Difference between revisions of "LINC00857"

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(Created page with "==Annotated Information== ===Approved Symbol=== LINC00857 ===Approved Name=== long intergenic non-protein coding RNA 857 ===Previous Symbols=== _ ===Synonyms=== _ ===Chromosom...")
 
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==Annotated Information==
 
==Annotated Information==
−
===Approved Symbol===
+
===Name===
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LINC00857
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Approved symbol: LINC00857
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===Approved Name===
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−
long intergenic non-protein coding RNA 857
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Approved name: long intergenic non-protein coding RNA 857
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===Previous Symbols===
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−
_
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HGNC ID: HGNC:45114
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===Synonyms===
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−
_
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RefSeq ID: NR_038464
 +
 
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Ensembl ID: ENSG00000237523
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 +
LncBook ID: [https://bigd.big.ac.cn/lncbook/transcript?transid=HSALNT0165271 HSALNT0165271]
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===Chromosome===
 
===Chromosome===
 
10q22.3
 
10q22.3
−
===RefSeq ID===
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−
NR_038464
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===Characteristics ===
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===OMIM ID===
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[[File:Functional domains of 7SK RNA..png|right|thumb|Functional domains of 7SK RNA([https://www.ncbi.nlm.nih.gov/pubmed/19246988 (Diribarne 2009)])]]
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_
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−
===Ensembl ID===
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Please input characteristics information here.
−
ENSG00000237523
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===pubmed IDs===
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===Expression===
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26862852
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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 ([http://www.ncbi.nlm.nih.gov/pubmed/20668672 (Castle 2010)]).
 +
 
 +
===Regulation===
 +
In the 7SK ribonucleoprotein, Larp7 binds directly to 3′ terminus of 7SK RNA ([https://www.ncbi.nlm.nih.gov/pubmed/18281698 (Krueger 2008)]) ([https://www.ncbi.nlm.nih.gov/pubmed/18483487 (Markert 2008)]), and prevents degradation of 7SK in vivo ([https://www.ncbi.nlm.nih.gov/pubmed/18281698 (Krueger 2008)]).
 +
 
 +
===Function===
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[[File:Model of hLarp7 recognition of the 7SK.png|right|thumb|Model of hLarp7 recognition of the 7SK 3′end and mechanism of assembly of core 7SK RNP([https://www.ncbi.nlm.nih.gov/pubmed/29946027 (Eichhorn 2018)])]]
 +
 
 +
===Disease===
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colon adenocarcinoma <ref name="ref1" />
 +
 
 +
===Evolution===
 +
Please input evolution information here.
 +
 
 +
==Labs working on this lncRNA==
 +
Please input related labs here.
 +
 
 +
==References==
 +
<references>
 +
<ref name="ref1"> Shahriyari L. Effect of normalization methods on the performance of supervised
 +
learning algorithms applied to HTSeq-FPKM-UQ data sets: 7SK RNA expression as a
 +
predictor of survival in patients with colon adenocarcinoma. Brief Bioinform.
 +
2017 Nov 3. doi: 10.1093/bib/bbx153.
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</ref>(1)
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</references>
 +
 
 
===Sequence===
 
===Sequence===
 
>gi|336285291|ref|NR_038464.1| Homo sapiens long intergenic non-protein coding RNA 857 (LINC00857), long non-coding RNA
 
>gi|336285291|ref|NR_038464.1| Homo sapiens long intergenic non-protein coding RNA 857 (LINC00857), long non-coding RNA
 
