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SLC66A1 solute carrier family 66 member 1 [ Homo sapiens (human) ]

Gene ID: 54896, updated on 17-Jun-2024

Summary

Official Symbol
SLC66A1provided by HGNC
Official Full Name
solute carrier family 66 member 1provided by HGNC
Primary source
HGNC:HGNC:26001
See related
Ensembl:ENSG00000040487 MIM:614760; AllianceGenome:HGNC:26001
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
LAAT1; PQLC2; LAAT-1
Summary
Enables L-arginine transmembrane transporter activity and L-lysine transmembrane transporter activity. Involved in L-arginine transmembrane transport; amino acid homeostasis; and lysine transport. Located in lysosomal membrane. Is integral component of organelle membrane. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in testis (RPKM 2.3), adrenal (RPKM 1.8) and 25 other tissues See more
Orthologs
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Genomic context

See SLC66A1 in Genome Data Viewer
Location:
1p36.13
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (19312326..19334463)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (19135861..19158016)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (19638820..19658922)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903867 Neighboring gene uncharacterized LOC100506730 Neighboring gene RNA, U6 small nuclear 1099, pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:19638229-19638728 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 353 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19641943-19642442 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:19644916-19645106 Neighboring gene aldo-keto reductase family 7 member A2 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19661163-19661664 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19661665-19662164 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:19663848-19664812 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19665979-19666480 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19667246-19668220 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 299 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:19679737-19680421 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19682496-19682996 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19682997-19683497 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_1531 Neighboring gene capping actin protein of muscle Z-line subunit beta Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19685462-19685962 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:19696541-19697233 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_1534 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 300 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 301 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr1:19727675-19728354 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:19729033-19729710 Neighboring gene uncharacterized LOC124903868 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:19745938-19746438 Neighboring gene RNA, 7SL, cytoplasmic 277, pseudogene

Genomic regions, transcripts, and products

Expression

  • 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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • FLJ20320, FLJ23906, FLJ26661, FLJ26665

Gene Ontology Provided by GOA

Component Evidence Code Pubs
located_in intracellular membrane-bounded organelle IDA
Inferred from Direct Assay
more info
 
is_active_in lysosomal membrane IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in lysosomal membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in lysosomal membrane TAS
Traceable Author Statement
more info
 
located_in organelle membrane IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
lysosomal amino acid transporter 1 homolog
Names
PQ loop repeat containing 2
PQ-loop repeat-containing protein 2

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_001040125.2NP_001035214.1  lysosomal amino acid transporter 1 homolog isoform 1

    See identical proteins and their annotated locations for NP_001035214.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AK125580, BC015324, DA202894, DA560373
    Consensus CDS
    CCDS195.2
    UniProtKB/Swiss-Prot
    B3KWQ5, Q6ZMJ3, Q6ZP27, Q6ZP29, Q9NXC7
    Related
    ENSP00000364295.3, ENST00000375153.8
    Conserved Domains (1) summary
    pfam04193
    Location:183238
    PQ-loop; PQ loop repeat
  2. NM_001040126.2NP_001035215.1  lysosomal amino acid transporter 1 homolog isoform 2

    See identical proteins and their annotated locations for NP_001035215.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an alternate segment in the 5' UTR and an alternate exon compared to variant 1. The resulting isoform (2) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    BC015324, DA202894
    Consensus CDS
    CCDS30618.1
    UniProtKB/TrEMBL
    A0A024RAA1
    Related
    ENSP00000383395.2, ENST00000400548.6
    Conserved Domains (1) summary
    pfam04193
    Location:119173
    PQ-loop; PQ loop repeat
  3. NM_001287531.2NP_001274460.1  lysosomal amino acid transporter 1 homolog isoform 3 precursor

    See identical proteins and their annotated locations for NP_001274460.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) lacks an alternate segment in the 5' UTR, an alternate exon, and uses an alternate splice junction at the 5' end of an exon compared to variant 1. The resulting isoform (3) is shorter at the N-terminus compared to isoform 1.
    Source sequence(s)
    AK172745, BC015324, DA202894
    UniProtKB/Swiss-Prot
    Q6ZP29
    Conserved Domains (1) summary
    pfam04193
    Location:73127
    PQ-loop; PQ loop repeat
  4. NM_017765.3NP_060235.2  lysosomal amino acid transporter 1 homolog isoform 1

    See identical proteins and their annotated locations for NP_060235.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate segment in the 5' UTR compared to variant 1. Variants 1 and 2 both encode the same isoform (1).
    Source sequence(s)
    AK125580, AK130171, BC015324, DA202894
    Consensus CDS
    CCDS195.2
    UniProtKB/Swiss-Prot
    B3KWQ5, Q6ZMJ3, Q6ZP27, Q6ZP29, Q9NXC7
    Related
    ENSP00000364297.3, ENST00000375155.7
    Conserved Domains (1) summary
    pfam04193
    Location:183238
    PQ-loop; PQ loop repeat

RNA

  1. NR_109848.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (5) uses an alternate 3' exon structure 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)
    AK000327, AL035413

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

    Range
    19312326..19334463
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047423401.1XP_047279357.1  lysosomal amino acid transporter 1 homolog isoform X3

  2. XM_011541634.4XP_011539936.1  lysosomal amino acid transporter 1 homolog isoform X3

    Conserved Domains (1) summary
    pfam04193
    Location:3897
    PQ-loop; PQ loop repeat
  3. XM_005245916.3XP_005245973.1  lysosomal amino acid transporter 1 homolog isoform X2

    See identical proteins and their annotated locations for XP_005245973.1

    UniProtKB/Swiss-Prot
    B3KWQ5, Q6ZMJ3, Q6ZP27, Q6ZP29, Q9NXC7
    Conserved Domains (1) summary
    pfam04193
    Location:183238
    PQ-loop; PQ loop repeat
  4. XM_047423394.1XP_047279350.1  lysosomal amino acid transporter 1 homolog isoform X1

RNA

  1. XR_001737253.2 RNA Sequence

  2. XR_001737254.2 RNA Sequence

  3. XR_007061310.1 RNA Sequence

  4. XR_007061311.1 RNA Sequence

  5. XR_007061312.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060925.1 Alternate T2T-CHM13v2.0

    Range
    19135861..19158016
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054337249.1XP_054193224.1  lysosomal amino acid transporter 1 homolog isoform X3

  2. XM_054337250.1XP_054193225.1  lysosomal amino acid transporter 1 homolog isoform X3

  3. XM_054337248.1XP_054193223.1  lysosomal amino acid transporter 1 homolog isoform X2

    UniProtKB/Swiss-Prot
    B3KWQ5, Q6ZMJ3, Q6ZP27, Q6ZP29, Q9NXC7
  4. XM_054337247.1XP_054193222.1  lysosomal amino acid transporter 1 homolog isoform X1

RNA

  1. XR_008486077.1 RNA Sequence

  2. XR_008486079.1 RNA Sequence

  3. XR_008486076.1 RNA Sequence

  4. XR_008486078.1 RNA Sequence

  5. XR_008486080.1 RNA Sequence