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DALRD3 DALR anticodon binding domain containing 3 [ Homo sapiens (human) ]

Gene ID: 55152, updated on 17-Jun-2024

Summary

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Official Symbol
DALRD3provided by HGNC
Official Full Name
DALR anticodon binding domain containing 3provided by HGNC
Primary source
HGNC:HGNC:25536
See related
Ensembl:ENSG00000178149 MIM:618904; AllianceGenome:HGNC:25536
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
DEE86; EIEE86
Summary
The exact function of this gene is not known. It encodes a protein with a DALR anticodon binding domain similar to that of class Ia aminoacyl tRNA synthetases. This gene is located in a cluster of genes (with a complex sense-anti-sense genome architecture) on chromosome 3, and contains two micro RNA (miRNA) precursors (mir-425 and mir-191) in one of its introns. Preferential expression of this gene (the miRNAs and other genes in the cluster) in testis suggests a role of this gene in spermatogenesis (PMID:19906709). [provided by RefSeq, Feb 2013]
Expression
Ubiquitous expression in testis (RPKM 22.8), prostate (RPKM 21.2) and 25 other tissues See more
Orthologs
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Genomic context

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See DALRD3 in Genome Data Viewer
Location:
3p21.31
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (49015488..49021505, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (49043528..49049545, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (49052921..49058938, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene ariadne RBR E3 ubiquitin protein ligase 2 Neighboring gene uncharacterized LOC124909376 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:49026394-49026957 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:49026958-49027520 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14344 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:49028085-49028646 Neighboring gene uncharacterized LOC124906235 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:49043602-49044590 Neighboring gene prolyl 4-hydroxylase, transmembrane Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14345 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14346 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:49051026-49051863 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:49054789-49055560 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19849 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:49058641-49059410 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14349 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14350 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14351 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14352 Neighboring gene WD repeat domain 6 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:49065964-49066566 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:49066567-49067168 Neighboring gene NADH:ubiquinone oxidoreductase complex assembly factor 3 Neighboring gene microRNA 425 Neighboring gene microRNA 191 Neighboring gene inosine monophosphate dehydrogenase 2 Neighboring gene glutamine rich 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:49097169-49097668 Neighboring gene RNA, 7SL, cytoplasmic 182, pseudogene

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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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Related articles in PubMed

  1. Integrative analysis of the human cis-antisense gene pairs, miRNAs and their transcription regulation patterns. Grinchuk OV, et al. Nucleic Acids Res, 2010 Jan. PMID 19906709, Free PMC Article
  2. DALRD3 encodes a protein mutated in epileptic encephalopathy that targets arginine tRNAs for 3-methylcytosine modification. Lentini JM, et al. Nat Commun, 2020 May 19. PMID 32427860, Free PMC Article
  3. Estrogen mediated-activation of miR-191/425 cluster modulates tumorigenicity of breast cancer cells depending on estrogen receptor status. Di Leva G, et al. PLoS Genet, 2013. PMID 23505378, Free PMC Article
  4. The palmitoyl acyltransferase HIP14 shares a high proportion of interactors with huntingtin: implications for a role in the pathogenesis of Huntington's disease. Butland SL, et al. Hum Mol Genet, 2014 Aug 1. PMID 24705354, Free PMC Article
  5. Impaired plasma membrane localization of ubiquitin ligase complex underlies 3-M syndrome development. Wang P, et al. J Clin Invest, 2019 Jul 25. PMID 31343991, Free PMC Article

See all (19) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. DALRD3 encodes a protein mutated in epileptic encephalopathy that targets arginine tRNAs for 3-methylcytosine modification.
    Title: DALRD3 encodes a protein mutated in epileptic encephalopathy that targets arginine tRNAs for 3-methylcytosine modification.
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

Associated conditions

Description Tests
Developmental and epileptic encephalopathy, 86
MedGen: C5394462 OMIM: 618910 GeneReviews: Not available
not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ10496

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ATP binding IEA
Inferred from Electronic Annotation
more info
  
enables arginine-tRNA ligase activity IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables tRNA binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables tRNA binding IDA
Inferred from Direct Assay
more info
 PubMed 
Process Evidence Code Pubs
involved_in arginyl-tRNA aminoacylation IEA
Inferred from Electronic Annotation
more info
  
involved_in tRNA C3-cytosine methylation IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in tRNA C3-cytosine methylation IMP
Inferred from Mutant Phenotype
more info
 PubMed 

General protein information

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Preferred Names
DALR anticodon-binding domain-containing protein 3

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

  1. NG_033126.1 RefSeqGene

    Range
    7492..10584
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001009996.3 → NP_001009996.1  DALR anticodon-binding domain-containing protein 3 isoform 1

