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

    Gene ID: 55152, updated on 2-Nov-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
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (49015488..49021505, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (49043528..49049545, complement)
    RS_2024_09 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 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. The RNA binding protein MEX3A promotes tumor progression of breast cancer by post-transcriptional regulation of IGFBP4. Chen W, et al. Breast Cancer Res Treat, 2023 Oct. PMID 37433992, Free PMC Article

    See all (22) 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_2024_08

    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

      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

    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

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

    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

    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

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

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