Lnc-IRX3-4:2

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CRNDE, a lncRNA and displays a very time- and tissue-specific pattern of expression, is the most upregulated lncRNA in gliomas ,which may associated with a "stemness" signature.

Contents

Annotated Information

Name

CRNDE, colorectal neoplasia differentially expressed (HGNC nomenclature)

LINC00180, LOC643911, "long intergenic non-protein coding RNA 180"[1]

Charcteristics

Human CRNDE gene locus[1]

CRNDE, a lncRNA gene whose locus is low potential coding transcripts, is transcribed from chromosome 16 on the strand opposite to the adjacent IRX5 gene, with which it may share a bidirectional promoter.

Cellular Localization

The transcripts of CRNDE that have retained intronic sequence are highly enriched in the nucleus[1].


Function

CRNDE is the most upregulated lncRNA in gliomas and in other cancers, it is associated with a “stemness” signature. In ESC, the function of CRNDE may be to suppress lineage-determining genes. During the differentiation of certain lineages (e.g., ectodermal cell types), CRNDE levels are known to rise further, perhaps in order to suppress genes that specify alternate cell fates. In cancers of tissues where CRNDE is aberrantly expressed, its high elevation may again help to suppress lineage markers and revert the cells to a less differentiated state[1].

Expression

CRNDE displays tissue-specific and temporal expression patterns, in that it has little to no expression in many normal adult tissues, such as colorectal mucosa, white blood cells, and liver, while tissues with high CRNDE expression include testis, breast, skin, parotid gland, and bronchial epithelium.CRNDE was differentially expressed in colorectal neoplasia relative to normal colorectal tissue. CRNDE expression is elevated in neoplastic diseases, especially cancers of the blood and brain[1].

While CRNDE expression is most often elevated in cancers, in some cases it is lower than in normal control tissue. For example, in contrast to clear cell carcinomas and Type I papillary tumors of the kidney, chromophobe tumors and oncocytomas show significantly downregulated expression of CRNDE.[1]

CRNDE features high expression in high risk group of papillary thyroid cancer [2].

Disease

gliomas, colorectal cancer, acute myeloid leukemias(AML), hepatocelluar carcinoma(HCC), prostate cancer [1].

papillary thyroid cancer [2]

Labs working on this lncRNA

CSIRO Animal, Food and Health Sciences, Preventative Health Flagship, Commonwealth Scientific and Industrial Research Organisation, Sydney, NSW, Australia [1]

Department of Gastrointestinal Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang.Autonomous Region, P.R. China [1]

References

  1. 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 Ellis BC, Molloy PL, Graham LD. CRNDE: A Long Non-Coding RNA Involved in CanceR, Neurobiology, and DEvelopment[J]. Frontiers in genetics. 2012,3:270.
  2. 2.0 2.1 Luo YH, Liang L, He RQ, Wen DY, Deng GF, Yang H, He Y, Ma W, Cai XY, Chen JQ, Chen G. RNA-sequencing investigation identifies an effective risk score generated by three novel lncRNAs for the survival of papillary thyroid cancer patients.Oncotarget. 2017 May 26.

Basic Information

Transcript ID

lnc-IRX3-4:2

Source

LNCipedia2.1

Same with

CRNDE ,LINC00180,LOC643911

Classification

intergenic

Length

1034 nt

Genomic location

chr16-:54952778..54963079

Exon number

5

Exons

54952778..54953121,54954210..54954322,54957497..54957562,54959013..54959125,54962682..54963079

Genome context

Sequence
000001 CATGGAGACG GGAAGCTGGC TGCAGCGGCG GCGGGGACCG TGGGGCCGAG GTGGCTGCCA GCCGGCCAAT GTCTAAGCGA 000080
000081 GGCGGAGCGG CCCAGGCGGC CCGAGCCTGG GGGAGCGCGC AGCCGGCCAG TGGCGGCCTC GCCGGCGGCC TCTTCCCGGG 000160
000161 CTCGCAGTAG GCCCGAGTCG TCGCCGGGAG CTCCTGGGAG CAGCGTCCCC GCCCTGCTCC CCTCGCTCCC GCCTCTTGCG 000240
000241 GCCCCACGGC CCCTCAGCGC CCGCCCCCGG CTCCGCCCGC CGCAGCCGCA GCCCCTGGCG CTAACGGTCG GTAACGGCCC 000320
000321 GCGCGCGCCG CCCGCCGGGG GCTCGCGCCA GCCACGAGGG AGCGTCCGCG GCCCGCGCGC CCGCGCGGCG GAGGAGAGGT 000400
000401 GTTAAGTGTG ATGCTTCCAT AATACATTTG GATGCTGTCA GCTAAGTTCA CTTCTGAACT AAGGGGTTCC TCCAAATGTT 000480
000481 GGCTGAAATT CATCCCAAGG CTGGTCTGCA AAGTCTGCAA TTCATAATGG AGCTACTGTA CTGGCTATTG GAAGGAGGAG 000560
000561 ATTCTGAAGA TAAGGAGGTA AAACCTGTTT AGAAATTAAA AATGAGTTAC GATTTAAAGA AAATTCAGAT GACTCATTGT 000640
000641 GAGTGCTAGT TCTCTTGTAG GATGCCACTG GAAATGTTGA AATGAAAAAT ATTCAGCCGT TGGTCTTTGA AATTTCCTGT 000720
000721 GATGTGTTTC AATCTAGATG CAAAGAACAT GGAAAAATCA AAGTGCTCGA GTGGTTTAAA TATGTTTTGG GTATTCCTGT 000800
000801 TTATAGACTA TAATACTTTT CCAATTAAAA TCCTCAGTTG TCACGCAGAA GAAGGTTAAG CTGTATTTGA TTGCCAGTTT 000880
000881 TACTGAAAAT GCTTAGTATT TTACAGTATC ACCAAATATA TTTTGTTTAG CCAAGGTATA GGAAAAATAA AATAAATTGT 000960
000961 ATAGGTTGAC TTTTTTCTAA AATGTCTTTA TTGGATTGAA TGAATGTTTA TACCTGAAAA AAAAAGGTTC AAAA
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