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    LOC374443 C-type lectin domain family 2 member D pseudogene [ Homo sapiens (human) ]

    Gene ID: 374443, updated on 22-Oct-2024

    Summary

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    Gene symbol
    LOC374443
    Gene description
    C-type lectin domain family 2 member D pseudogene
    See related
    Ensembl:ENSG00000284634
    Gene type
    pseudo
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Expression
    Broad expression in lymph node (RPKM 5.9), appendix (RPKM 3.9) and 23 other tissues See more
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    Genomic context

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    See LOC374443 in Genome Data Viewer
    Location:
    12p13.31
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (9617284..9658415)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (9503534..9544658)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 12 NC_000012.11 (9769880..9811011)

    Chromosome 12 - NC_000012.12Genomic Context describing neighboring genes Neighboring gene alpha-2-macroglobulin like 1 pseudogene Neighboring gene RAN binding protein 6 pseudogene Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr12:9721455-9722278 Neighboring gene killer cell lectin like receptor B1 Neighboring gene RNA, U6 small nuclear 700, pseudogene Neighboring gene uncharacterized LOC105369728 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5942 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5943 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4229 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5944 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5945 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4230 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5946 Neighboring gene GOT2 pseudogene 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5947 Neighboring gene C-type lectin domain family 2 member D Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5948 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 4231 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5949 Neighboring gene long intergenic non-protein coding RNA 2390 Neighboring gene nucleophosmin 1 pseudogene 7

    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. Distinct class of putative "non-conserved" promoters in humans: comparative studies of alternative promoters of human and mouse genes. Tsuritani K, et al. Genome Res, 2007 Jul. PMID 17567985, Free PMC Article
    2. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039

    GeneRIFs: Gene References Into Functions

    Phenotypes

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    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)

    General gene information

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    Markers

    Other Names

    • CLR pseudogene

    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_002814.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks an internal exon, compared to variant 1.
      Source sequence(s)
      AA713965, AC010186, AK096274
      Related
      ENST00000575094.6

    2. NR_046444.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript.
      Source sequence(s)
      AA713965, AC010186, BX110220

    3. NR_046445.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' exon and internal exons, compared to variant 1.
      Source sequence(s)
      AA713965, AC010186, BP871964, BX436430

    4. NR_046446.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' exon and internal exons, compared to variant 1.
      Source sequence(s)
      AA713965, AC010186, AK096274, BF128895, DR002819
      Related
      ENST00000803960.1

    5. NR_046447.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in the 5' exon and lacks an internal exon, compared to variant 1.
      Source sequence(s)
      AA713965, AC010186, AK096274, DA835472
      Related
      ENST00000803963.1

    6. NR_046448.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) differs in the 5' exon and an internal exon, compared to variant 1.
      Source sequence(s)
      AA713965, AC010186, AY084051

    7. NR_046449.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (7) differs in the 5' exon and lacks an internal exon, compared to variant 1.
      Source sequence(s)
      AA713965, AC010186, AK096274, CD700936

    8. NR_046450.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (8) differs in the 5' exon and internal exons, compared to variant 1.
      Source sequence(s)
      AA713965, AC010186, BG754872

    9. NR_046451.1 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (9) differs in the 5' exon and lacks an internal exon, compared to variant 1.
      Source sequence(s)
      AA713965, AC010186, CD174827, DB131244
      Related
      ENST00000803958.1

    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_000012.12 Reference GRCh38.p14 Primary Assembly

      Range
      9617284..9658415
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060936.1 Alternate T2T-CHM13v2.0

      Range
      9503534..9544658
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version

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