DDX55 DEAD-box helicase 55 [Homo sapiens (human)] - Gene

Summary

Official Symbol: DDX55provided by HGNC
Official Full Name: DEAD-box helicase 55provided by HGNC
Primary source: HGNC:HGNC:20085
See related: Ensembl:ENSG00000111364 MIM:620176; AllianceGenome:HGNC:20085
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
Summary: This gene encodes a member of protein family containing a characteristic Asp-Glu-Ala-Asp (DEAD) motif. These proteins are putative RNA helicases, and may be involved in a range of nuclear processes including translational initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Multiple alternatively spliced transcript variants have been found for this gene. Pseudogenes have been identified on chromosomes 1 and 12. [provided by RefSeq, Feb 2016]
Expression: Ubiquitous expression in lymph node (RPKM 4.3), bone marrow (RPKM 4.0) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 12q24.31

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	12	NC_000012.12 (123602099..123620943)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	12	NC_060936.1 (123600963..123619807)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	12	NC_000012.11 (124086646..124105490)

Chromosome 12 - NC_000012.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

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?

The DExD box ATPase DDX55 is recruited to domain IV of the 28S ribosomal RNA by its C-terminal region.
Title: The DExD box ATPase DDX55 is recruited to domain IV of the 28S ribosomal RNA by its C-terminal region.

Submit: New GeneRIF Correction

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

EBI GWAS Catalog

Description
Genome-wide association and longitudinal analyses reveal genetic loci linking pubertal height growth, pubertal timing and childhood adiposity. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
Knockdown of DEAD (Asp-Glu-Ala-Asp) box polypeptide 55 (DDX55) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

GC29S0405 (e-PCR)
- UniSTS:464646

STS-N26791 (e-PCR)
- UniSTS:26396

G38154 (e-PCR)
- UniSTS:53341

G20768 (e-PCR)
- UniSTS:18855

A006F32 (e-PCR)
- UniSTS:18856

WI-12310 (e-PCR)
- UniSTS:82089

RH98764 (e-PCR)
- UniSTS:87754

SHGC-149620 (e-PCR)
- UniSTS:177119

G64577 (e-PCR)
- UniSTS:163836

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent H2AZ histone chaperone activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent H3-H4 histone complex chaperone activity	IEA Inferred from Electronic Annotation more info
enables DNA clamp loader activity	IEA Inferred from Electronic Annotation more info
enables RNA binding	HDA more info	PubMed
enables RNA helicase activity	IEA Inferred from Electronic Annotation more info
enables chromatin extrusion motor activity	IEA Inferred from Electronic Annotation more info
enables cohesin loader activity	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in chromatin looping	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytosol	IDA Inferred from Direct Assay more info
located_in membrane	HDA more info	PubMed
is_active_in nucleolus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleolus	IDA Inferred from Direct Assay more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info

General protein information

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Preferred Names: ATP-dependent RNA helicase DDX55

Names: DEAD (Asp-Glu-Ala-Asp) box polypeptide 55; DEAD box protein 55; epididymis secretory sperm binding protein

NP_065987.1

EC 3.6.4.13

XP_011536910.1

EC 3.6.4.13

XP_016875199.1

EC 3.6.4.13

XP_016875200.1

EC 3.6.4.13

XP_016875201.1

EC 3.6.4.13

XP_016875204.1

EC 3.6.4.13

XP_016875205.1

EC 3.6.4.13

XP_016875210.1

EC 3.6.4.13

XP_047285177.1

EC 3.6.4.13

XP_047285178.1

EC 3.6.4.13

XP_047285179.1

EC 3.6.4.13

XP_047285180.1

EC 3.6.4.13

XP_047285181.1

EC 3.6.4.13

XP_047285182.1

EC 3.6.4.13

XP_047285183.1

EC 3.6.4.13

XP_047285184.1

EC 3.6.4.13

XP_047285185.1

EC 3.6.4.13

XP_054228667.1

EC 3.6.4.13

XP_054228668.1

EC 3.6.4.13

XP_054228669.1

EC 3.6.4.13

XP_054228670.1

EC 3.6.4.13

XP_054228671.1

EC 3.6.4.13

XP_054228672.1

EC 3.6.4.13

XP_054228673.1

EC 3.6.4.13

XP_054228674.1

EC 3.6.4.13

XP_054228675.1

EC 3.6.4.13

XP_054228676.1

EC 3.6.4.13

XP_054228677.1

EC 3.6.4.13

XP_054228678.1

EC 3.6.4.13

XP_054228679.1

EC 3.6.4.13

XP_054228680.1

EC 3.6.4.13

XP_054228681.1

EC 3.6.4.13

XP_054228682.1

EC 3.6.4.13

XP_054228683.1

EC 3.6.4.13

XP_054228684.1

EC 3.6.4.13

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.