<dnaseq>GACCGCGAAGGCCAGCTTCTTCGAAAGGCCCATTTTTCTCCGTGGCTGAGCGAATGCTCCTAGAATACCACGTTTATAATAAATCATGTAGGGTGGAATTCCTGCTGGATGTATACACCTTTCTGCATCAGAGCTCTTCAAACCCAGAATGGTGAATAGCTACCCCTGGGCTTACCCTTTTATAATTTTCAACAAACCTGCGTTTAGCCCCGGCTAGGTGCCAGCAAGTTGCTAGGGACTGAGGAGGCTCTGCAGAGGACCCGAGCTGAGGCCCTAATCCTCAAGGCCAATGGCAGGGGTCACCGCCCAGGCACCCCCAGAGAACGCGGTGTGAAGGAAAAGACACCAAACTCGGTGTTCAAATGTGTGGGATCTATTCTAGTTCTGATTCTGACACTTGCAAGTCATGCATCCTCCGAGCCTCGGCTTTCTCACCTATAAAATCTTCAACGTGACCTATAAAAATCCATAAAATCACCCCTGCTTCATTGTTTCCCAGGGCTCATAGAAACATCATACAAGGTGGAGAAGAGTACCCAAGAAGGACAAGCTTGGAATGGGGCCCCCTCCCCAGGCTGGAGATCAGACATTGTTGGAGAAGGTATCATTGCAGCCCCCTACATAGCAGAGAGATTTGCTGAGTTGCATAGTCTAGAGCTGGTTGCAATTATTGGACAAGCAGGAAACAAACCTCCACAGCCCATGCGAGCCACACTGCTGGGTTGAGTGTATGAGCATGTAGAATGATTGGGTCTCCAGTGCGGACAGAAGGCATGGATCGCGTGGTGCCTGTGTTGGGAGGATACTAAGAGGGCGATCACCATGCCAGGACAAGACTAGTTGCCTGGGATCTTCTGGGCACGTGACTGGAGCAGAGTACCACTGGATCTCCTCACACCAGCCAGACCCAGGAAGAGAAGCTCCTTTCACCTGCACTGTTCTCTCAGCACCCTCCACGGAGAAAGCTTCATGTTATGCTTAGTGTACAGGAGAAATGCTCATGGGAATCCTGTCCATTATCACAGAGCAGGTATTAGTGGGTGAATATGGAGCTGAGAAGTAATAAGTTGTAACTGGCATAGATATCATGGGGATATTTGAAGAACGCTGTGAACACATATGCATGGGTCCATGTATTCATGAGTGTGCACATATGTGTAATTATTCATACAATTCATGGTGGATACTACTTCGAGGGTGTTCACAGACCCCAGGCAGAGAGCGCCTGGAGGGAAAATTATCCAAGGCAGGCCCATTCATAGTTCCAGGACAGCCAGAAGAAAGCCTCCGTTAAGCACCAGAAGTCTCCGGGGCAGGTGGGGCCAGGCAGCATGAAAGAATTGGCCGCAAGAGTTCCAAACCCTGTCCCAATTATGGAGGGTGACTTTTCTTTGTCCTCCTTCTCCATTCCCTTCCATATTGCTCATGCATCCAAAGGGAGACCTGAAGACTCTCTAGCAGGGCAAGGCCATTTTCTTTTGGCATTTTTCTCTCCCCAGAGTCTAGCTGATTATCAGCTTAGACACACAGCAGGCTATGTGCTGTGAACAACAGGCATCCTGGGTTATTTTACAAACTCATGGATAGTCATTTTGAAACCACCTTTGCAAAATTGTGACTGAAACAGTGAAAGAGAGCTAACTTAACCAGCTCCATCTTGTTTCTAACCTCCAAGCTGTCTTTGTTCATTCCTGGGCGTAGGCTGAACTAACTTTGGGAGAAACTTAGTTTGTAGTTATAGTTTAAACAAAGACTGTGACAGCCCTTTCCCAATGCAGACCTCCTTCTTGTCTGGGGACTAGACTAACATTAGCCACAGGATTAGAAATTACGGTTTAGGAGTCACGCAGCTGGAGGCTACAAGATTCTGACCCTCCCTAAACTGCTTCTAAGATCAGTGCTTGAGACATGTTGCAGACCCCGCACTTGCTGGATCAGCTGACGCCACACAGATGGATAAACTGCCTCGTCTGATCTTGTGGCCCCCACCCGGGAACTGACGAAGCGCAAGAAGACAGCTTCGACTCCCTGTGAGTTCATCCCTGACCAACCAGCACTCCTGGCTCACTGGCTTCCCCCTACCAAGTTATGCTTAAAAATTCTGCTCCCCGAATTCTCGAGGAGACTGATTTGAGTGATAATAAAACTCCAGTCTCCCGCAAAAAAAAAAA</dnaseq>
 
