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CCDC162P coiled-coil domain containing 162, pseudogene [ Homo sapiens (human) ]

Gene ID: 221262, updated on 5-Mar-2024

Summary

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Official Symbol
CCDC162Pprovided by HGNC
Official Full Name
coiled-coil domain containing 162, pseudogeneprovided by HGNC
Primary source
HGNC:HGNC:21565
See related
Ensembl:ENSG00000203799 AllianceGenome:HGNC:21565
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
CCDC162; C6orf183; C6orf184; C6orf185
Summary
This gene is the ortholog of the mouse coiled-coil domain containing 162 gene. This locus is transcribed, but is represented as a unitary pseudogene because there are multiple changes in the coding sequence, including multiple changes that result in premature stop codons, relative to the mouse coding sequence. Transcripts from this locus are expected to encode truncated proteins, and may be candidates for nonsense-mediated decay (NMD). [provided by RefSeq, Sep 2018]
Expression
Biased expression in colon (RPKM 1.8), testis (RPKM 1.4) and 11 other tissues See more
Orthologs
all
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Genomic context

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Location:
6q21
Exon count:
46
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (109165831..109354948)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (110343879..110532985)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (109487034..109676151)

Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene armadillo repeat containing 2 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:109241738-109242648 Neighboring gene ARMC2 antisense RNA 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:109266564-109267120 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:109272427-109272928 Neighboring gene MPRA-validated peak6016 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17456 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24918 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24919 Neighboring gene sestrin 1 Neighboring gene Sharpr-MPRA regulatory region 5156 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:109367051-109367618 Neighboring gene RNA, U6 small nuclear 653, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24920 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17457 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24921 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:109422661-109423052 Neighboring gene centrosomal protein 57 like 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:109515122-109515622 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:109562791-109563990 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:109572150-109572928 Neighboring gene uncharacterized LOC124901374 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr6:109612245-109613444 Neighboring gene small nucleolar RNA U13 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:109625443-109625633 Neighboring gene MPRA functional variant 6:109625879:G:A red blood cell enhancer Neighboring gene patched domain containing 3 pseudogene 3 Neighboring gene OCT4 hESC enhancer GRCh37_chr6:109649788-109650315 Neighboring gene RNY3 pseudogene 11 Neighboring gene ribosomal protein L7 pseudogene 28 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17458 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:109703563-109704072 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24923 Neighboring gene Sharpr-MPRA regulatory region 15445 Neighboring gene CD164 molecule Neighboring gene ReSE screen-validated silencer GRCh37_chr6:109761883-109762088 Neighboring gene peptidylprolyl isomerase like 6 Neighboring gene sphingomyelin phosphodiesterase 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
  • 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. Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium. Ganesh SK, et al. Nat Genet, 2009 Nov. PMID 19862010, Free PMC Article
  2. Seventy-five genetic loci influencing the human red blood cell. van der Harst P, et al. Nature, 2012 Dec 20. PMID 23222517, Free PMC Article
  3. Genome-wide association study of hematological and biochemical traits in a Japanese population. Kamatani Y, et al. Nat Genet, 2010 Mar. PMID 20139978
  4. The sequence of the human genome. Venter JC, et al. Science, 2001 Feb 16. PMID 11181995
  5. The DNA sequence and analysis of human chromosome 6. Mungall AJ, et al. Nature, 2003 Oct 23. PMID 14574404

See all (8) citations in PubMed

GeneRIFs: Gene References Into Functions

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium.
EBI GWAS Catalog
Seventy-five genetic loci influencing the human red blood cell.
EBI GWAS Catalog

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

Homology

Clone Names

  • FLJ37396, MGC129804, MGC149201

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_152435.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AK094715, AL355305, AL359711, AL359712, BC107113, BC128119, BG572220, CR735618, DV080116, DY655452, EB710335
    Related
    ENST00000368966.10

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_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    109165831..109354948
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    110343879..110532985
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001277339.1: Suppressed sequence

    Description
    NM_001277339.1: This RefSeq was removed because currently it is thought that this locus represents a unitary pseudogene.

  2. NM_173671.1: Suppressed sequence

    Description
    NM_173671.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.

  3. NR_028595.1: Suppressed sequence

    Description
    NR_028595.1: This RefSeq was removed because currently there is insufficient support for the transcript.
Nucleotide Protein
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