Isca1 (iron-sulfur cluster assembly 1) - Rat Genome Database

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Gene: Isca1 (iron-sulfur cluster assembly 1) Rattus norvegicus
Analyze
Symbol: Isca1
Name: iron-sulfur cluster assembly 1
RGD ID: 727792
Description: Predicted to enable 2 iron, 2 sulfur cluster binding activity. Predicted to be involved in iron-sulfur cluster assembly and protein maturation by iron-sulfur cluster transfer. Predicted to be active in mitochondrion. Human ortholog(s) of this gene implicated in multiple mitochondrial dysfunctions syndrome 5. Orthologous to human ISCA1 (iron-sulfur cluster assembly 1); PARTICIPATES IN mitochondrial iron-sulfur cluster protein biogenesis pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3,4-methylenedioxymethamphetamine; ammonium chloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Hbld2; HESB like domain containing 2; HesB protein; HESB-like domain-containing protein 2; hIscA; iron sulfur assembly protein IscA; iron-sulfur assembly protein IscA; iron-sulfur cluster assembly 1 homolog (S. cerevisiae); iron-sulfur cluster assembly 1 homolog, mitochondrial; LOC290985
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: Isca1-ps1  
Candidate Gene For: Kidm52
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2174,905,291 - 4,917,955 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl174,905,287 - 4,917,955 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx174,924,890 - 4,937,662 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0176,466,859 - 6,479,549 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0174,921,330 - 4,934,105 (+)NCBIRnor_WKY
Rnor_6.0175,281,727 - 5,294,386 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl175,281,727 - 5,294,384 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0177,507,069 - 7,519,772 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41710,808,966 - 10,821,681 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11710,808,965 - 10,821,679 (+)NCBI
Celera175,026,823 - 5,039,495 (+)NCBICelera
Cytogenetic Map17p14NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IBA)
mitochondrion  (IBA,IEA)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
# Reference Title Reference Citation
1. hIscA: a protein implicated in the biogenesis of iron-sulfur clusters. Cozar-Castellano I, etal., Biochim Biophys Acta 2004 Aug 2;1700(2):179-88.
2. 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.
3. Iron-sulfur cluster biogenesis in mammalian cells: New insights into the molecular mechanisms of cluster delivery. Maio N and Rouault TA, Biochim Biophys Acta. 2015 Jun;1853(6):1493-512. doi: 10.1016/j.bbamcr.2014.09.009. Epub 2014 Sep 19.
4. NCBI rat LocusLink and RefSeq merged data October 15, 2003 NCBI rat LocusLink and RefSeq merged data October 15, 2003
5. GOA pipeline RGD automated data pipeline
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. [Initial characterization of a new miniature animal model in the rat: studies on anatomy, pituitary hormones and GH mRNA in miniature rat Ishikawa] Serizawa N Nippon Naibunpi Gakkai Zasshi 1993 Jan 20;69(1):33-45.
8. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
9. Knockout of ISCA1 causes early embryonic death in rats. Yang X, etal., Animal Model Exp Med. 2019 Mar 12;2(1):18-24. doi: 10.1002/ame2.12059. eCollection 2019 Mar.
Additional References at PubMed
PMID:15489334   PMID:18614015  