    See identical proteins and their annotated locations for NP_001009996.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    BC047683, DB045082
    Consensus CDS
    CCDS33754.1
    UniProtKB/Swiss-Prot
    Q5D0E6, Q7Z5S7, Q86WY1, Q8N105, Q8NA89, Q9NVU8
    UniProtKB/TrEMBL
    B7Z727
    Related
    ENSP00000344989.4, ENST00000341949.9
    Conserved Domains (1) summary
    smart00836
    Location:403 → 543
    DALR_1; DALR anticodon binding domain

  2. NM_001276405.2 → NP_001263334.1  DALR anticodon-binding domain-containing protein 3 isoform 3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) uses an alternate acceptor splice site at an internal exon in the 3' coding region that causes a frameshift, compared to variant 1. The resulting isoform (3) has a shorter and distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AC137630, BC054493, DB045082
    Consensus CDS
    CCDS63632.1
    UniProtKB/TrEMBL
    B7Z727
    Related
    ENSP00000410623.2, ENST00000441576.6

  3. NM_018114.6 → NP_060584.3  DALR anticodon-binding domain-containing protein 3 isoform 2

    See identical proteins and their annotated locations for NP_060584.3

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) contains an alternate 5' terminal exon and uses an in-frame downstream start codon compared to variant 1. The encoded isoform (2) has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AC137630, AK093204, BC054493, HY047953
    Consensus CDS
    CCDS2783.1
    UniProtKB/TrEMBL
    C9JJG6
    Related
    ENSP00000323265.5, ENST00000313778.9
    Conserved Domains (1) summary
    smart00836
    Location:236 → 376
    DALR_1; DALR anticodon binding domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    49015488..49021505 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017006723.2 → XP_016862212.1  DALR anticodon-binding domain-containing protein 3 isoform X6

    UniProtKB/TrEMBL
    C9JJG6

  2. XM_047448438.1 → XP_047304394.1  DALR anticodon-binding domain-containing protein 3 isoform X5

    UniProtKB/TrEMBL
    C9JJG6
    Related
    ENSP00000403770.1, ENST00000440857.5

  3. XM_006713219.3 → XP_006713282.1  DALR anticodon-binding domain-containing protein 3 isoform X4

    See identical proteins and their annotated locations for XP_006713282.1

    Conserved Domains (1) summary
    smart00836
    Location:236 → 408
    DALR_1; DALR anticodon binding domain

  4. XM_047448437.1 → XP_047304393.1  DALR anticodon-binding domain-containing protein 3 isoform X3

    UniProtKB/Swiss-Prot
    Q5D0E6, Q7Z5S7, Q86WY1, Q8N105, Q8NA89, Q9NVU8
    UniProtKB/TrEMBL
    B7Z727

  5. XM_047448436.1 → XP_047304392.1  DALR anticodon-binding domain-containing protein 3 isoform X1

  6. XM_011533891.3 → XP_011532193.1  DALR anticodon-binding domain-containing protein 3 isoform X2

    Conserved Domains (1) summary
    cl12020
    Location:403 → 464
    Anticodon_Ia_like; Anticodon-binding domain of class Ia aminoacyl tRNA synthetases and similar domains

  7. XM_011533893.3 → XP_011532195.1  DALR anticodon-binding domain-containing protein 3 isoform X7

    UniProtKB/TrEMBL
    C9JA38
    Related
    ENSP00000397385.2, ENST00000420952.2

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    49043528..49049545 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054347061.1 → XP_054203036.1  DALR anticodon-binding domain-containing protein 3 isoform X6

    UniProtKB/TrEMBL
    C9JJG6

  2. XM_054347060.1 → XP_054203035.1  DALR anticodon-binding domain-containing protein 3 isoform X5

    UniProtKB/TrEMBL
    C9JJG6

  3. XM_054347059.1 → XP_054203034.1  DALR anticodon-binding domain-containing protein 3 isoform X4

  4. XM_054347058.1 → XP_054203033.1  DALR anticodon-binding domain-containing protein 3 isoform X3

    UniProtKB/TrEMBL
    B7Z727

  5. XM_054347056.1 → XP_054203031.1  DALR anticodon-binding domain-containing protein 3 isoform X1

  6. XM_054347057.1 → XP_054203032.1  DALR anticodon-binding domain-containing protein 3 isoform X2

  7. XM_054347062.1 → XP_054203037.1  DALR anticodon-binding domain-containing protein 3 isoform X7

    UniProtKB/TrEMBL
    C9JA38
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5D0E6.2 GenPept UniProtKB/Swiss-Prot:Q5D0E6

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