Human Gene CLPB (ENST00000538039.6_11) from GENCODE V47lift37
  Description: caseinolytic mitochondrial matrix peptidase chaperone subunit B, transcript variant 2 (from RefSeq NM_001258392.3)
Gencode Transcript: ENST00000538039.6_11
Gencode Gene: ENSG00000162129.15_20
Transcript (Including UTRs)
   Position: hg19 chr11:71,996,539-72,145,575 Size: 149,037 Total Exon Count: 16 Strand: -
Coding Region
   Position: hg19 chr11:72,004,411-72,145,518 Size: 141,108 Coding Exon Count: 16 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:71,996,539-72,145,575)mRNA (may differ from genome)Protein (677 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: CLPB_HUMAN
DESCRIPTION: RecName: Full=Caseinolytic peptidase B protein homolog; AltName: Full=Suppressor of potassium transport defect 3;
FUNCTION: May function as a regulatory ATPase and be related to secretion/protein trafficking process.
SIMILARITY: Belongs to the clpA/clpB family.
SIMILARITY: Contains 4 ANK repeats.

-  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: CLPB
Diseases sorted by gene-association score: 3-methylglutaconic aciduria, type vii, with cataracts, neurologic involvement and neutropenia* (1650), clpb deficiency* (400), 3-methylglutaconic aciduria (30), neutropenia (18), human monocytic ehrlichiosis (7), tularemia (5)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  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: 144.35 RPKM in Testis
Total median expression: 257.78 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 -11.9057-0.209 Picture PostScript Text
3' UTR -3084.627872-0.392 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
IPR003593 - AAA+_ATPase
IPR002110 - Ankyrin_rpt
IPR020683 - Ankyrin_rpt-contain_dom
IPR013093 - ATPase_AAA-2
IPR001270 - Chaprnin_ClpA/B
IPR019489 - Clp_ATPase_C

Pfam Domains:
PF00004 - ATPase family associated with various cellular activities (AAA)
PF00023 - Ankyrin repeat
PF00158 - Sigma-54 interaction domain
PF06414 - Zeta toxin
PF07724 - AAA domain (Cdc48 subfamily)
PF07728 - AAA domain (dynein-related subfamily)
PF10431 - C-terminal, D2-small domain, of ClpB protein
PF12796 - Ankyrin repeats (3 copies)
PF13606 - Ankyrin repeat
PF13637 - Ankyrin repeats (many copies)
PF13857 - Ankyrin repeats (many copies)

SCOP Domains:
140860 - Pseudo ankyrin repeat-like
52540 - P-loop containing nucleoside triphosphate hydrolases
53795 - PEP carboxykinase-like
48403 - Ankyrin repeat

ModBase Predicted Comparative 3D Structure on Q9H078
FrontTopSide
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 orthologGenome Browser
Gene DetailsGene Details   Gene Details
Gene SorterGene Sorter   Gene Sorter
 RGDEnsembl  SGD
     Protein Sequence
     Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003674 molecular_function
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0016887 ATPase activity

