LINC00339

Annotated Information

Name

Approved symbol: LINC00339

Approved name: long intergenic non-protein coding RNA 339

HGNC ID: HGNC:25011

Previous symbols: NCRNA00339

Previous names: non-protein coding RNA 339

Alias symbols: HSPC157

RefSeq ID: NR_109762

Ensembl ID: ENSG00000218510

LncBook ID: HSALNT0002923

Chromosome

1p36.12

Characteristics

Functional domains of 7SK RNA((Diribarne 2009))

~330 nt in vertebrates*. Transcribed by RNAP III, GC-rich sequence forming conserved secondary structures (especially 3' and 5' stem-loop motifs).

The 7SK gene is located on chromosome 6, and chromosome 6 is the sole human chromosome that produces 7SK RNA ((Driscoll 1994))

7SK RNA is capped at its 5' end by BCDIN3, a specific methylase methylphosphate capping enzyme (MePCE) ((Jeronimo 2007)).

RNAP II was recently found to bind near 7SK promoter, as well as many other known Pol III genes, suggesting that RNAP II may also play a role in regulating their transcription ((Raha 2010)).

In invertebrates, 7SK homologs may have different sizes (such as >400 nt and ~130 nt in drosophilids and nematodes, respectively). ((Gruber 2008)) ((Marz 2009))

Expression

Nuclear, highly abundant (one of the most abundant small RNAs in vertebrate cells), first isolated from HeLa nuclear extracts, but ubiquitously expressed.

RNA sequencing from 11 humans tissues confirmed ubiquitous high expression of 7SK with expression in some tissues being higher than any mRNA ((Castle 2010)).

Regulation

Intergenic SNP (rs6426749) at 1p36.12 acts as a strong long-range allele-specific enhancer to regulate the expression of LINC00339.

Function

Model of hLarp7 recognition of the 7SK 3′end and mechanism of assembly of core 7SK RNP((Eichhorn 2018))

LINC00339 might influence bone metabolism by modulating expression of CDC42.

Disease

Osteoporosis

Evolution

Please input evolution information here.

Labs working on this lncRNA

• Key Laboratory of Biomedical Information Engineering of Ministry of Education, and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, P. R. China.

References

Sequence

>gi|564473412|ref|NR_109761.1| Homo sapiens long intergenic non-protein coding RNA 339 (LINC00339), transcript variant 4, long non-coding RNA

000001 GACTTCCGGT TCCCGCGCGG CGCTCCAAAG CTCGGGGAGT GGTGGTCTCC CTTTCCTGGA GTCATTTGTG GGAGTTAGGG 000080
000081 TCTTATCCTG ATCTTTCCTC GTCCCCCGCT CCCCCGTCCT CCGAGGTGGC AGCTGCATCG GGGGTCATAC TACACATCGA 000160
000161 TCGGGACCTT AGTCATGTTG TGATATGGAC AGCTTTCTTA CCAGTACTCA TAAGCCTGCT TCATTTTTTA CGTGGCGGCA 000240
000241 CCACTGAGTG GTTGACGAAG TCTGGAACGT TTTTTCTTAG AGTTCCAGAA TTGAGACTGA AGTGTACCCA GAGACACAAA 000320
000321 GAAATACAGA AGTCCAGAAT GATCAAATGA GATCACTACC CAATGAAATG ATGGGCCGAG GAGCCAGAAG TTGTCCTACT 000400
000401 ACCTGCTTTC CAGGTCCAGA TTCCACGAGA GCCTTCTGGG CTCCCACCAG AGACCCTCAG TGAAGACTCT GTTGAAGACT 000480
000481 TTAAGACCAT GCTAGAAAGC CTCCCGGCAG AGGTTCAGGA AGTTCTGCTA TGAGGATGCA GCTGGCCCCA GGGATGTCCT 000560
000561 CAGGCATCTC TAGGACCTTG CTGGACGGTG GTGGCTGAGA CCTGATATCC ACACAAAGGA GCAGACTGTG GAAATGCTGG 000640
000641 TGCAGGAGCA ATTCCAGGCT GTCCTGCCCG AGGAGCTCAG AGCTCAAGCA CAGAGATGTC AGCCTGGAAT CAGAATCACT 000720
000721 GGCTAAGTCT TGCTGCTTGC TTCTTGCTCA GCCTGCATAT GAGAAGTCAA CCAAGCATTC TCTTGGATGC AAGATCCAAC 000800
000801 TGCACCCATG GGAAATCTGA ACTTCCACTT TCTTTGAGCT TGTCTTTGGT TGTAATAAGA ATCCATCAAA ACCCATGTCT 000880
000881 GGATCTCTCT TTGGCTGAGG CAGCTTTATT TCCTACAGAA AGAGTTTCTC TGTCCTCTTG TTAGGACAAT CAGCCTGCTG 000960
000961 CTTTGGGCTT TTCCAAGAGC CTATTTTTCA TCTGCTGGAT GCCTCTTTTT TTTTTTTTTT TTTTTTTTGC ACTGTGTGAC 001040
001041 ATGCTTTAAT ATATATATTT TTTATGTATC CAAAGAGGTA ATCAACTTTA ACTTTCAGAA TTCATGAATC TTGGTTTGGT 001120
001121 GGCATGAATG AAAGGTTATG TAACCCCACC AGTAACTCAT TTGGGGTGCC CTTGAAATAT TAAAGTTTGG TCCTCAATAA 001200
001201 AT