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

Gene ID: 374443, updated on 10-Oct-2023

Summary

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Gene symbol
LOC374443
Gene description
C-type lectin domain family 2 member D pseudogene
See related
Ensembl:ENSG00000291107
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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Location:
12p13.31
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 12 NC_000012.12 (9617284..9658415)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 12 NC_060936.1 (9503534..9544658)
105.20220307 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)

Genotypes

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
    ENST00000575094.5

  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

  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

  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

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_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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