Biological Process:
GO:0034605 cellular response to heat

Cellular Component:
GO:0005575 cellular_component
GO:0005739 mitochondrion


-  Descriptions from all associated GenBank mRNAs
  BC006404 - Homo sapiens ClpB caseinolytic peptidase B homolog (E. coli), mRNA (cDNA clone MGC:13160 IMAGE:4304523), complete cds.
HM005551 - Homo sapiens clone HTL-S-11 testicular secretory protein Li 11 mRNA, complete cds.
AK023214 - Homo sapiens cDNA FLJ13152 fis, clone NT2RP3003385, highly similar to Mus musculus SKD3 mRNA.
AL136909 - Homo sapiens mRNA; cDNA DKFZp434O209 (from clone DKFZp434O209).
AK302069 - Homo sapiens cDNA FLJ53237 complete cds, highly similar to Caseinolytic peptidase B protein.
AK302006 - Homo sapiens cDNA FLJ53235 complete cds, highly similar to Caseinolytic peptidase B protein.
AK302158 - Homo sapiens cDNA FLJ53238 complete cds, highly similar to Caseinolytic peptidase B protein.
EU176435 - Synthetic construct Homo sapiens clone IMAGE:100006511; FLH194218.01X; RZPDo839G0979D ClpB caseinolytic peptidase B homolog (E. coli) (CLPB) gene, encodes complete protein.
KJ894846 - Synthetic construct Homo sapiens clone ccsbBroadEn_04240 CLPB gene, encodes complete protein.
EU176772 - Synthetic construct Homo sapiens clone IMAGE:100011541; FLH194217.01L; RZPDo839D03256D ClpB caseinolytic peptidase B homolog (E. coli) (CLPB) gene, encodes complete protein.
CU675391 - Synthetic construct Homo sapiens gateway clone IMAGE:100017775 5' read CLPB mRNA.
JD277901 - Sequence 258925 from Patent EP1572962.
JD319391 - Sequence 300415 from Patent EP1572962.
JD117157 - Sequence 98181 from Patent EP1572962.
JD441452 - Sequence 422476 from Patent EP1572962.
JD425351 - Sequence 406375 from Patent EP1572962.
JD308315 - Sequence 289339 from Patent EP1572962.
JD308316 - Sequence 289340 from Patent EP1572962.
JD435526 - Sequence 416550 from Patent EP1572962.
JD245796 - Sequence 226820 from Patent EP1572962.
JD364946 - Sequence 345970 from Patent EP1572962.
JD513629 - Sequence 494653 from Patent EP1572962.
JD293414 - Sequence 274438 from Patent EP1572962.
JD523078 - Sequence 504102 from Patent EP1572962.
JD431834 - Sequence 412858 from Patent EP1572962.
JD161644 - Sequence 142668 from Patent EP1572962.
JD080582 - Sequence 61606 from Patent EP1572962.
JD398808 - Sequence 379832 from Patent EP1572962.
JD070575 - Sequence 51599 from Patent EP1572962.
JD447593 - Sequence 428617 from Patent EP1572962.
JD447592 - Sequence 428616 from Patent EP1572962.
JD457243 - Sequence 438267 from Patent EP1572962.
JD388525 - Sequence 369549 from Patent EP1572962.
JD457242 - Sequence 438266 from Patent EP1572962.
JD491985 - Sequence 473009 from Patent EP1572962.
JD281396 - Sequence 262420 from Patent EP1572962.
JD295677 - Sequence 276701 from Patent EP1572962.
JD350212 - Sequence 331236 from Patent EP1572962.
JD168580 - Sequence 149604 from Patent EP1572962.
JD208753 - Sequence 189777 from Patent EP1572962.
JD158959 - Sequence 139983 from Patent EP1572962.
JD213230 - Sequence 194254 from Patent EP1572962.
JD110073 - Sequence 91097 from Patent EP1572962.
JD353036 - Sequence 334060 from Patent EP1572962.
JD106559 - Sequence 87583 from Patent EP1572962.
JD069605 - Sequence 50629 from Patent EP1572962.
JD363824 - Sequence 344848 from Patent EP1572962.
JD082558 - Sequence 63582 from Patent EP1572962.
JD186912 - Sequence 167936 from Patent EP1572962.
JD265446 - Sequence 246470 from Patent EP1572962.
JD186514 - Sequence 167538 from Patent EP1572962.
JD123530 - Sequence 104554 from Patent EP1572962.
JD423438 - Sequence 404462 from Patent EP1572962.
JD196793 - Sequence 177817 from Patent EP1572962.
JD429842 - Sequence 410866 from Patent EP1572962.
JD339626 - Sequence 320650 from Patent EP1572962.
JD147594 - Sequence 128618 from Patent EP1572962.
JD107318 - Sequence 88342 from Patent EP1572962.
JD464296 - Sequence 445320 from Patent EP1572962.
AL834484 - Homo sapiens mRNA; cDNA DKFZp434P1321 (from clone DKFZp434P1321).
JD132033 - Sequence 113057 from Patent EP1572962.
JD061502 - Sequence 42526 from Patent EP1572962.
BC006257 - Homo sapiens ClpB caseinolytic peptidase B homolog (E. coli), mRNA (cDNA clone IMAGE:3946730), complete cds.
JD150219 - Sequence 131243 from Patent EP1572962.
JD376530 - Sequence 357554 from Patent EP1572962.
JD364976 - Sequence 346000 from Patent EP1572962.
KJ903326 - Synthetic construct Homo sapiens clone ccsbBroadEn_12720 CLPB gene, encodes complete protein.
JD160672 - Sequence 141696 from Patent EP1572962.

-  Other Names for This Gene
  Alternate Gene Symbols: B4DXJ7, B4DXP7, B4DXW4, CLPB , CLPB_HUMAN, E7EWN6, ENST00000538039.1, ENST00000538039.2, ENST00000538039.3, ENST00000538039.4, ENST00000538039.5, F8W7P6, NM_001258392, Q8ND11, Q9H078, Q9H8Y0, SKD3, uc324qdb.1, uc324qdb.2
UCSC ID: ENST00000538039.6_11
RefSeq Accession: NM_001258392.3
Protein: Q9H078 (aka CLPB_HUMAN)

-  GeneReviews for This Gene
  GeneReviews article(s) related to gene CLPB:
clpb-def (CLPB Deficiency)

-  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.