Genomics

Comparative Map Data
Isca1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2174,905,291 - 4,917,955 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl174,905,287 - 4,917,955 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx174,924,890 - 4,937,662 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0176,466,859 - 6,479,549 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0174,921,330 - 4,934,105 (+)NCBIRnor_WKY
Rnor_6.0175,281,727 - 5,294,386 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl175,281,727 - 5,294,384 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0177,507,069 - 7,519,772 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41710,808,966 - 10,821,681 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11710,808,965 - 10,821,679 (+)NCBI
Celera175,026,823 - 5,039,495 (+)NCBICelera
Cytogenetic Map17p14NCBI
ISCA1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38986,264,546 - 86,282,538 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl986,264,546 - 86,283,102 (-)EnsemblGRCh38hg38GRCh38
GRCh37988,879,461 - 88,897,453 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36988,069,281 - 88,087,310 (-)NCBINCBI36Build 36hg18NCBI36
Build 34986,109,015 - 86,127,044NCBI
Celera959,449,572 - 59,467,604 (-)NCBICelera
Cytogenetic Map9q21.33NCBI
HuRef958,702,212 - 58,720,322 (-)NCBIHuRef
CHM1_1989,025,905 - 89,043,932 (-)NCBICHM1_1
T2T-CHM13v2.0998,415,772 - 98,433,767 (-)NCBIT2T-CHM13v2.0
Isca1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391359,903,229 - 59,917,603 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1359,903,223 - 59,917,624 (-)EnsemblGRCm39 Ensembl
GRCm381359,755,415 - 59,769,789 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1359,755,409 - 59,769,810 (-)EnsemblGRCm38mm10GRCm38
MGSCv371359,856,776 - 59,871,150 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361359,765,038 - 59,779,412 (-)NCBIMGSCv36mm8
Celera1360,813,565 - 60,829,332 (-)NCBICelera
Cytogenetic Map13B2NCBI
Isca1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554321,335,481 - 1,349,847 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554321,335,481 - 1,349,852 (+)NCBIChiLan1.0ChiLan1.0
ISCA1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1985,467,139 - 85,485,107 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl985,467,145 - 85,485,107 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0957,410,328 - 57,428,477 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
Isca1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947120,048,452 - 120,064,421 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366801,673,666 - 1,689,635 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049366801,673,666 - 1,689,646 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LOC100513185
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11670,893,220 - 70,893,762 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21676,999,935 - 77,000,396 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ISCA1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11296,900,619 - 96,915,611 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1296,897,849 - 96,915,540 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603885,250,660 - 85,266,902 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Isca1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462480911,099,485 - 11,114,917 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462480911,099,483 - 11,114,917 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Isca1
34 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:324
Count of miRNA genes:180
Interacting mature miRNAs:211
Transcripts:ENSRNOT00000024781
Prediction methods:Microtar, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590316Scort21Serum corticosterone level QTL 214.750.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17122871563Rat
10401807Kidm52Kidney mass QTL 52kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17131701463Rat
70184BpQTLcluster14Blood pressure QTL cluster 143.38arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)17131990913Rat
631207Niddm41Non-insulin dependent diabetes mellitus QTL 41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)17137830672Rat
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17160781592Rat
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17169599340Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17169599340Rat
1641902Colcr7Colorectal carcinoma resistance QTL 73.350.0044intestine integrity trait (VT:0010554)benign colorectal tumor surface area measurement (CMO:0001799)17211514921881669Rat
1300123Bp194Blood pressure QTL 1942.82arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)17211514934551001Rat
631499Stl1Serum triglyceride level QTL 13.6blood triglyceride amount (VT:0002644)blood triglyceride level (CMO:0000118)17327139827389946Rat
2324619Coatc4Coat color QTL 40.001coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)17429913021293263Rat
2324619Coatc4Coat color QTL 40.001coat/hair pigmentation trait (VT:0010463)pigmented dorsal coat/hair area to total dorsal coat/hair area ratio (CMO:0001811)17429913021293263Rat
1354613Kidm14Kidney mass QTL 146.2kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)17429913035837242Rat
1354596Bw32Body weight QTL 324.5body mass (VT:0001259)body weight (CMO:0000012)17429913060781592Rat
1354630Cm34Cardiac mass QTL 348.7heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)17429913069599340Rat
1354638Insul1Insulin level QTL 14.8blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)17429913069599340Rat
1354651Lmblg2Limb length QTL 26tibia length (VT:0004357)tibia length (CMO:0000450)17429913069599340Rat
2293648Bmd31Bone mineral density QTL 314.50.0001femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)17435448727028127Rat
2293664Bmd28Bone mineral density QTL 285.10.0001femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)17435448727028127Rat
2303627Vencon8Ventilatory control QTL 80.001respiration trait (VT:0001943)tidal volume (CMO:0000222)17452803849528038Rat
10054088Scort28Serum corticosterone level QTL 282.040.0102blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17452803849528038Rat

