Difference between revisions of "ENST00000427391.1"
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==Annotated Information==
===Transcriptomic Nomeclature===
Please input transcriptomic nomeclature information here.
===Functio...") |
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| − | + | ''FIRRE'', through a 156 bp repeating sequence and interacting with the nuclear matrix factor hnRNPU, localized across a ~5 Mb domain on the X-chromosome and modulate the topological organization of multiple chromosomes. | |
==Annotated Information== | ==Annotated Information== | ||
| − | === | + | ===Name=== |
| − | + | ''FIRRE'', firre intergenic repeating RNA element (HGNC nomenclature) | |
| + | |||
| + | "functional intergenic repeating RNA element", LINC01200<ref name="ref1" /> | ||
| + | |||
| + | LncBook ID: [https://bigd.big.ac.cn/lncbook/transcript?transid=HSALNT0288976 HSALNT0288976] | ||
===Function=== | ===Function=== | ||
| − | + | [[File:Firre forms cis and several trans chromosomal contacts.jpg|right|thumb|300px|'''Firre forms cis and several trans chromosomal contacts'''<ref name="ref1" />]] | |
| − | = | + | Firre has important roles in both cell physiology and nuclear architecture. It may serve to interface with and modulate the topological organization of multiple chromosomes <ref name="ref1" />. |
| − | |||
===Expression=== | ===Expression=== | ||
| − | + | Firre localization across at least five distinct trans-chromosomal loci, which reside in spatial proximity to the Firre genomic locus on the X-chromosome <ref name="ref1" />. | |
| − | === | + | ===Cellular Localization=== |
| − | + | Firre is nuclear-localized and forms expression foci on both X-chromosomes prior to, and after X-chromosome inactivation <ref name="ref1" />. | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
==Labs working on this lncRNA== | ==Labs working on this lncRNA== | ||
| − | + | Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA <ref name="ref1" />. | |
==References== | ==References== | ||
| − | + | <references> | |
| − | + | <ref name="ref1"> Hacisuleyman E, Goff LA, Trapnell C, Williams A, Henao-Mejia J, Sun L, et al. Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre[J]. Nature structural & molecular biology. 2014,21(2):198-206.</ref>(1) | |
| + | </references> | ||
{{basic| | {{basic| | ||
tID = ENST00000427391.1| | tID = ENST00000427391.1| | ||
source = Gencode19| | source = Gencode19| | ||
| − | same = lnc-FRMD7-1:1| | + | same = lnc-FRMD7-1:1,''FIRRE''| |
classification = intergenic| | classification = intergenic| | ||
