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    SLC66A2 solute carrier family 66 member 2 [ Homo sapiens (human) ]

    Gene ID: 80148, updated on 27-Nov-2024

    Summary

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    Official Symbol
    SLC66A2provided by HGNC
    Official Full Name
    solute carrier family 66 member 2provided by HGNC
    Primary source
    HGNC:HGNC:26188
    See related
    Ensembl:ENSG00000122490 AllianceGenome:HGNC:26188
    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
    PQLC1
    Summary
    Predicted to be involved in phospholipid translocation and retrograde transport, endosome to Golgi. Predicted to be located in cytosol and membrane. Predicted to be active in endosome and trans-Golgi network. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Ubiquitous expression in fat (RPKM 15.1), testis (RPKM 10.4) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See SLC66A2 in Genome Data Viewer
    Location:
    18q23
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (79902420..79951653, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (80178398..80227221, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (77662420..77711653, complement)

    Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene CTDP1 divergent transcript Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:77438928-77439435 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:77439436-77439944 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77441560-77442068 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77442069-77442575 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77457803-77458304 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77458305-77458804 Neighboring gene ReSE screen-validated silencer GRCh37_chr18:77471187-77471379 Neighboring gene CTD phosphatase subunit 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_50709 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77557221-77557817 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77576519-77577020 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77577021-77577520 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13545 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr18:77585975-77587174 Neighboring gene potassium voltage-gated channel modifier subfamily G member 2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77601626-77602126 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9578 Neighboring gene Sharpr-MPRA regulatory region 1017 Neighboring gene Sharpr-MPRA regulatory region 1467 Neighboring gene Sharpr-MPRA regulatory region 11655 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr18:77664167-77664802 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr18:77672372-77673288 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9579 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9580 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9581 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9582 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9583 Neighboring gene uncharacterized LOC124904336 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr18:77717730-77718328 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr18:77718329-77718926 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr18:77720052-77720736 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13547 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9584 Neighboring gene heat shock factor binding protein 1 like 1 Neighboring gene thioredoxin like 4A

    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. A germline-specific class of small RNAs binds mammalian Piwi proteins. Girard A, et al. Nature, 2006 Jul 13. PMID 16751776
    2. RNA-binding activity of TRIM25 is mediated by its PRY/SPRY domain and is required for ubiquitination. Choudhury NR, et al. BMC Biol, 2017 Nov 8. PMID 29117863, Free PMC Article
    3. Toward an understanding of the protein interaction network of the human liver. Wang J, et al. Mol Syst Biol, 2011 Oct 11. PMID 21988832, Free PMC Article
    4. A reference map of the human binary protein interactome. Luck K, et al. Nature, 2020 Apr. PMID 32296183, Free PMC Article
    5. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039

    See all (8) 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

    • FLJ22378

    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 phospholipid translocation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in retrograde transport, endosome to Golgi IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in trans-Golgi network IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    solute carrier family 66 member 2
    Names
    PQ loop repeat containing 1
    PQ-loop repeat-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_001146343.2 → NP_001139815.1  solute carrier family 66 member 2 isoform 2

      See identical proteins and their annotated locations for NP_001139815.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks two exons in the coding region, which results in a frameshift and an early stop codon compared to variant 1. The encoded isoform (2) is shorter compared to isoform 1.
      Source sequence(s)
      AC114341, AK026031, AK301881
      Consensus CDS
      CCDS54192.1
      UniProtKB/TrEMBL
      B7Z8S3
      Related
      ENSP00000465546.1, ENST00000590381.5
      Conserved Domains (1) summary
      pfam04193
      Location:17 → 77
      PQ-loop; PQ loop repeat

    2. NM_001146345.2 → NP_001139817.1  solute carrier family 66 member 2 isoform 3

      See identical proteins and their annotated locations for NP_001139817.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an in-frame exon in the coding region, compared to variant 1. The encoded isoform (3) is shorter compared to isoform 1.
      Source sequence(s)
      AC114341, AK026031, DB475520
      Consensus CDS
      CCDS54193.1
      UniProtKB/Swiss-Prot
      Q8N2U9
      Related
      ENSP00000350188.3, ENST00000357575.8
      Conserved Domains (1) summary
      pfam04193
      Location:152 → 212
      PQ-loop; PQ loop repeat

    3. NM_025078.5 → NP_079354.2  solute carrier family 66 member 2 isoform 1

      See identical proteins and their annotated locations for NP_079354.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).
      Source sequence(s)
      AC114341, AK026031, BC030140, DB475520
      Consensus CDS
      CCDS12020.1
      UniProtKB/Swiss-Prot
      B7Z7D9, G5E989, Q8N2U9, Q9H6D0
      Related
      ENSP00000380880.2, ENST00000397778.7
      Conserved Domains (1) summary
      pfam04193
      Location:170 → 230
      PQ-loop; PQ loop repeat

