Sdhaf4 (succinate dehydrogenase complex assembly factor 4) - Rat Genome Database

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Gene: Sdhaf4 (succinate dehydrogenase complex assembly factor 4) Rattus norvegicus
Analyze
Symbol: Sdhaf4
Name: succinate dehydrogenase complex assembly factor 4
RGD ID: 1588998
Description: Orthologous to human SDHAF4 (succinate dehydrogenase complex assembly factor 4); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A; tetrachloromethane.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: hypothetical protein LOC685888; LOC685888; succinate dehydrogenase assembly factor 4, mitochondrial
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
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
GRCr8933,904,667 - 33,912,813 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl933,904,667 - 33,912,813 (-)EnsemblGRCr8
mRatBN7.2926,408,332 - 26,416,478 (-)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx934,918,115 - 34,926,261 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0940,036,410 - 40,044,557 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0938,346,158 - 38,354,304 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0930,243,261 - 30,251,478 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl930,243,610 - 30,251,388 (-)Ensemblrn6Rnor6.0
Rnor_5.0929,067,898 - 29,076,116 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4922,713,335 - 22,721,491 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera923,945,793 - 23,953,994 (-)NCBICelera
Cytogenetic Map9q13NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:18614015   PMID:19805818   PMID:24954416   PMID:34800366  


Genomics

Comparative Map Data
Sdhaf4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8933,904,667 - 33,912,813 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl933,904,667 - 33,912,813 (-)EnsemblGRCr8
mRatBN7.2926,408,332 - 26,416,478 (-)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx934,918,115 - 34,926,261 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0940,036,410 - 40,044,557 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0938,346,158 - 38,354,304 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0930,243,261 - 30,251,478 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl930,243,610 - 30,251,388 (-)Ensemblrn6Rnor6.0
Rnor_5.0929,067,898 - 29,076,116 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4922,713,335 - 22,721,491 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera923,945,793 - 23,953,994 (-)NCBICelera
Cytogenetic Map9q13NCBI
SDHAF4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38670,566,930 - 70,598,428 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl670,566,917 - 70,589,569 (+)Ensemblhg38GRCh38
GRCh37671,276,633 - 71,299,272 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36671,333,346 - 71,355,327 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34671,333,345 - 71,355,327NCBI
Celera671,665,041 - 71,687,022 (+)NCBICelera
Cytogenetic Map6q13NCBI
HuRef668,474,783 - 68,496,774 (+)NCBIHuRef
CHM1_1671,442,976 - 71,464,957 (+)NCBICHM1_1
T2T-CHM13v2.0671,747,474 - 71,770,117 (+)NCBIT2T-CHM13v2.0
Sdhaf4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39124,035,020 - 24,044,721 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl124,035,020 - 24,044,737 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38123,995,939 - 24,005,640 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl123,995,939 - 24,005,656 (-)Ensemblmm10GRCm38
MGSCv37124,002,778 - 24,012,479 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36123,950,221 - 23,959,915 (-)NCBIMGSCv36mm8
Celera123,832,137 - 23,841,860 (-)NCBICelera
Cytogenetic Map1A5NCBI
cM Map19.86NCBI
Sdhaf4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554885,628,341 - 5,645,707 (+)Ensembl
ChiLan1.0NW_0049554885,628,297 - 5,644,384 (+)NCBIChiLan1.0ChiLan1.0
SDHAF4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2590,554,858 - 90,576,863 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1688,480,060 - 88,509,848 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0668,402,024 - 68,424,420 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1671,700,165 - 71,722,131 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl671,700,165 - 71,722,125 (+)EnsemblpanPan2panpan1.1
SDHAF4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11233,080,545 - 33,089,944 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1233,069,013 - 33,089,930 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1232,927,894 - 32,948,859 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01233,608,662 - 33,629,628 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1233,608,696 - 33,629,614 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11233,139,123 - 33,160,035 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01233,180,881 - 33,201,819 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01233,293,517 - 33,314,461 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Sdhaf4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494668,294,307 - 68,306,697 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366182,451,675 - 2,466,150 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049366182,451,717 - 2,461,676 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SDHAF4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1174,410,081 - 4,432,885 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl174,410,932 - 4,432,841 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366605810,414,639 - 10,437,421 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Sdhaf4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248199,320,368 - 9,336,572 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046248199,320,343 - 9,336,196 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Sdhaf4
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v14101,353,144 - 101,361,746 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Sdhaf4
55 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:124
Count of miRNA genes:101
Interacting mature miRNAs:112
Transcripts:ENSRNOT00000035033
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
2303170Bp332Blood pressure QTL 3323.730.027arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)9671488884474983Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9534647950346479Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9875049253750492Rat
1300180Bw14Body weight QTL 143.776body mass (VT:0001259)body weight (CMO:0000012)93125043268875676Rat
61450Ciaa3CIA Autoantibody QTL 36.5blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)92956766474567664Rat
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92956766483835942Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)949664545496645Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9621499551214995Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9875049253750492Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9141763315Rat
7207805Bmd88Bone mineral density QTL 884femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)93125043265651574Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9534647950416711Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)949664545496645Rat
1600365Mcs20Mammary carcinoma susceptibility QTL 203mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)92103143049025574Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)949664545496645Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9621499551214995Rat
1598823Memor16Memory QTL 161.9exploratory behavior trait (VT:0010471)difference between duration of physical contact or close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)93145606157460683Rat

