Difference between revisions of "Lnc-IRX3-4:2"
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| − | CRNDE | + | ''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. |
==Annotated Information== | ==Annotated Information== | ||
| − | === | + | ===Name=== |
''CRNDE'', colorectal neoplasia differentially expressed (HGNC nomenclature) | ''CRNDE'', colorectal neoplasia differentially expressed (HGNC nomenclature) | ||
| − | |||
| + | ''LINC00180'', ''LOC643911'', "long intergenic non-protein coding RNA 180"<ref name="ref1" /> | ||
| + | |||
| + | ===Charcteristics=== | ||
| + | [[File:Human CRNDE gene locus.jpg|right|thumb|400px|'''Human CRNDE gene locus'''<ref name="ref1" />]] | ||
| + | |||
| + | 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=== | ===Cellular Localization=== | ||
| − | The transcripts of CRNDE that have retained intronic sequence are highly enriched in the nucleus | + | The transcripts of CRNDE that have retained intronic sequence are highly enriched in the nucleus<ref name="ref1" />. |
| − | |||
===Function=== | ===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 | + | ''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<ref name="ref1" />. |
| − | = | ||
| − | |||
===Expression=== | ===Expression=== | ||
| − | ''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 | + | 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<ref name="ref1" />. |
| + | 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''.<ref name="ref1" /> | ||
| + | CRNDE features high expression in high risk group of papillary thyroid cancer <ref name="ref2" />. | ||
===Disease=== | ===Disease=== | ||
| − | gliomas, colorectal cancer, acute myeloid leukemias(AML), hepatocelluar carcinoma(HCC), prostate cancer | + | gliomas, colorectal cancer, acute myeloid leukemias(AML), hepatocelluar carcinoma(HCC), prostate cancer <ref name="ref1" />. |
| + | papillary thyroid cancer <ref name="ref2" /> | ||
==Labs working on this lncRNA== | ==Labs working on this lncRNA== | ||
| − | CSIRO Animal, Food and Health Sciences, Preventative Health Flagship, Commonwealth Scientific and Industrial Research Organisation, Sydney, NSW, Australia | + | CSIRO Animal, Food and Health Sciences, Preventative Health Flagship, Commonwealth Scientific and Industrial Research Organisation, Sydney, NSW, Australia <ref name="ref1" /> |
| + | Department of Gastrointestinal Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang.Autonomous Region, P.R. China <ref name="ref1" /> | ||
==References== | ==References== | ||
<references> | <references> | ||
| − | <ref name="ref1"> | + | <ref name="ref1">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.</ref>( |
| + | <ref name="ref2">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. </ref> | ||
</references> | </references> | ||
| − | |||
{{basic| | {{basic| | ||
tID = lnc-IRX3-4:2| | tID = lnc-IRX3-4:2| | ||
source = LNCipedia2.1| | source = LNCipedia2.1| | ||
| − | same = ,| | + | same =''CRNDE'' ,''LINC00180'',''LOC643911''| |
classification = intergenic| | classification = intergenic| | ||
length = 1034 nt| | length = 1034 nt| | ||
Latest revision as of 09:36, 27 March 2018
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
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
- ↑ 1.0 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.
- ↑ 2.0 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 |
