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CLMAT3 colorectal liver metastasis associated transcript 3 [ Homo sapiens (human) ]

Gene ID: 101927096, updated on 17-Sep-2024

Summary

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Official Symbol
CLMAT3provided by HGNC
Official Full Name
colorectal liver metastasis associated transcript 3provided by HGNC
Primary source
HGNC:HGNC:52287
See related
Ensembl:ENSG00000249035 AllianceGenome:HGNC:52287
Gene type
ncRNA
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
SPARC-AS1; CTB-113P19.1
Expression
Broad expression in fat (RPKM 19.7), placenta (RPKM 11.8) and 18 other tissues See more
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Genomic context

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See CLMAT3 in Genome Data Viewer
Location:
5q33.1
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 5 NC_000005.10 (151676945..151687910)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 5 NC_060929.1 (152215924..152226891)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 5 NC_000005.9 (151056506..151067471)

Chromosome 5 - NC_000005.10Genomic Context describing neighboring genes Neighboring gene solute carrier family 36 member 1 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82555 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_82563 Neighboring gene FAT atypical cadherin 2 Neighboring gene microRNA 6499 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23458 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr5:150950930-150951442 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:150974668-150975189 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:150998970-150999648 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:150999649-151000325 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr5:151003759-151004958 Neighboring gene uncharacterized LOC105378231 Neighboring gene uncharacterized LOC124901116 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23459 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23460 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr5:151042798-151043997 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr5:151063929-151064758 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:151065587-151066416 Neighboring gene H3K27ac hESC enhancer GRCh37_chr5:151066417-151067244 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr5:151079020-151079841 Neighboring gene secreted protein acidic and cysteine rich Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16525 Neighboring gene MPRA-validated peak5542 silencer Neighboring gene Sharpr-MPRA regulatory region 9564 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 16526 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23461 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23462 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23463 Neighboring gene MPRA-validated peak5544 silencer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23464 Neighboring gene MPRA-validated peak5543 silencer Neighboring gene RN7SK pseudogene 232 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr5:151109002-151109538 Neighboring gene Sharpr-MPRA regulatory region 608 Neighboring gene Sharpr-MPRA regulatory regions 4972 and 759 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr5:151124409-151125608 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23466 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 23467 Neighboring gene ATOX1 antisense RNA 1 Neighboring gene antioxidant 1 copper chaperone

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. Aberrant expression of long noncoding RNAs in colorectal cancer with liver metastasis. Ye LC, et al. Tumour Biol, 2015 Nov. PMID 26050227
  2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article

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 variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

General gene information

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Other Names

  • SPARC antisense RNA 1

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_109873.1 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC011374
    Related
    ENST00000510576.6

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_000005.10 Reference GRCh38.p14 Primary Assembly

    Range
    151676945..151687910
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060929.1 Alternate T2T-CHM13v2.0

    Range
    152215924..152226891
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version

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