Markers in Region
RH133392  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2926,408,462 - 26,408,654 (+)MAPPERmRatBN7.2
Rnor_6.0930,243,404 - 30,243,595NCBIRnor6.0
Rnor_5.0929,068,041 - 29,068,232UniSTSRnor5.0
RGSC_v3.4922,713,478 - 22,713,669UniSTSRGSC3.4
Celera923,945,936 - 23,946,127UniSTS
RH 3.4 Map9245.5UniSTS
Cytogenetic Map9q13UniSTS
RH143909  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2926,414,285 - 26,414,404 (+)MAPPERmRatBN7.2
Rnor_6.0930,249,227 - 30,249,345NCBIRnor6.0
Rnor_5.0929,073,864 - 29,073,982UniSTSRnor5.0
RGSC_v3.4922,719,301 - 22,719,423UniSTSRGSC3.4
Celera923,951,743 - 23,951,861UniSTS
RH 3.4 Map9247.3UniSTS
Cytogenetic Map9q13UniSTS
RH135085  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2926,417,095 - 26,417,314 (+)MAPPERmRatBN7.2
Rnor_6.0930,252,035 - 30,252,253NCBIRnor6.0
Rnor_5.0929,076,672 - 29,076,890UniSTSRnor5.0
RGSC_v3.4922,722,113 - 22,722,331UniSTSRGSC3.4
Celera923,954,551 - 23,954,769UniSTS
RH 3.4 Map9245.5UniSTS
Cytogenetic Map9q13UniSTS


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 89 59 6 353 189 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000035033   ⟹   ENSRNOP00000030072
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl930,243,610 - 30,251,388 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000127123   ⟹   ENSRNOP00000104596
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl933,904,667 - 33,912,813 (-)Ensembl
RefSeq Acc Id: NM_001399405   ⟹   NP_001386334
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8933,904,667 - 33,912,813 (-)NCBI
mRatBN7.2926,408,332 - 26,416,478 (-)NCBI
RefSeq Acc Id: NM_001399406   ⟹   NP_001386335
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8933,904,667 - 33,912,813 (-)NCBI
mRatBN7.2926,408,332 - 26,416,478 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001386334 (Get FASTA)   NCBI Sequence Viewer  
  NP_001386335 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM18618 (Get FASTA)   NCBI Sequence Viewer  
  EDM18620 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000104596
  ENSRNOP00000104596.1
Ensembl Acc Id: ENSRNOP00000030072   ⟸   ENSRNOT00000035033
RefSeq Acc Id: NP_001386334   ⟸   NM_001399405
- Peptide Label: isoform 1
- UniProtKB: A6JJB2 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001386335   ⟸   NM_001399406
- Peptide Label: isoform 2
- UniProtKB: A6JJB3 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000104596   ⟸   ENSRNOT00000127123

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A7Q3-F1-model_v2 AlphaFold D4A7Q3 1-104 view protein structure

Transcriptome

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

Promoters
RGD ID:13696583
Promoter ID:EPDNEW_R7105
Type:multiple initiation site
Name:Sdhaf4_1
Description:succinate dehydrogenase complex assembly factor 4
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_6.0930,251,414 - 30,251,474EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1588998 AgrOrtholog
BioCyc Gene G2FUF-27965 BioCyc
Ensembl Genes ENSRNOG00000028087 Ensembl
  ENSRNOG00000072946 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000127123 ENTREZGENE
  ENSRNOT00000127123.1 UniProtKB/TrEMBL
InterPro SDHF4 UniProtKB/TrEMBL
NCBI Gene 685888 ENTREZGENE
PANTHER SUCCINATE DEHYDROGENASE ASSEMBLY FACTOR 4, MITOCHONDRIAL UniProtKB/TrEMBL
  SUCCINATE DEHYDROGENASE ASSEMBLY FACTOR 4, MITOCHONDRIAL UniProtKB/TrEMBL
Pfam DUF1674 UniProtKB/TrEMBL
PhenoGen Sdhaf4 PhenoGen
RatGTEx ENSRNOG00000028087 RatGTEx
  ENSRNOG00000072946 RatGTEx
UniProt A0ABK0LIQ3_RAT UniProtKB/TrEMBL
  A6JJB2 ENTREZGENE, UniProtKB/TrEMBL
  A6JJB3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-04-03 Sdhaf4  succinate dehydrogenase complex assembly factor 4  LOC685888  hypothetical protein LOC685888  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC685888  hypothetical protein LOC685888  LOC684207  similar to CG7224-PA, isoform A  Data merged from RGD:1592738 1643240 APPROVED
2006-11-20 LOC684207  similar to CG7224-PA, isoform A      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC685888  hypothetical protein LOC685888      Symbol and Name status set to provisional 70820 PROVISIONAL