DCAF4 DDB1 and CUL4 associated factor 4 [Homo sapiens (human)] - Gene

Summary

Official Symbol: DCAF4provided by HGNC
Official Full Name: DDB1 and CUL4 associated factor 4provided by HGNC
Primary source: HGNC:HGNC:20229
See related: Ensembl:ENSG00000119599 MIM:616372; AllianceGenome:HGNC:20229
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: WDR21; WDR21A
Summary: This gene encodes a WD repeat-containing protein that interacts with the Cul4-Ddb1 E3 ligase macromolecular complex. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2009]
Expression: Ubiquitous expression in thyroid (RPKM 4.7), testis (RPKM 3.5) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 14q24.2

Exon count:: 19

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	14	NC_000014.9 (72926464..72962098)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	14	NC_060938.1 (67132127..67167702)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	14	NC_000014.8 (73393172..73428806)

Chromosome 14 - NC_000014.9 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

our results suggest that rs12587742 is associated with an increased lung cancer risk, possibly by up-regulating mRNA expression and decreasing methylation status of DCAF4.
Title: Functional variants in DCAF4 associated with lung cancer risk in European populations.
Genome-wide association (GWA) meta-analysis and de novo genotyping of 20 022 individuals revealed a novel association (p=6.4x10(-10)) between LTL and rs2535913, which lies within DCAF4
Title: DCAF4, a novel gene associated with leucocyte telomere length.
The minor allele of WDR21A may induce a good response to inhaled corticosteroids possibly through competition with the Gbeta(1) proteins for binding to GRs
Title: Association between WDR21A polymorphisms and airway responsiveness to inhaled corticosteroids in asthmatic patients.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

G38243 (e-PCR)
- UniSTS:13089

G38186 (e-PCR)
- UniSTS:45612

SHGC-146741 (e-PCR)
- UniSTS:175406

sY3084 (e-PCR)
- UniSTS:515126

G38086 (e-PCR)
- UniSTS:72819

G35972 (e-PCR)
- UniSTS:30335

WI-13373 (e-PCR)
- UniSTS:82854

G38285 (e-PCR)
- UniSTS:6070

G38281 (e-PCR)
- UniSTS:67255

G38199 (e-PCR)
- UniSTS:39617

G38183 (e-PCR)
- UniSTS:80580

G38190 (e-PCR)
- UniSTS:57034

G59495 (e-PCR)
- UniSTS:136659

G38165 (e-PCR)
- UniSTS:56050

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in protein ubiquitination	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of Cul4-RING E3 ubiquitin ligase complex	IBA Inferred from Biological aspect of Ancestor more info
part_of Cul4-RING E3 ubiquitin ligase complex	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info

General protein information

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Preferred Names: DDB1- and CUL4-associated factor 4

Names: WD repeat domain 21A; WD repeat-containing protein 21A

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_047140.1 RefSeqGene

Range

5133..38372

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001163508.2 → NP_001156980.1 DDB1- and CUL4-associated factor 4 isoform 4

Status: REVIEWED

Description

Transcript Variant: This variant (4) uses two alternate in-frame splice sites in the coding region, compared to variant 1, resulting in an isoform (4) that is shorter than isoform 1.

Source sequence(s)

AK027745, AK315499, AL442663, BC018979, DC314513

Consensus CDS

CCDS55926.1

UniProtKB/TrEMBL

B2RDD6

Related

ENSP00000452131.1, ENST00000555042.5

Conserved Domains (3) summary

COG2319
Location:310 → 475

WD40; WD40 repeat [General function prediction only]

sd00039
Location:286 → 316

7WD40; WD40 repeat [structural motif]

cl02567
Location:363 → 463

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001163509.2 → NP_001156981.1 DDB1- and CUL4-associated factor 4 isoform 5

Status: REVIEWED

Description

Transcript Variant: This variant (5) uses two alternate splice sites in the coding region and uses an alternate translational start codon, compared to variant 1. The encoded isoform (5) has a distinct N-terminus and is shorter than isoform 1.

Source sequence(s)

AK027745, AK297742, AL442663, BC018979, DC314513

UniProtKB/TrEMBL

B4DN30

Conserved Domains (3) summary

COG2319
Location:265 → 460

WD40; WD40 repeat [General function prediction only]

sd00039
Location:264 → 301

7WD40; WD40 repeat [structural motif]

cl02567
Location:265 → 448

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001352447.2 → NP_001339376.1 DDB1- and CUL4-associated factor 4 isoform 6

Status: REVIEWED

Source sequence(s)

AC007160, AL442663

UniProtKB/TrEMBL

B4DMQ0

Conserved Domains (2) summary

sd00039
Location:71 → 108

7WD40; WD40 repeat [structural motif]

cl25539
Location:124 → 255

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001352448.3 → NP_001339377.1 DDB1- and CUL4-associated factor 4 isoform 7

Status: REVIEWED

Source sequence(s)

AC007160, AL442663

UniProtKB/TrEMBL

B2RDD6

Conserved Domains (2) summary

sd00039
Location:285 → 322

7WD40; WD40 repeat [structural motif]

cl25539
Location:315 → 434

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_001352449.2 → NP_001339378.1 DDB1- and CUL4-associated factor 4 isoform 8

Status: REVIEWED

Description

Transcript Variant: This variant (8) encodes the longest isoform (8).

