Human Gene IDH3B (ENST00000380843.9_10) from GENCODE V47lift37
  Description: isocitrate dehydrogenase (NAD(+)) 3 non-catalytic subunit beta, transcript variant 6 (from RefSeq NR_136344.2)
Gencode Transcript: ENST00000380843.9_10
Gencode Gene: ENSG00000101365.22_14
Transcript (Including UTRs)
   Position: hg19 chr20:2,639,041-2,644,862 Size: 5,822 Total Exon Count: 12 Strand: -
Coding Region
   Position: hg19 chr20:2,639,397-2,644,834 Size: 5,438 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesGeneReviewsModel Information
Methods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr20:2,639,041-2,644,862)mRNA (may differ from genome)Protein (385 aa)
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UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: IDH3B_HUMAN
DESCRIPTION: RecName: Full=Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial; EC=1.1.1.41; AltName: Full=Isocitric dehydrogenase subunit beta; AltName: Full=NAD(+)-specific ICDH subunit beta; Flags: Precursor;
CATALYTIC ACTIVITY: Isocitrate + NAD(+) = 2-oxoglutarate + CO(2) + NADH.
COFACTOR: Binds 1 magnesium or manganese ion per subunit (By similarity).
SUBUNIT: Heterooligomer of subunits alpha, beta, and gamma in the apparent ratio of 2:1:1 (By similarity).
SUBCELLULAR LOCATION: Mitochondrion.
DISEASE: Defects in IDH3B are the cause of retinitis pigmentosa type 46 (RP46) [MIM:612572]. RP is a retinal dystrophy belonging to the group of pigmentary retinopathies. RP is characterized by retinal pigment deposits visible on fundus examination and primary loss of rod photoreceptor cells followed by secondary loss of cone photoreceptors. Patients typically have night vision blindness and loss of midperipheral visual field. As their condition progresses, they lose their far peripheral visual field and eventually central vision as well.
SIMILARITY: Belongs to the isocitrate and isopropylmalate dehydrogenases family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: IDH3B
Diseases sorted by gene-association score: retinitis pigmentosa 46* (1229), idh3b-related retinitis pigmentosa* (100), retinitis pigmentosa* (47), retinitis pigmentosa 28 (10)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 55.61 RPKM in Brain - Cerebellum
Total median expression: 1804.77 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -7.5028-0.268 Picture PostScript Text
3' UTR -115.10356-0.323 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR019818 - IsoCit/isopropylmalate_DH_CS
IPR001804 - Isocitrate/isopropylmalate_DH
IPR004434 - Isocitrate_DH_NAD
IPR024084 - IsoPropMal-DH-like_dom

Pfam Domains:
PF00180 - Isocitrate/isopropylmalate dehydrogenase

SCOP Domains:
53659 - Isocitrate/Isopropylmalate dehydrogenase-like

ModBase Predicted Comparative 3D Structure on O43837
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGDEnsembl   
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000287 magnesium ion binding
GO:0004449 isocitrate dehydrogenase (NAD+) activity
GO:0009055 electron carrier activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0051287 NAD binding

Biological Process:
GO:0006099 tricarboxylic acid cycle
GO:0006102 isocitrate metabolic process
GO:0022900 electron transport chain
GO:0055114 oxidation-reduction process

Cellular Component:
GO:0005634 nucleus
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix


-  Descriptions from all associated GenBank mRNAs
  LF205900 - JP 2014500723-A/13403: Polycomb-Associated Non-Coding RNAs.
LF205901 - JP 2014500723-A/13404: Polycomb-Associated Non-Coding RNAs.
AL050094 - Homo sapiens mRNA; cDNA DKFZp586P0718 (from clone DKFZp586P0718); partial cds.
BC019037 - Homo sapiens isocitrate dehydrogenase 3 (NAD+) beta, mRNA (cDNA clone IMAGE:4591114).
AF023265 - Homo sapiens NAD+-specific isocitrate dehydrogenase beta subunit isoform A mRNA, nuclear gene encoding mitochondrial product, complete cds.
AF023266 - Homo sapiens NAD+-specific isocitrate dehydrogenase beta subunit isoform B mRNA, nuclear gene encoding mitochondrial product, complete cds.
U49283 - Human NAD+-specific isocitrate dehydrogenase beta subunit precursor, mRNA, nuclear gene encoding mitochondrial protein, complete cds.
BC001960 - Homo sapiens isocitrate dehydrogenase 3 (NAD+) beta, mRNA (cDNA clone MGC:903 IMAGE:3536921), complete cds.
BX647393 - Homo sapiens mRNA; cDNA DKFZp686K18144 (from clone DKFZp686K18144).
AK001905 - Homo sapiens cDNA FLJ11043 fis, clone PLACE1004437, highly similar to Human NAD+-specific isocitrate dehydrogenase beta subunit precursor, mRNA.
LF349511 - JP 2014500723-A/157014: Polycomb-Associated Non-Coding RNAs.
JD115758 - Sequence 96782 from Patent EP1572962.
JD145363 - Sequence 126387 from Patent EP1572962.
JD540573 - Sequence 521597 from Patent EP1572962.
JD163030 - Sequence 144054 from Patent EP1572962.
JD055951 - Sequence 36975 from Patent EP1572962.
JD415853 - Sequence 396877 from Patent EP1572962.
LF349512 - JP 2014500723-A/157015: Polycomb-Associated Non-Coding RNAs.
JD051538 - Sequence 32562 from Patent EP1572962.
JD097834 - Sequence 78858 from Patent EP1572962.
DQ892561 - Synthetic construct clone IMAGE:100005191; FLH187527.01X; RZPDo839A05150D isocitrate dehydrogenase 3 (NAD+) beta (IDH3B) gene, encodes complete protein.
AK315641 - Homo sapiens cDNA, FLJ96729, Homo sapiens isocitrate dehydrogenase 3 (NAD+) beta (IDH3B),nuclear gene encoding mitochondrial protein, transcript variant 1,mRNA.
KJ891425 - Synthetic construct Homo sapiens clone ccsbBroadEn_00819 IDH3B gene, encodes complete protein.
KR709841 - Synthetic construct Homo sapiens clone CCSBHm_00006474 IDH3B (IDH3B) mRNA, encodes complete protein.
DQ895776 - Synthetic construct Homo sapiens clone IMAGE:100010236; FLH187523.01L; RZPDo839A05149D isocitrate dehydrogenase 3 (NAD+) beta (IDH3B) gene, encodes complete protein.
DQ895816 - Synthetic construct Homo sapiens clone IMAGE:100010276; FLH263711.01L; RZPDo839E09149D isocitrate dehydrogenase 3 (NAD+) beta (IDH3B) gene, encodes complete protein.
EU831924 - Synthetic construct Homo sapiens clone HAIB:100066953; DKFZo008C0123 isocitrate dehydrogenase 3 (NAD+) beta protein (IDH3B) gene, encodes complete protein.
EU832019 - Synthetic construct Homo sapiens clone HAIB:100067048; DKFZo004C0124 isocitrate dehydrogenase 3 (NAD+) beta protein (IDH3B) gene, encodes complete protein.
LF349513 - JP 2014500723-A/157016: Polycomb-Associated Non-Coding RNAs.
AK309488 - Homo sapiens cDNA, FLJ99529.
CU674954 - Synthetic construct Homo sapiens gateway clone IMAGE:100017146 5' read IDH3B mRNA.
LF349515 - JP 2014500723-A/157018: Polycomb-Associated Non-Coding RNAs.
AK300485 - Homo sapiens cDNA FLJ57795 complete cds, highly similar to Isocitrate dehydrogenase [NAD] subunit beta, mitochondrial precursor (EC 1.1.1.41).
LF349516 - JP 2014500723-A/157019: Polycomb-Associated Non-Coding RNAs.
JD418884 - Sequence 399908 from Patent EP1572962.
JD085296 - Sequence 66320 from Patent EP1572962.
JD221673 - Sequence 202697 from Patent EP1572962.
JD094610 - Sequence 75634 from Patent EP1572962.
LF349517 - JP 2014500723-A/157020: Polycomb-Associated Non-Coding RNAs.
JD152082 - Sequence 133106 from Patent EP1572962.
JD243109 - Sequence 224133 from Patent EP1572962.
JD206067 - Sequence 187091 from Patent EP1572962.
JD231181 - Sequence 212205 from Patent EP1572962.
LF349518 - JP 2014500723-A/157021: Polycomb-Associated Non-Coding RNAs.
JD346917 - Sequence 327941 from Patent EP1572962.
JD385258 - Sequence 366282 from Patent EP1572962.
LF349519 - JP 2014500723-A/157022: Polycomb-Associated Non-Coding RNAs.
JD267875 - Sequence 248899 from Patent EP1572962.
JD406181 - Sequence 387205 from Patent EP1572962.
MA585088 - JP 2018138019-A/157014: Polycomb-Associated Non-Coding RNAs.
MA585089 - JP 2018138019-A/157015: Polycomb-Associated Non-Coding RNAs.
MA585090 - JP 2018138019-A/157016: Polycomb-Associated Non-Coding RNAs.
MA585092 - JP 2018138019-A/157018: Polycomb-Associated Non-Coding RNAs.
MA585093 - JP 2018138019-A/157019: Polycomb-Associated Non-Coding RNAs.
MA585094 - JP 2018138019-A/157020: Polycomb-Associated Non-Coding RNAs.
MA585095 - JP 2018138019-A/157021: Polycomb-Associated Non-Coding RNAs.
MA585096 - JP 2018138019-A/157022: Polycomb-Associated Non-Coding RNAs.
MA441477 - JP 2018138019-A/13403: Polycomb-Associated Non-Coding RNAs.
MA441478 - JP 2018138019-A/13404: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  BioCyc Knowledge Library
PWY66-398 - TCA cycle
PWY66-407 - superpathway of conversion of glucose to acetyl CoA and entry into the TCA cycle

Reactome (by CSHL, EBI, and GO)

Protein O43837 (Reactome details) participates in the following event(s):

R-HSA-70967 isocitrate + NAD+ => alpha-ketoglutarate + CO2 + NADH + H+ [IDH3]
R-HSA-71403 Citric acid cycle (TCA cycle)
R-HSA-71406 Pyruvate metabolism and Citric Acid (TCA) cycle
R-HSA-1428517 The citric acid (TCA) cycle and respiratory electron transport
R-HSA-1430728 Metabolism

-  Other Names for This Gene
  Alternate Gene Symbols: B2RDR1, D3DVX2, D3DVX3, ENST00000380843.1, ENST00000380843.2, ENST00000380843.3, ENST00000380843.4, ENST00000380843.5, ENST00000380843.6, ENST00000380843.7, ENST00000380843.8, IDH3B_HUMAN, NR_136344, O43837, O95106, Q5JXS8, Q9NQ06, Q9NQ07, Q9NUZ0, Q9UEX0, Q9UG99, uc318pwp.1, uc318pwp.2
UCSC ID: ENST00000380843.9_10
RefSeq Accession: NM_006899.5
Protein: O43837 (aka IDH3B_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene IDH3B:
rp-overview (Nonsyndromic Retinitis Pigmentosa Overview)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.