mRNA and Protein(s)

NM_020936.3 → NP_065987.1 ATP-dependent RNA helicase DDX55

See identical proteins and their annotated locations for NP_065987.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the protein.

Source sequence(s)

AA403154, AB046815, AC055713, BC030020, BU619784

Consensus CDS

CCDS9251.1

UniProtKB/Swiss-Prot

Q658L6, Q8IYH0, Q8NHQ9, Q9HCH7

UniProtKB/TrEMBL

A0A384N652

Related

ENSP00000238146.3, ENST00000238146.9

Conserved Domains (3) summary

cd18787
Location:242 → 372

SF2_C_DEAD; C-terminal helicase domain of the DEAD box helicases

cd17960
Location:20 → 224

DEADc_DDX55; DEAD-box helicase domain of DEAD box protein 55

pfam13959
Location:405 → 462

DUF4217; Domain of unknown function (DUF4217)

RNA

NR_135104.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate internal splice site compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AA403154, AB046815, AC117503, AK301043, BU619784, DA806426
NR_135105.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate internal splice site compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AC055713, AC117503

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_000012.12 Reference GRCh38.p14 Primary Assembly

Range

123602099..123620943

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047429221.1 → XP_047285177.1 ATP-dependent RNA helicase DDX55 isoform X3
XM_047429222.1 → XP_047285178.1 ATP-dependent RNA helicase DDX55 isoform X4
XM_017019711.2 → XP_016875200.1 ATP-dependent RNA helicase DDX55 isoform X2

UniProtKB/TrEMBL

A0A384N652
XM_017019710.2 → XP_016875199.1 ATP-dependent RNA helicase DDX55 isoform X1

UniProtKB/TrEMBL

A0A384N652
XM_017019715.2 → XP_016875204.1 ATP-dependent RNA helicase DDX55 isoform X5

UniProtKB/TrEMBL

F5H5U2
XM_017019716.2 → XP_016875205.1 ATP-dependent RNA helicase DDX55 isoform X6

UniProtKB/TrEMBL

F5H5U2
XM_047429227.1 → XP_047285183.1 ATP-dependent RNA helicase DDX55 isoform X11
XM_047429224.1 → XP_047285180.1 ATP-dependent RNA helicase DDX55 isoform X8
XM_011538608.4 → XP_011536910.1 ATP-dependent RNA helicase DDX55 isoform X14

UniProtKB/TrEMBL

Q8TEC9

Conserved Domains (3) summary

smart00487
Location:24 → 228

DEXDc; DEAD-like helicases superfamily

cd00268
Location:9 → 224

DEADc; DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif ...

pfam00271
Location:252 → 366

Helicase_C; Helicase conserved C-terminal domain
XM_017019721.2 → XP_016875210.1 ATP-dependent RNA helicase DDX55 isoform X15

UniProtKB/TrEMBL

Q8TEC9
XM_047429229.1 → XP_047285185.1 ATP-dependent RNA helicase DDX55 isoform X13
XM_047429225.1 → XP_047285181.1 ATP-dependent RNA helicase DDX55 isoform X9
XM_047429226.1 → XP_047285182.1 ATP-dependent RNA helicase DDX55 isoform X10
XM_047429228.1 → XP_047285184.1 ATP-dependent RNA helicase DDX55 isoform X12
XM_017019712.2 → XP_016875201.1 ATP-dependent RNA helicase DDX55 isoform X3

UniProtKB/TrEMBL

A0A384N652
XM_047429223.1 → XP_047285179.1 ATP-dependent RNA helicase DDX55 isoform X7