Human Gene KLHL20 (uc001gjc.3) Description and Page Index
  Description: Homo sapiens kelch-like family member 20 (KLHL20), mRNA.
RefSeq Summary (NM_014458): The protein encoded by this gene is a member of the kelch family of proteins, which is characterized by a 44-56 amino acid repeat motif. The kelch motif appears in many different polypeptide contexts and contains multiple potential protein-protein contact sites. Members of this family are present both throughout the cell and extracellularly, with diverse activities. [provided by RefSeq, Jul 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR1660809.43618.1, SRR1660803.104669.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000209884.5/ ENSP00000209884.4 RefSeq Select criteria :: based on conservation, expression ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr1:173,684,080-173,755,840 Size: 71,761 Total Exon Count: 12 Strand: +
Coding Region
   Position: hg19 chr1:173,685,183-173,754,385 Size: 69,203 Coding Exon Count: 11 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:173,684,080-173,755,840)mRNA (may differ from genome)Protein (609 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
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Wikipedia

-  Comments and Description Text from UniProtKB
  ID: KLH20_HUMAN
DESCRIPTION: RecName: Full=Kelch-like protein 20; AltName: Full=Kelch-like ECT2-interacting protein; AltName: Full=Kelch-like protein X;
FUNCTION: Substrate-specific adapter of a BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex involved in interferon response. The BCR(KLHL20) E3 ubiquitin ligase complex mediates the ubiquitination of DAPK1, leading to its degradation by the proteasome, thereby acting as a negative regulator of apoptosis. Also acts as a regulator of endothelial migration during angiogenesis by controlling the activation of Rho GTPases.
PATHWAY: Protein modification; protein ubiquitination.
SUBUNIT: Component of the BCR(KLHL20) E3 ubiquitin ligase complex, at least composed of CUL3, KLHL20 and RBX1. Interacts with DAPK1. Interacts with F-actin. Interacts with IFN-gamma (IFNG).
INTERACTION: P29590:PML; NbExp=4; IntAct=EBI-714379, EBI-295890;
SUBCELLULAR LOCATION: Cytoplasm, perinuclear region. Nucleus. Note=Localizes in the perinuclear region in normal conditions. Following IFN-alpha or IFN-gamma treatment, it is relocalized and sequestrated to the PML nuclear bodies, preventing DAPK1 ubiquitination.
SIMILARITY: Contains 1 BACK (BTB/Kelch associated) domain.
SIMILARITY: Contains 1 BTB (POZ) domain.
SIMILARITY: Contains 6 Kelch repeats.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): KLHL20
CDC HuGE Published Literature: KLHL20
Positive Disease Associations: Macular Degeneration
Related Studies:
  1. Macular Degeneration
    , , . [PubMed 0]
  2. Macular Degeneration
    , , . [PubMed 0]
  3. Macular Degeneration
    , , . [PubMed 0]
           more ... click here to view the complete list

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

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 9.23 RPKM in Testis
Total median expression: 260.54 RPKM



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

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -51.90179-0.290 Picture PostScript Text
3' UTR -301.151455-0.207 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
IPR011705 - BACK
IPR000210 - BTB/POZ-like
IPR011333 - BTB/POZ_fold
IPR013069 - BTB_POZ
IPR015916 - Gal_Oxidase_b-propeller
IPR017096 - Kelch-like_gigaxonin
IPR006652 - Kelch_1

Pfam Domains:
PF00651 - BTB/POZ domain
PF01344 - Kelch motif
PF07646 - Kelch motif
PF07707 - BTB And C-terminal Kelch
PF13415 - Galactose oxidase, central domain
PF13418 - Galactose oxidase, central domain
PF13964 - Kelch motif

SCOP Domains:
50960 - TolB, C-terminal domain
63825 - YWTD domain
63829 - Calcium-dependent phosphotriesterase
69304 - Tricorn protease N-terminal domain
101898 - NHL repeat
50965 - Galactose oxidase, central domain
50969 - YVTN repeat-like/Quinoprotein amine dehydrogenase
50993 - Prolyl oligopeptidase, N-terminal domain
54695 - POZ domain

ModBase Predicted Comparative 3D Structure on Q9Y2M5
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 orthologNo ortholog
Gene Details     
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0003779 actin binding
GO:0004842 ubiquitin-protein transferase activity
GO:0005515 protein binding
GO:0019964 interferon-gamma binding

