Human Gene KLHDC3 (ENST00000326974.9_4) from GENCODE V47lift37
  Description: kelch domain containing 3, transcript variant 1 (from RefSeq NM_057161.4)
Gencode Transcript: ENST00000326974.9_4
Gencode Gene: ENSG00000124702.19_8
Transcript (Including UTRs)
   Position: hg19 chr6:42,981,987-42,989,032 Size: 7,046 Total Exon Count: 11 Strand: +
Coding Region
   Position: hg19 chr6:42,984,931-42,988,471 Size: 3,541 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:42,981,987-42,989,032)mRNA (may differ from genome)Protein (382 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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HGNCMGIOMIMPubMedReactomeUniProtKB
WikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: KLDC3_HUMAN
DESCRIPTION: RecName: Full=Kelch domain-containing protein 3; AltName: Full=Protein Peas; AltName: Full=Testis intracellular mediator protein;
FUNCTION: May be involved in meiotic recombination process.
SUBCELLULAR LOCATION: Cytoplasm. Note=Also found in meiotic chromatin (By similarity).
SIMILARITY: Contains 5 Kelch 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


-  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: 207.58 RPKM in Testis
Total median expression: 2879.18 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 -80.30159-0.505 Picture PostScript Text
3' UTR -234.80561-0.419 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
IPR015915 - Kelch-typ_b-propeller
IPR011498 - Kelch_2

Pfam Domains:
PF01344 - Kelch motif
PF07646 - Kelch motif
PF13415 - Galactose oxidase, central domain
PF13418 - Galactose oxidase, central domain
PF13854 - Kelch motif
PF13964 - Kelch motif

SCOP Domains:
117281 - Kelch motif
63825 - YWTD domain
63829 - Calcium-dependent phosphotriesterase
69304 - Tricorn protease N-terminal domain
89372 - Fucose-specific lectin
101898 - NHL repeat
50965 - Galactose oxidase, central domain
75011 - 3-carboxy-cis,cis-mucoante lactonizing enzyme
101908 - Putative isomerase YbhE
50969 - YVTN repeat-like/Quinoprotein amine dehydrogenase
50974 - Nitrous oxide reductase, N-terminal domain
50998 - Quinoprotein alcohol dehydrogenase-like
51004 - C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
82171 - DPP6 N-terminal domain-like

ModBase Predicted Comparative 3D Structure on Q9BQ90
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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 orthologGenome BrowserNo ortholog
Gene DetailsGene Details Gene DetailsGene Details 
Gene SorterGene Sorter Gene SorterGene Sorter 
 RGDEnsembl WormBase 
    Protein Sequence 
    Alignment 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003682 chromatin binding
GO:0005515 protein binding

Biological Process:
GO:0007131 reciprocal meiotic recombination
GO:0036498 IRE1-mediated unfolded protein response
GO:0051321 meiotic cell cycle

Cellular Component:
GO:0000790 nuclear chromatin
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol


-  Descriptions from all associated GenBank mRNAs
  LF210871 - JP 2014500723-A/18374: Polycomb-Associated Non-Coding RNAs.
AK308917 - Homo sapiens cDNA, FLJ98958.
BC012987 - Homo sapiens kelch domain containing 3, mRNA (cDNA clone IMAGE:3637377), containing frame-shift errors.
AB055925 - Homo sapiens mRNA for PEAS, complete cds.
AK290384 - Homo sapiens cDNA FLJ76706 complete cds, highly similar to Homo sapiens kelch domain containing 3 (KLHDC3), mRNA.
BC041793 - Homo sapiens kelch domain containing 3, mRNA (cDNA clone MGC:34006 IMAGE:5288540), complete cds.
BC045612 - Homo sapiens kelch domain containing 3, mRNA (cDNA clone MGC:33896 IMAGE:5313255), complete cds.
BC007296 - Homo sapiens kelch domain containing 3, mRNA (cDNA clone MGC:15673 IMAGE:3349731), complete cds.
BC009460 - Homo sapiens kelch domain containing 3, mRNA (cDNA clone MGC:15936 IMAGE:3537223), complete cds.
BC021546 - Homo sapiens kelch domain containing 3, mRNA (cDNA clone MGC:2490 IMAGE:3351635), complete cds.
BC001789 - Homo sapiens kelch domain containing 3, mRNA (cDNA clone MGC:2612 IMAGE:3355470), complete cds.
BC000295 - Homo sapiens kelch domain containing 3, mRNA (cDNA clone MGC:8340 IMAGE:2819570), complete cds.
BC001793 - Homo sapiens kelch domain containing 3, mRNA (cDNA clone MGC:3124 IMAGE:3352397), complete cds.
AK302336 - Homo sapiens cDNA FLJ58305 complete cds, highly similar to Kelch domain-containing protein 3.
AK097719 - Homo sapiens cDNA FLJ40400 fis, clone TESTI2037103.
JD090939 - Sequence 71963 from Patent EP1572962.
JD041005 - Sequence 22029 from Patent EP1572962.
KJ906410 - Synthetic construct Homo sapiens clone ccsbBroadEn_16080 KLHDC3 gene, encodes complete protein.
CU674138 - Synthetic construct Homo sapiens gateway clone IMAGE:100018186 5' read KLHDC3 mRNA.
CU679365 - Synthetic construct Homo sapiens gateway clone IMAGE:100017154 5' read KLHDC3 mRNA.
AB529130 - Synthetic construct DNA, clone: pF1KB5004, Homo sapiens KLHDC3 gene for kelch domain containing 3, without stop codon, in Flexi system.
KJ895301 - Synthetic construct Homo sapiens clone ccsbBroadEn_04695 KLHDC3 gene, encodes complete protein.
HQ448243 - Synthetic construct Homo sapiens clone IMAGE:100071644; CCSB006522_01 kelch domain containing 3 (KLHDC3) gene, encodes complete protein.
KJ903663 - Synthetic construct Homo sapiens clone ccsbBroadEn_13057 KLHDC3 gene, encodes complete protein.
DQ590099 - Homo sapiens piRNA piR-57211, complete sequence.
KJ904965 - Synthetic construct Homo sapiens clone ccsbBroadEn_14359 KLHDC3 gene, encodes complete protein.
CU692278 - Synthetic construct Homo sapiens gateway clone IMAGE:100020857 5' read KLHDC3 mRNA.
BC126937 - Homo sapiens cDNA clone IMAGE:40023412, **** WARNING: chimeric clone ****.
DQ574215 - Homo sapiens piRNA piR-42327, complete sequence.
DQ590131 - Homo sapiens piRNA piR-57243, complete sequence.
JD507483 - Sequence 488507 from Patent EP1572962.
JD171171 - Sequence 152195 from Patent EP1572962.
JD081845 - Sequence 62869 from Patent EP1572962.
JD393057 - Sequence 374081 from Patent EP1572962.
JD550574 - Sequence 531598 from Patent EP1572962.
JD282429 - Sequence 263453 from Patent EP1572962.
JD515930 - Sequence 496954 from Patent EP1572962.
JD516473 - Sequence 497497 from Patent EP1572962.
JD116254 - Sequence 97278 from Patent EP1572962.
JD500864 - Sequence 481888 from Patent EP1572962.
JD424198 - Sequence 405222 from Patent EP1572962.
JD469126 - Sequence 450150 from Patent EP1572962.
JD171999 - Sequence 153023 from Patent EP1572962.
JD278729 - Sequence 259753 from Patent EP1572962.
JD131806 - Sequence 112830 from Patent EP1572962.
JD131807 - Sequence 112831 from Patent EP1572962.
JD163626 - Sequence 144650 from Patent EP1572962.
JD293765 - Sequence 274789 from Patent EP1572962.
JD510345 - Sequence 491369 from Patent EP1572962.
JD086027 - Sequence 67051 from Patent EP1572962.
JD399063 - Sequence 380087 from Patent EP1572962.
JD481894 - Sequence 462918 from Patent EP1572962.
JD402564 - Sequence 383588 from Patent EP1572962.
MA446448 - JP 2018138019-A/18374: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q9BQ90 (Reactome details) participates in the following event(s):

R-HSA-381038 XBP1(S) activates chaperone genes
R-HSA-381070 IRE1alpha activates chaperones
R-HSA-381119 Unfolded Protein Response (UPR)
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: A8K2W9, ENST00000326974.1, ENST00000326974.2, ENST00000326974.3, ENST00000326974.4, ENST00000326974.5, ENST00000326974.6, ENST00000326974.7, ENST00000326974.8, KLDC3_HUMAN, KLHDC3 , NM_057161, PEAS , Q9BQ90, uc317sen.1, uc317sen.2
UCSC ID: ENST00000326974.9_4
RefSeq Accession: NM_057161.4
Protein: Q9BQ90 (aka KLDC3_HUMAN)

-  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.