<dnaseq>GACCGCGAAGGCCAGCTTCTTCGAAAGGCCCATTTTTCTCCGTGGCTGAGCGAATGCTCCTAGAATACCACGTTTATAATAAATCATGTAGGGTGGAATTCCTGCTGGATGTATACACCTTTCTGCATCAGAGCTCTTCAAACCCAGAATGGTGAATAGCTACCCCTGGGCTTACCCTTTTATAATTTTCAACAAACCTGCGTTTAGCCCCGGCTAGGTGCCAGCAAGTTGCTAGGGACTGAGGAGGCTCTGCAGAGGACCCGAGCTGAGGCCCTAATCCTCAAGGCCAATGGCAGGGGTCACCGCCCAGGCACCCCCAGAGAACGCGGTGTGAAGGAAAAGACACCAAACTCGGTGTTCAAATGTGTGGGATCTATTCTAGTTCTGATTCTGACACTTGCAAGTCATGCATCCTCCGAGCCTCGGCTTTCTCACCTATAAAATCTTCAACGTGACCTATAAAAATCCATAAAATCACCCCTGCTTCATTGTTTCCCAGGGCTCATAGAAACATCATACAAGGTGGAGAAGAGTACCCAAGAAGGACAAGCTTGGAATGGGGCCCCCTCCCCAGGCTGGAGATCAGACATTGTTGGAGAAGGTATCATTGCAGCCCCCTACATAGCAGAGAGATTTGCTGAGTTGCATAGTCTAGAGCTGGTTGCAATTATTGGACAAGCAGGAAACAAACCTCCACAGCCCATGCGAGCCACACTGCTGGGTTGAGTGTATGAGCATGTAGAATGATTGGGTCTCCAGTGCGGACAGAAGGCATGGATCGCGTGGTGCCTGTGTTGGGAGGATACTAAGAGGGCGATCACCATGCCAGGACAAGACTAGTTGCCTGGGATCTTCTGGGCACGTGACTGGAGCAGAGTACCACTGGATCTCCTCACACCAGCCAGACCCAGGAAGAGAAGCTCCTTTCACCTGCACTGTTCTCTCAGCACCCTCCACGGAGAAAGCTTCATGTTATGCTTAGTGTACAGGAGAAATGCTCATGGGAATCCTGTCCATTATCACAGAGCAGGTATTAGTGGGTGAATATGGAGCTGAGAAGTAATAAGTTGTAACTGGCATAGATATCATGGGGATATTTGAAGAACGCTGTGAACACATATGCATGGGTCCATGTATTCATGAGTGTGCACATATGTGTAATTATTCATACAATTCATGGTGGATACTACTTCGAGGGTGTTCACAGACCCCAGGCAGAGAGCGCCTGGAGGGAAAATTATCCAAGGCAGGCCCATTCATAGTTCCAGGACAGCCAGAAGAAAGCCTCCGTTAAGCACCAGAAGTCTCCGGGGCAGGTGGGGCCAGGCAGCATGAAAGAATTGGCCGCAAGAGTTCCAAACCCTGTCCCAATTATGGAGGGTGACTTTTCTTTGTCCTCCTTCTCCATTCCCTTCCATATTGCTCATGCATCCAAAGGGAGACCTGAAGACTCTCTAGCAGGGCAAGGCCATTTTCTTTTGGCATTTTTCTCTCCCCAGAGTCTAGCTGATTATCAGCTTAGACACACAGCAGGCTATGTGCTGTGAACAACAGGCATCCTGGGTTATTTTACAAACTCATGGATAGTCATTTTGAAACCACCTTTGCAAAATTGTGACTGAAACAGTGAAAGAGAGCTAACTTAACCAGCTCCATCTTGTTTCTAACCTCCAAGCTGTCTTTGTTCATTCCTGGGCGTAGGCTGAACTAACTTTGGGAGAAACTTAGTTTGTAGTTATAGTTTAAACAAAGACTGTGACAGCCCTTTCCCAATGCAGACCTCCTTCTTGTCTGGGGACTAGACTAACATTAGCCACAGGATTAGAAATTACGGTTTAGGAGTCACGCAGCTGGAGGCTACAAGATTCTGACCCTCCCTAAACTGCTTCTAAGATCAGTGCTTGAGACATGTTGCAGACCCCGCACTTGCTGGATCAGCTGACGCCACACAGATGGATAAACTGCCTCGTCTGATCTTGTGGCCCCCACCCGGGAACTGACGAAGCGCAAGAAGACAGCTTCGACTCCCTGTGAGTTCATCCCTGACCAACCAGCACTCCTGGCTCACTGGCTTCCCCCTACCAAGTTATGCTTAAAAATTCTGCTCCCCGAATTCTCGAGGAGACTGATTTGAGTGATAATAAAACTCCAGTCTCCCGCAAAAAAAAAAA</dnaseq>