Source sequence(s)

AC007160, AL442663

UniProtKB/TrEMBL

B2RDD6

Conserved Domains (2) summary

sd00039
Location:286 → 323

7WD40; WD40 repeat [structural motif]

cl25539
Location:287 → 470

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_015604.4 → NP_056419.2 DDB1- and CUL4-associated factor 4 isoform 1

See identical proteins and their annotated locations for NP_056419.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes isoform 1.

Source sequence(s)

AK027745, AK315499, AL442663, BC018979, DC314513

Consensus CDS

CCDS9809.1

UniProtKB/Swiss-Prot

B4DUT6, G3V522, Q86U31, Q8IV10, Q8WV16, Q96K22, Q9Y4P5

UniProtKB/TrEMBL

B2RDD6

Related

ENSP00000351147.2, ENST00000358377.7

Conserved Domains (3) summary

COG2319
Location:301 → 481

WD40; WD40 repeat [General function prediction only]

sd00039
Location:285 → 322

7WD40; WD40 repeat [structural motif]

cl02567
Location:286 → 469

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_181340.3 → NP_851937.1 DDB1- and CUL4-associated factor 4 isoform 2

See identical proteins and their annotated locations for NP_851937.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region, and uses a downstream translational start codon, compared to variant 1. The encoded isoform (2) is shorter at the N-terminus, compared to isoform 1.

Source sequence(s)

AK027745, AL442663, BC018979, BC035901, DC314513

Consensus CDS

CCDS9810.1

UniProtKB/TrEMBL

G3V3D6

Related

ENSP00000377781.2, ENST00000394234.6

Conserved Domains (2) summary

sd00039
Location:185 → 222

7WD40; WD40 repeat [structural motif]

cl25539
Location:186 → 369

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
NM_181341.3 → NP_851938.2 DDB1- and CUL4-associated factor 4 isoform 3

See identical proteins and their annotated locations for NP_851938.2

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate in-frame splice site and lacks two alternate exons in the coding region, compared to variant 1, resulting in an isoform (3) that is shorter than isoform 1.

Source sequence(s)

AK027745, AK300786, AL442663, BC018979, DC314513

Consensus CDS

CCDS41968.2

UniProtKB/TrEMBL

B2RDD6

Related

ENSP00000426178.1, ENST00000509153.5

Conserved Domains (3) summary

COG2319
Location:241 → 421

WD40; WD40 repeat [General function prediction only]

sd00039
Location:225 → 262

7WD40; WD40 repeat [structural motif]

cl02567
Location:278 → 409

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

RNA

NR_147990.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AC007160, AL442663

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000014.9 Reference GRCh38.p14 Primary Assembly

Range

72926464..72962098

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017021205.2 → XP_016876694.1 DDB1- and CUL4-associated factor 4 isoform X5

UniProtKB/TrEMBL

B2RDD6

Conserved Domains (2) summary

sd00039
Location:286 → 323

7WD40; WD40 repeat [structural motif]

cl25539
Location:287 → 470

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
XM_017021206.2 → XP_016876695.1 DDB1- and CUL4-associated factor 4 isoform X5

UniProtKB/TrEMBL

B2RDD6

Conserved Domains (2) summary

sd00039
Location:286 → 323

7WD40; WD40 repeat [structural motif]

cl25539
Location:287 → 470

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
XM_017021213.3 → XP_016876702.1 DDB1- and CUL4-associated factor 4 isoform X6

UniProtKB/TrEMBL

B4DN30

Conserved Domains (3) summary

COG2319
Location:265 → 460

WD40; WD40 repeat [General function prediction only]

sd00039
Location:264 → 301

7WD40; WD40 repeat [structural motif]

cl02567
Location:265 → 448

WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
XM_047431256.1 → XP_047287212.1 DDB1- and CUL4-associated factor 4 isoform X3
XM_047431257.1 → XP_047287213.1 DDB1- and CUL4-associated factor 4 isoform X4
XM_047431254.1 → XP_047287210.1 DDB1- and CUL4-associated factor 4 isoform X1
XM_047431255.1 → XP_047287211.1 DDB1- and CUL4-associated factor 4 isoform X2
XM_047431259.1 → XP_047287215.1 DDB1- and CUL4-associated factor 4 isoform X6
XM_047431258.1 → XP_047287214.1 DDB1- and CUL4-associated factor 4 isoform X6
XM_047431260.1 → XP_047287216.1 DDB1- and CUL4-associated factor 4 isoform X7