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    SLC66A1LP solute carrier family 66 member 1 like, pseudogene [ Homo sapiens (human) ]

    Gene ID: 152078, updated on 2-Nov-2024

    Summary

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    Official Symbol
    SLC66A1LPprovided by HGNC
    Official Full Name
    solute carrier family 66 member 1 like, pseudogeneprovided by HGNC
    Primary source
    HGNC:HGNC:25146
    See related
    Ensembl:ENSG00000293490 AllianceGenome:HGNC:25146
    Gene type
    pseudo
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    PQLC2L; C3orf55; SLC66A1L; SLC66A2L
    Summary
    Predicted to enable L-lysine transmembrane transporter activity. Predicted to be involved in L-lysine transmembrane transport. Predicted to be active in lysosomal membrane. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Biased expression in fat (RPKM 5.2), thyroid (RPKM 2.0) and 4 other tissues See more
    Orthologs
    all
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    Genomic context

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    See SLC66A1LP in Genome Data Viewer
    Location:
    3q25.32
    Exon count:
    7
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (157543312..157601094)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (160317934..160375697)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (157261101..157318883)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC101928236 Neighboring gene uncharacterized LOC105374179 Neighboring gene VISTA enhancer hs2571 Neighboring gene NANOG hESC enhancer GRCh37_chr3:156973526-156974057 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:156992312-156992853 Neighboring gene ventricular zone expressed PH domain containing 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:157216797-157217361 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:157217362-157217925 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:157220998-157221232 Neighboring gene CRISPRi-validated cis-regulatory element chr3.4666 Neighboring gene pentraxin 3 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_65660 Neighboring gene VISTA enhancer hs638 Neighboring gene RN7SK pseudogene 46 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr3:157737752-157738378 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:157751099-157752298 Neighboring gene hs1251 and hs1262 enhancers downstream of SHOX2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20743 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:157820715-157821322 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14847 Neighboring gene SHOX homeobox 2

    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. Cystinosin, MPDU1, SWEETs and KDELR belong to a well-defined protein family with putative function of cargo receptors involved in vesicle trafficking. Saudek V. PLoS One, 2012. PMID 22363504, Free PMC Article
    2. Creation of genome-wide protein expression libraries using random activation of gene expression. Harrington JJ, et al. Nat Biotechnol, 2001 May. PMID 11329013
    3. Generation and analysis of 280,000 human expressed sequence tags. Hillier LD, et al. Genome Res, 1996 Sep. PMID 8889549
    4. CFTR interactome mapping using the mammalian membrane two-hybrid high-throughput screening system. Lim SH, et al. Mol Syst Biol, 2022 Feb. PMID 35156780, Free PMC Article
    5. hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes. Lamesch P, et al. Genomics, 2007 Mar. PMID 17207965, Free PMC Article

    See all (9) 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 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

    Other Names

    • PQ loop repeat containing 2 like
    • PQ-loop repeat-containing protein 2-like

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables L-lysine transmembrane transporter activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in L-lysine transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    is_active_in lysosomal membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    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.

    RNA

    1. NR_024016.3 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) includes an alternate exon in the 3' end, compared to variant 1. The transcript is sufficiently abundant to represent as a RefSeq record; however, the predicted protein is not represented because the product is significantly truncated.
      Source sequence(s)
      AC084212, AI377021, BE905784, BX113701
      Related
      ENST00000468043.8

    2. NR_166162.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC084212

    3. NR_166163.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC084212
      Related
      ENST00000651011.1

    4. NR_166164.1 RNA Sequence

      Status: VALIDATED

      Source sequence(s)
      AC084212
      Related
      ENST00000651325.1

    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
      157543312..157601094
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      160317934..160375697
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001099777.3: Suppressed sequence

      Description
      NM_001099777.3: This RefSeq was removed because it is now thought that this gene is a pseudogene.

    2. NM_001130001.2: Suppressed sequence

      Description
      NM_001130001.2: This RefSeq was removed because it is now thought that this gene is a pseudogene.

    3. NM_001130002.2: Suppressed sequence

      Description
      NM_001130002.2: This RefSeq was removed because it is now thought that this gene is a pseudogene.

    4. NM_001243729.1: Suppressed sequence

      Description
      NM_001243729.1: This RefSeq was removed because it is now thought that this gene is a pseudogene.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A1A4F0.2 GenPept UniProtKB/Swiss-Prot:A1A4F0

    Gene LinkOut

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

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