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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

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