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    GATD1 glutamine amidotransferase class 1 domain containing 1 [ Homo sapiens (human) ]

    Gene ID: 347862, updated on 10-Dec-2024

    Summary

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    Official Symbol
    GATD1provided by HGNC
    Official Full Name
    glutamine amidotransferase class 1 domain containing 1provided by HGNC
    Primary source
    HGNC:HGNC:26616
    See related
    Ensembl:ENSG00000177225 AllianceGenome:HGNC:26616
    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
    Fy-5; PDDC1; FERRY5
    Summary
    Predicted to enable glyoxalase III activity. Predicted to be involved in methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione. Located in extracellular exosome. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Ubiquitous expression in adrenal (RPKM 7.5), brain (RPKM 7.2) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See GATD1 in Genome Data Viewer
    Location:
    11p15.5
    Exon count:
    8
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (767222..777487, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (818734..828922, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (767222..777487, complement)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105376509 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:742971-743670 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:743671-744369 Neighboring gene hESC enhancers GRCh37_chr11:746448-747096 and GRCh37_chr11:747097-747745 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3025 Neighboring gene transaldolase 1 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr11:762588-763787 Neighboring gene ReSE screen-validated silencer GRCh37_chr11:765339-765752 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3026 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3027 Neighboring gene uncharacterized LOC124900301 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3028 Neighboring gene GATD1 divergent transcript Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:783107-783794 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr11:783795-784482 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 3029 Neighboring gene cell cycle exit and neuronal differentiation 1

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. The Rab5 effector FERRY links early endosomes with mRNA localization. Schuhmacher JS, et al. Mol Cell, 2023 Jun 1. PMID 37267905
    2. Elevation of hsa-miR-7-5p level mediated by CtBP1-p300-AP1 complex targets ATXN1 to trigger NF-κB-dependent inflammation response. Lou LQ, et al. J Mol Med (Berl), 2023 Mar. PMID 36629882
    3. BCAR1 promotes proliferation and cell growth in lung adenocarcinoma via upregulation of POLR2A. Mao CG, et al. Thorac Cancer, 2020 Nov. PMID 33001583, Free PMC Article
    4. Global Interactome Mapping of Mitochondrial Intermembrane Space Proteases Identifies a Novel Function for HTRA2. Botham A, et al. Proteomics, 2019 Dec. PMID 31617661
    5. CLEC16A interacts with retromer and TRIM27, and its loss impairs endosomal trafficking and neurodevelopment. Smits DJ, et al. Hum Genet, 2023 Mar. PMID 36538041, Free PMC Article

    See all (20) citations in PubMed

    GeneRIFs: Gene References Into Functions

    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

    Homology

    Clone Names

    • FLJ34283, FLJ35497, MGC131881, MGC138350

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables glyoxalase III activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in lactate biosynthetic process IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in early endosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in extracellular exosome HDA PubMed 

    General protein information

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    Preferred Names
    glutamine amidotransferase-like class 1 domain-containing protein 1
    Names
    Parkinson disease 7 domain containing 1
    ferry endosomal RAB5 effector complex subunit 5
    glutamine amidotransferase like class 1 domain containing 1
    parkinson disease 7 domain-containing protein 1

    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)

    1. NM_001318818.2 → NP_001305747.1  glutamine amidotransferase-like class 1 domain-containing protein 1 isoform 2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.
      Source sequence(s)
      AK293559, AP006621, BU625376
      UniProtKB/TrEMBL
      B7Z1J9
      Conserved Domains (2) summary
      cd03141
      Location:8 → 166
      GATase1_Hsp31_like; Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Escherichia coli Hsp31 protein
      COG0693
      Location:31 → 154
      ThiJ; Putative intracellular protease/amidase [General function prediction only]

    2. NM_001318820.2 → NP_001305749.1  glutamine amidotransferase-like class 1 domain-containing protein 1 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an alternate exon and differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (3) lacks an alternate internal segment and is shorter at the C-terminus compared to variant 1.
      Source sequence(s)
      AK293559, AP006621, BC143416, BU625376, DC364167
      UniProtKB/TrEMBL
      B7ZKW3
      Conserved Domains (1) summary
      cl00020
      Location:12 → 180
      GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain

    3. NM_001318821.2 → NP_001305750.1  glutamine amidotransferase-like class 1 domain-containing protein 1 isoform 4 precursor

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (4) is shorter at the C-terminus compared to isoform 1.
      Source sequence(s)
      AP006621, BC143418, BU625376, DC364167
      UniProtKB/TrEMBL
      B7ZKW4
      Conserved Domains (2) summary
      cd03141
      Location:12 → 216
      GATase1_Hsp31_like; Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Escherichia coli Hsp31 protein
      COG0693
      Location:21 → 204
      ThiJ; Putative intracellular protease/amidase [General function prediction only]