Biological Process:
GO:0006895 Golgi to endosome transport
GO:0007010 cytoskeleton organization
GO:0015031 protein transport
GO:0016567 protein ubiquitination
GO:0035455 response to interferon-alpha
GO:0043066 negative regulation of apoptotic process
GO:0043161 proteasome-mediated ubiquitin-dependent protein catabolic process
GO:0043687 post-translational protein modification
GO:1990390 protein K33-linked ubiquitination

Cellular Component:
GO:0005634 nucleus
GO:0005737 cytoplasm
GO:0005794 Golgi apparatus
GO:0005802 trans-Golgi network
GO:0005829 cytosol
GO:0015629 actin cytoskeleton
GO:0016605 PML body
GO:0030424 axon
GO:0030425 dendrite
GO:0031463 Cul3-RING ubiquitin ligase complex
GO:0042995 cell projection
GO:0048471 perinuclear region of cytoplasm


-  Descriptions from all associated GenBank mRNAs
  AK308048 - Homo sapiens cDNA, FLJ97996.
AK300755 - Homo sapiens cDNA FLJ57439 complete cds, highly similar to Kelch-like protein 20.
AK001430 - Homo sapiens cDNA FLJ10568 fis, clone NT2RP2002986, highly similar to Kelch-like protein 20.
JD499289 - Sequence 480313 from Patent EP1572962.
JD407413 - Sequence 388437 from Patent EP1572962.
AB026190 - Homo sapiens mRNA for Kelch motif containing protein, complete cds.
JD222591 - Sequence 203615 from Patent EP1572962.
JD540793 - Sequence 521817 from Patent EP1572962.
JD471442 - Sequence 452466 from Patent EP1572962.
JD178384 - Sequence 159408 from Patent EP1572962.
BC063418 - Homo sapiens kelch-like 20 (Drosophila), mRNA (cDNA clone MGC:74874 IMAGE:5221643), complete cds.
BC005253 - Homo sapiens kelch-like 20 (Drosophila), mRNA (cDNA clone IMAGE:3951189), complete cds.
KJ902465 - Synthetic construct Homo sapiens clone ccsbBroadEn_11859 KLHL20 gene, encodes complete protein.
AB527537 - Synthetic construct DNA, clone: pF1KB5990, Homo sapiens KLHL20 gene for kelch-like protein 20, without stop codon, in Flexi system.
AJ844466 - Homo sapiens partial mRNA for KLEIP (kelch-like ECT2 interacting protein), (KLHLX gene).
JD558143 - Sequence 539167 from Patent EP1572962.
JD345377 - Sequence 326401 from Patent EP1572962.

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

Protein Q9Y2M5 (Reactome details) participates in the following event(s):

R-HSA-8955241 CAND1 binds cytosolic CRL E3 ubiquitin ligases
R-HSA-983157 Interaction of E3 with substrate and E2-Ub complex
R-HSA-983147 Release of E3 from polyubiquitinated substrate
R-HSA-8955289 COMMDs displace CAND1 from cytosolic CRL E3 ubiquitin ligase complexes
R-HSA-8956040 COP9 signalosome deneddylates cytosolic CRL E3 ubiquitin ligase complexes
R-HSA-983140 Transfer of Ub from E2 to substrate and release of E2
R-HSA-8951664 Neddylation
R-HSA-983168 Antigen processing: Ubiquitination & Proteasome degradation
R-HSA-597592 Post-translational protein modification
R-HSA-983169 Class I MHC mediated antigen processing & presentation
R-HSA-392499 Metabolism of proteins
R-HSA-1280218 Adaptive Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: B3KMA0, KLEIP, KLH20_HUMAN, NM_014458, NP_055273, Q5TZF2, Q5ZF45, Q9H457, Q9Y2M5
UCSC ID: uc001gjc.3
RefSeq Accession: NM_014458
Protein: Q9Y2M5 (aka KLH20_HUMAN)
CCDS: CCDS1310.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_014458.3
exon count: 12CDS single in 3' UTR: no RNA size: 3505
ORF size: 1830CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 3267.00frame shift in genome: no % Coverage: 98.83
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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.