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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
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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

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