    4. NM_001318822.2 → NP_001305751.1  glutamine amidotransferase-like class 1 domain-containing protein 1 isoform 5

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) lacks two alternate exons and differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (5) is shorter at the N- and C-termini and lacks an alternate in-frame segment compared to isoform 1.
      Source sequence(s)
      AP006621, BC143415, BU625376, DC364167
      Conserved Domains (1) summary
      cl00020
      Location:14 → 130
      GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain

    5. NM_001318823.2 → NP_001305752.1  glutamine amidotransferase-like class 1 domain-containing protein 1 isoform 6

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) lacks an alternate exon and differs in the 3' UTR and coding sequence compared to variant 1. The resulting isoform (6) is shorter at the N- and C-termini compared to isoform 1.
      Source sequence(s)
      AP006621, BC143422, BU625376, DC364167
      Conserved Domains (2) summary
      cd03141
      Location:8 → 166
      GATase1_Hsp31_like; Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Escherichia coli Hsp31 protein
      COG0693
      Location:31 → 154
      ThiJ; Putative intracellular protease/amidase [General function prediction only]

    6. NM_001318824.2 → NP_001305753.1  glutamine amidotransferase-like class 1 domain-containing protein 1 isoform 7

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (7) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AP006621, BC143420, BU625376, DC364167
      Consensus CDS
      CCDS81530.1
      UniProtKB/Swiss-Prot
      Q8NB37
      Related
      ENSP00000431183.1, ENST00000524550.5
      Conserved Domains (1) summary
      cl00020
      Location:12 → 180
      GAT_1; Type 1 glutamine amidotransferase (GATase1)-like domain

    7. NM_001410955.1 → NP_001397884.1  glutamine amidotransferase-like class 1 domain-containing protein 1 isoform 8 precursor

      Status: VALIDATED

      Source sequence(s)
      AP006621
      Consensus CDS
      CCDS91400.1
      UniProtKB/TrEMBL
      E9PLI5
      Related
      ENSP00000433322.1, ENST00000526325.5

    8. NM_182612.4 → NP_872418.1  glutamine amidotransferase-like class 1 domain-containing protein 1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_872418.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AK293559, AP006621, BU625376, DC364167
      Consensus CDS
      CCDS7713.1
      UniProtKB/Swiss-Prot
      B7ZKW5, Q2NL76, Q6ZQY0, Q8NAE0, Q8NB37
      Related
      ENSP00000321691.8, ENST00000319863.13
      Conserved Domains (2) summary
      cd03141
      Location:12 → 216
      GATase1_Hsp31_like; Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Escherichia coli Hsp31 protein
      COG0693
      Location:21 → 204
      ThiJ; Putative intracellular protease/amidase [General function prediction only]

    RNA

    1. NR_134867.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (8) lacks an alternate exon and uses an alternate splice junction compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AP006621, BC143423, BU625376, DC364167

    2. NR_134868.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (9) uses an alternate splice junction compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AP006621, BC143421, BU625376, DC364167

    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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      767222..777487 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_017017668.2 → XP_016873157.1  glutamine amidotransferase-like class 1 domain-containing protein 1 isoform X3

    2. XM_047426880.1 → XP_047282836.1  glutamine amidotransferase-like class 1 domain-containing protein 1 isoform X2

    3. XM_011520064.3 → XP_011518366.1  glutamine amidotransferase-like class 1 domain-containing protein 1 isoform X1

      Conserved Domains (2) summary
      cd03141
      Location:12 → 184
      GATase1_Hsp31_like; Type 1 glutamine amidotransferase (GATase1)-like domain found in proteins similar to Escherichia coli Hsp31 protein
      COG0693
      Location:13 → 187
      ThiJ; Putative intracellular protease/amidase [General function prediction only]

    4. XM_017017662.2 → XP_016873151.1  glutamine amidotransferase-like class 1 domain-containing protein 1 isoform X4

    RNA

    1. XR_242802.4 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      818734..828922 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054368660.1 → XP_054224635.1  glutamine amidotransferase-like class 1 domain-containing protein 1 isoform X3

    2. XM_054368659.1 → XP_054224634.1  glutamine amidotransferase-like class 1 domain-containing protein 1 isoform X2

    3. XM_054368658.1 → XP_054224633.1  glutamine amidotransferase-like class 1 domain-containing protein 1 isoform X1

    RNA

    1. XR_008488393.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NB37.1 GenPept UniProtKB/Swiss-Prot:Q8NB37

    Gene LinkOut

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