Markers in Region
RH136798  
Rat AssemblyChrPosition (strand)SourceJBrowse
Celera175,037,959 - 5,038,105UniSTS
Celera165,136,495 - 5,136,641UniSTS
Cytogenetic Map17p14UniSTS
Cytogenetic Map16p15UniSTS


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 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000024781   ⟹   ENSRNOP00000024781
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl174,905,287 - 4,917,952 (+)Ensembl
Rnor_6.0 Ensembl175,281,727 - 5,294,384 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000117636   ⟹   ENSRNOP00000078686
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl174,905,323 - 4,917,955 (+)Ensembl
RefSeq Acc Id: NM_181626   ⟹   NP_853657
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2174,905,291 - 4,917,955 (+)NCBI
Rnor_6.0175,281,727 - 5,294,386 (+)NCBI
Rnor_5.0177,507,069 - 7,519,772 (+)NCBI
RGSC_v3.41710,808,966 - 10,821,681 (+)RGD
Celera175,026,823 - 5,039,495 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_853657 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH70929 (Get FASTA)   NCBI Sequence Viewer  
  AAH78677 (Get FASTA)   NCBI Sequence Viewer  
  AAP29778 (Get FASTA)   NCBI Sequence Viewer  
  EDL93876 (Get FASTA)   NCBI Sequence Viewer  
  Q80W96 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_853657   ⟸   NM_181626
- Peptide Label: precursor
- UniProtKB: Q80W96 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000024781   ⟸   ENSRNOT00000024781
RefSeq Acc Id: ENSRNOP00000078686   ⟸   ENSRNOT00000117636
Protein Domains
Fe-S_biosyn

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q80W96-F1-model_v2 AlphaFold Q80W96 1-129 view protein structure

Transcriptome

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

Promoters
RGD ID:13700272
Promoter ID:EPDNEW_R10796
Type:multiple initiation site
Name:Isca1_1
Description:iron-sulfur cluster assembly 1
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_6.0175,281,713 - 5,281,773EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:727792 AgrOrtholog
BioCyc Gene G2FUF-10426 BioCyc
Ensembl Genes ENSRNOG00000018343 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000024781.5 UniProtKB/TrEMBL
  ENSRNOP00000078686 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000024781.7 UniProtKB/TrEMBL
  ENSRNOT00000117636 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.300.12 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7096424 IMAGE-MGC_LOAD
  IMAGE:7133788 IMAGE-MGC_LOAD
InterPro FeS_biogenesis UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FeS_cluster_insertion UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  FeS_cluster_insertion_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HesB-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:290985 UniProtKB/Swiss-Prot
MGC_CLONE MGC:91391 IMAGE-MGC_LOAD
  MGC:93032 IMAGE-MGC_LOAD
NCBI Gene 290985 ENTREZGENE
Pfam Fe-S_biosyn UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Isca1 PhenoGen
PROSITE HESB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF89360 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs TIGR00049 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0A0MXZ0_RAT UniProtKB/TrEMBL
  ISCA1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-08-14 Isca1  iron-sulfur cluster assembly 1  Isca1  iron-sulfur cluster assembly 1 homolog (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-04 Isca1  iron-sulfur cluster assembly 1 homolog (S. cerevisiae)  Hbld2  HESB like domain containing 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Hbld2  HESB like domain containing 2    HesB protein  Name updated 1299863 APPROVED
2004-09-10 Hbld2  HesB protein  LOC290985    Symbol and Name updated 1299863 APPROVED