Revision as of 01:05, 12 August 2019

Annotated Information

Name

Approved symbol: LINC00857

Approved name: long intergenic non-protein coding RNA 857

HGNC ID: HGNC:45114

RefSeq ID: NR_038464

Ensembl ID: ENSG00000237523

LncBook ID: HSALNT0165271

Chromosome

10q22.3

Characteristics

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

Please input characteristics information here.

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

In the 7SK ribonucleoprotein, Larp7 binds directly to 3′ terminus of 7SK RNA ((Krueger 2008)) ((Markert 2008)), and prevents degradation of 7SK in vivo ((Krueger 2008)).

Function

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

Disease

colon adenocarcinoma [1]

Evolution

Please input evolution information here.

Labs working on this lncRNA

Please input related labs here.

References

  1. ↑ Shahriyari L. Effect of normalization methods on the performance of supervised learning algorithms applied to HTSeq-FPKM-UQ data sets: 7SK RNA expression as a predictor of survival in patients with colon adenocarcinoma. Brief Bioinform. 2017 Nov 3. doi: 10.1093/bib/bbx153.

Sequence

>gi|336285291|ref|NR_038464.1| Homo sapiens long intergenic non-protein coding RNA 857 (LINC00857), long non-coding RNA

000001 GACCGCGAAG GCCAGCTTCT TCGAAAGGCC CATTTTTCTC CGTGGCTGAG CGAATGCTCC TAGAATACCA CGTTTATAAT 000080
000081 AAATCATGTA GGGTGGAATT CCTGCTGGAT GTATACACCT TTCTGCATCA GAGCTCTTCA AACCCAGAAT GGTGAATAGC 000160
000161 TACCCCTGGG CTTACCCTTT TATAATTTTC AACAAACCTG CGTTTAGCCC CGGCTAGGTG CCAGCAAGTT GCTAGGGACT 000240
000241 GAGGAGGCTC TGCAGAGGAC CCGAGCTGAG GCCCTAATCC TCAAGGCCAA TGGCAGGGGT CACCGCCCAG GCACCCCCAG 000320
000321 AGAACGCGGT GTGAAGGAAA AGACACCAAA CTCGGTGTTC AAATGTGTGG GATCTATTCT AGTTCTGATT CTGACACTTG 000400
000401 CAAGTCATGC ATCCTCCGAG CCTCGGCTTT CTCACCTATA AAATCTTCAA CGTGACCTAT AAAAATCCAT AAAATCACCC 000480
000481 CTGCTTCATT GTTTCCCAGG GCTCATAGAA ACATCATACA AGGTGGAGAA GAGTACCCAA GAAGGACAAG CTTGGAATGG 000560
000561 GGCCCCCTCC CCAGGCTGGA GATCAGACAT TGTTGGAGAA GGTATCATTG CAGCCCCCTA CATAGCAGAG AGATTTGCTG 000640