    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_000018.10 Reference GRCh38.p14 Primary Assembly

      Range
      79902420..79951653 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047437837.1 → XP_047293793.1  solute carrier family 66 member 2 isoform X15

    2. XM_047437831.1 → XP_047293787.1  solute carrier family 66 member 2 isoform X4

    3. XM_047437835.1 → XP_047293791.1  solute carrier family 66 member 2 isoform X13

    4. XM_047437830.1 → XP_047293786.1  solute carrier family 66 member 2 isoform X3

      UniProtKB/Swiss-Prot
      B7Z7D9, G5E989, Q8N2U9, Q9H6D0

    5. XM_047437828.1 → XP_047293784.1  solute carrier family 66 member 2 isoform X1

    6. XM_047437834.1 → XP_047293790.1  solute carrier family 66 member 2 isoform X11

    7. XM_047437829.1 → XP_047293785.1  solute carrier family 66 member 2 isoform X2

    8. XM_017026003.2 → XP_016881492.1  solute carrier family 66 member 2 isoform X9

      Conserved Domains (1) summary
      pfam04193
      Location:17 → 68
      PQ-loop; PQ loop repeat

    9. XM_024451267.1 → XP_024307035.1  solute carrier family 66 member 2 isoform X8

      UniProtKB/TrEMBL
      B3KW14
      Conserved Domains (1) summary
      pfam04193
      Location:87 → 147
      PQ-loop; PQ loop repeat

    10. XM_011526188.1 → XP_011524490.1  solute carrier family 66 member 2 isoform X12

      See identical proteins and their annotated locations for XP_011524490.1

      Conserved Domains (1) summary
      pfam04193
      Location:52 → 112
      PQ-loop; PQ loop repeat

    11. XM_017026001.3 → XP_016881490.1  solute carrier family 66 member 2 isoform X7

      Conserved Domains (1) summary
      pfam04193
      Location:89 → 149
      PQ-loop; PQ loop repeat

    12. XM_047437832.1 → XP_047293788.1  solute carrier family 66 member 2 isoform X5

    13. XM_017026000.2 → XP_016881489.1  solute carrier family 66 member 2 isoform X6

      Conserved Domains (1) summary
      pfam04193
      Location:17 → 68
      PQ-loop; PQ loop repeat

    14. XM_047437836.1 → XP_047293792.1  solute carrier family 66 member 2 isoform X14

      UniProtKB/TrEMBL
      K7ERV4
      Related
      ENSP00000468427.1, ENST00000593030.6

    15. XM_047437833.1 → XP_047293789.1  solute carrier family 66 member 2 isoform X10

    RNA

    1. XR_007066224.1 RNA Sequence

    2. XR_007066225.1 RNA Sequence

    3. XR_007066226.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060942.1 Alternate T2T-CHM13v2.0

      Range
      80178398..80227221 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054319162.1 → XP_054175137.1  solute carrier family 66 member 2 isoform X15

    2. XM_054319152.1 → XP_054175127.1  solute carrier family 66 member 2 isoform X4

    3. XM_054319160.1 → XP_054175135.1  solute carrier family 66 member 2 isoform X13

    4. XM_054319151.1 → XP_054175126.1  solute carrier family 66 member 2 isoform X3

      UniProtKB/Swiss-Prot
      B7Z7D9, G5E989, Q8N2U9, Q9H6D0

    5. XM_054319149.1 → XP_054175124.1  solute carrier family 66 member 2 isoform X1

    6. XM_054319158.1 → XP_054175133.1  solute carrier family 66 member 2 isoform X11

    7. XM_054319150.1 → XP_054175125.1  solute carrier family 66 member 2 isoform X2

    8. XM_054319156.1 → XP_054175131.1  solute carrier family 66 member 2 isoform X9

    9. XM_054319155.1 → XP_054175130.1  solute carrier family 66 member 2 isoform X8

      UniProtKB/TrEMBL
      B3KW14

    10. XM_054319159.1 → XP_054175134.1  solute carrier family 66 member 2 isoform X12

    11. XM_054319154.1 → XP_054175129.1  solute carrier family 66 member 2 isoform X7

    12. XM_054319153.1 → XP_054175128.1  solute carrier family 66 member 2 isoform X6

    13. XM_054319161.1 → XP_054175136.1  solute carrier family 66 member 2 isoform X14

      UniProtKB/TrEMBL
      K7ERV4

    14. XM_054319157.1 → XP_054175132.1  solute carrier family 66 member 2 isoform X10

    RNA

    1. XR_008485023.1 RNA Sequence

    2. XR_008485024.1 RNA Sequence

    3. XR_008485025.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8N2U9.1 GenPept UniProtKB/Swiss-Prot:Q8N2U9

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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