
Rnor_6.0 EnsemblX26,294,066 - 26,303,461 (+)Ensembl
RefSeq Acc Id: NM_001191732   ⟹   NP_001178661
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X28,505,417 - 28,514,812 (+)NCBI
mRatBN7.2X24,932,981 - 24,942,376 (+)NCBI
Rnor_6.0X26,294,066 - 26,303,461 (+)NCBI
Rnor_5.0X26,698,830 - 26,708,253 (+)NCBI
CeleraX25,352,867 - 25,362,262 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006256834   ⟹   XP_006256896
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X28,505,370 - 28,514,812 (+)NCBI
mRatBN7.2X24,932,944 - 24,942,376 (+)NCBI
Rnor_6.0X26,294,028 - 26,303,461 (+)NCBI
Rnor_5.0X26,698,830 - 26,708,253 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039099825   ⟹   XP_038955753
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X28,505,379 - 28,514,812 (+)NCBI
mRatBN7.2X24,932,943 - 24,942,376 (+)NCBI
RefSeq Acc Id: NP_001178661   ⟸   NM_001191732
- UniProtKB: D3ZL85 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256896   ⟸   XM_006256834
- Peptide Label: isoform X1
- UniProtKB: D3ZL85 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000034552   ⟸   ENSRNOT00000037862
RefSeq Acc Id: XP_038955753   ⟸   XM_039099825
- Peptide Label: isoform X2

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZL85-F1-model_v2 AlphaFold D3ZL85 1-274 view protein structure

Transcriptome

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

Promoters
RGD ID:13701782
Promoter ID:EPDNEW_R12305
Type:initiation region
Name:Hccs_1
Description:holocytochrome c synthase
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_6.0X26,294,083 - 26,294,143EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1563855 AgrOrtholog
BioCyc Gene G2FUF-2679 BioCyc
BioCyc Pathway PWY-8145 [cytochrome c biogenesis (system III type)] BioCyc
BioCyc Pathway Image PWY-8145 BioCyc
Ensembl Genes ENSRNOG00000025910 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000037862 ENTREZGENE
  ENSRNOT00000037862.7 UniProtKB/TrEMBL
InterPro Cyt_C/C1_haem_lyase UniProtKB/TrEMBL
KEGG Report rno:317444 UniProtKB/TrEMBL
NCBI Gene 317444 ENTREZGENE
PANTHER Cyto_heme_lyase UniProtKB/TrEMBL
  HOLOCYTOCHROME C-TYPE SYNTHASE UniProtKB/TrEMBL
Pfam Cyto_heme_lyase UniProtKB/TrEMBL
PhenoGen Hccs PhenoGen
PROSITE CYTO_HEME_LYASE_1 UniProtKB/TrEMBL
  CYTO_HEME_LYASE_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000025910 RatGTEx
UniProt D3ZL85 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2012-01-11 Hccs  holocytochrome c synthase  Hccs  holocytochrome c synthetase  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Hccs  holocytochrome c synthetase   Hccs_predicted  holocytochrome c synthetase (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Hccs_predicted  holocytochrome c synthetase (predicted)  RGD1563855_predicted  similar to Hccs protein (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1563855_predicted  similar to Hccs protein (predicted)  LOC317444  similar to Hccs protein  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC317444  similar to Hccs protein      Symbol and Name status set to provisional 70820 PROVISIONAL