000641 AGTTGCATAG TCTAGAGCTG GTTGCAATTA TTGGACAAGC AGGAAACAAA CCTCCACAGC CCATGCGAGC CACACTGCTG 000720
000721 GGTTGAGTGT ATGAGCATGT AGAATGATTG GGTCTCCAGT GCGGACAGAA GGCATGGATC GCGTGGTGCC TGTGTTGGGA 000800
000801 GGATACTAAG AGGGCGATCA CCATGCCAGG ACAAGACTAG TTGCCTGGGA TCTTCTGGGC ACGTGACTGG AGCAGAGTAC 000880
000881 CACTGGATCT CCTCACACCA GCCAGACCCA GGAAGAGAAG CTCCTTTCAC CTGCACTGTT CTCTCAGCAC CCTCCACGGA 000960
000961 GAAAGCTTCA TGTTATGCTT AGTGTACAGG AGAAATGCTC ATGGGAATCC TGTCCATTAT CACAGAGCAG GTATTAGTGG 001040
001041 GTGAATATGG AGCTGAGAAG TAATAAGTTG TAACTGGCAT AGATATCATG GGGATATTTG AAGAACGCTG TGAACACATA 001120
001121 TGCATGGGTC CATGTATTCA TGAGTGTGCA CATATGTGTA ATTATTCATA CAATTCATGG TGGATACTAC TTCGAGGGTG 001200
001201 TTCACAGACC CCAGGCAGAG AGCGCCTGGA GGGAAAATTA TCCAAGGCAG GCCCATTCAT AGTTCCAGGA CAGCCAGAAG 001280
001281 AAAGCCTCCG TTAAGCACCA GAAGTCTCCG GGGCAGGTGG GGCCAGGCAG CATGAAAGAA TTGGCCGCAA GAGTTCCAAA 001360
001361 CCCTGTCCCA ATTATGGAGG GTGACTTTTC TTTGTCCTCC TTCTCCATTC CCTTCCATAT TGCTCATGCA TCCAAAGGGA 001440
001441 GACCTGAAGA CTCTCTAGCA GGGCAAGGCC ATTTTCTTTT GGCATTTTTC TCTCCCCAGA GTCTAGCTGA TTATCAGCTT 001520
001521 AGACACACAG CAGGCTATGT GCTGTGAACA ACAGGCATCC TGGGTTATTT TACAAACTCA TGGATAGTCA TTTTGAAACC 001600
001601 ACCTTTGCAA AATTGTGACT GAAACAGTGA AAGAGAGCTA ACTTAACCAG CTCCATCTTG TTTCTAACCT CCAAGCTGTC 001680
001681 TTTGTTCATT CCTGGGCGTA GGCTGAACTA ACTTTGGGAG AAACTTAGTT TGTAGTTATA GTTTAAACAA AGACTGTGAC 001760
001761 AGCCCTTTCC CAATGCAGAC CTCCTTCTTG TCTGGGGACT AGACTAACAT TAGCCACAGG ATTAGAAATT ACGGTTTAGG 001840
001841 AGTCACGCAG CTGGAGGCTA CAAGATTCTG ACCCTCCCTA AACTGCTTCT AAGATCAGTG CTTGAGACAT GTTGCAGACC 001920
001921 CCGCACTTGC TGGATCAGCT GACGCCACAC AGATGGATAA ACTGCCTCGT CTGATCTTGT GGCCCCCACC CGGGAACTGA 002000
002001 CGAAGCGCAA GAAGACAGCT TCGACTCCCT GTGAGTTCAT CCCTGACCAA CCAGCACTCC TGGCTCACTG GCTTCCCCCT 002080
002081 ACCAAGTTAT GCTTAAAAAT TCTGCTCCCC GAATTCTCGA GGAGACTGAT TTGAGTGATA ATAAAACTCC AGTCTCCCGC 002160
002161 AAAAAAAAAA A
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