length = 2928 nt| | length = 2928 nt| | ||
| Line 42: | Line 41: | ||
sequence = <dnaseq>GACACGTGGTGCCTTCAGGCTCTGGGGCCTAGGACCTTTGTGGTAGCAGAGTCACTGCAGAGAACCAGACAATACCAGGTTGCTTATAAAAGGATGCCATGTGCTTGCTGGAGGTCCCAGGTGCAACCAAATTGCTTGCAGCTAGGAGGACCTTGAAGAGAAATGGGATCAGCCCGCCAAACCAAGAAGGGTTAGCACTTTTGCTAGGAGAGCTGACCACGCACAAACAGATGAGAACCAAAACCGAGTGAAGAGGATTGAAGATGAACCCACATTTTAAAAGTTCTTGTCTGCTGGAGGTGGCATTACCTGTGACCTCGCTTCACTTCTCCATACATGGCTGTTATAGCAGAAAATCCAGCTTTCTGAAGCATATTTCACGACATATGATGAGACTTATGTGATGTGAGACCTGAGAAAACTATGATAGAAAGAAGCAACTCAAGTTGCAAGGATATTCCTCATGTATCATGCAAGGATATTCCTCATATATCATGCTTTTTCTATCTTCTGCTCTTTGCCACCTGTGAGGTCCCTGAAAATGAAGGCCAATACTACCCAGATTTGAATATTCTAAGAGATTTCTCAAAAAGCTGATATTCATAATTTGAGAAGCAATCAAGAACAAACGTGTACTGAAACAGTTGGTGCAAAATCCTTATTGACCACAGATGGAATTCAGTAATTTATATTTCTTCGAAACATAGAAAAACGGAATACTGAGATCTGGTGGGGGGCCGGCGGCAGTCTGGGAGCGGCGCGCCATGTACACCATCATCAACGGGCCCAGCAAGTTGGTCGCGCAGCGCCGCACAGGTCTCACGCAGCAGCAGGTGAAGGGCCAGCTCCAGGAGCTCCTGAAAAGCCGGCAGCCCGCGCCGCCGACCTTGCAGCCCCAGCGGGCGCAGCCCTTCGCGCAGCCGCTGGGACCCTGGCCCCTGTCGAGTGCAGGGCCAAGGCTTGTGTTCAATCGTGTGAATCGCCGGCGGGACCCCTCCAAGTCCCCATCCCTCCAGGGGACCCAGGAGACCTACACACTGGCCCACAAGGAGAATGTCCGCTTTGTGTCCGAAGCCTGGCAGCAGAGACTAAGGTGTCAGTATGTTCTTCAAGCTGCTCTGCTCCTGGGCCCAAGCTATTCTCCTGCCTCAGCCTTCCAAGAAGCTGAAACTACAAGAACACAAGACTGTACCTGGCTTGCAAACACCATTGCTAATAAGAAGATATTACATGGATCCCTGAGGTCGGTCCCCAATACGACAAGACAATTTGATATCATAATAGAACACTGCAGAAACAATGCTGAGTGAAGAAGAGTAGAAATGGGAAGACTTGGTTGAGCGGAAACTGAGTTCTTGAAAAGAGGAGATGCTTGATGAGGGCATGGATCCCTGAGGTCTGCCCCAGTACTATAAGACAATTTGATGTAAGAAAACACAGCAGATATAATACTGAGTGAAGAAGAGTATAAATGAGAAGATTGGTTGTGCAGATACTGAGTTCATGAAAAGAGGAGATGATTGATGAGGCCAGGTGCGGTGACTCATGCCTGTAATCCCTGCACTTTGGGAGGCTGCGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGGAGACAGAGCATGGAAACCTAAGGTCTGTACCCAAAACTACAGGACTATTTGACATCATAATAAAACACTGCAGATATGATGCTGAGTAAGAGTAGAAATGGGAAGACTTGGTTGTGCAGTAACTGAGTTCTTGAAAAGAGGAGATGCTTGATGAGGGCATGGATCACTAAGGTCTGTTCCCAATACAAGAAGACTCTTTGACATCATAATAAAATACTGCAGATACGATGCTGAGTGAAAAAGAGTAGAAATGGGAAGACTTGGTTGTGCAGAAACTGAGTTCTTAAAGAGAGGAGATACTTTATGAGGGCTGGAGTGCACTGGAGCAATCCTGGCTGGCCAATACTGAGTTCTTGAAAACAGGAGATGCTTGATGAGGATGGGATCATCTAGTTGCAGGAAAACAAGGCTCAGGGTGCCTACTGATTCTACATTATGCTTGGTCCGGAGAGCTGCCTTGGACTCTCCAATGCAGCTGCCTCTGTTACCTTGACTCGTCTCAGATTTCATTGACCCAAGATGGGTCCTGGCACTAGGAATGTAAGACTGTCTCCATTCTTTTGGCTTGTTCCAGAGAAGCCCATGCAAGGTTCCTACTGACCATATGTTTCTTTCTTTTCTTTTGTTTTTTGAGACGGAGTTTCGCTGTTGTTGCCCAGGCTGGAGTGCAATGGCGCGATCTCCGCTCACTGCAACATCCGCCTCCCGGACTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCATGCGCCACCACGCCCGGCTAATTTTGTATTTCTAGTAGAGTTAGAGTTTCTCCATATTGGTCAGGCTGGTTTCGAACTCCTGGCCTCAGGTGATCTGCCCTCCTTGGCCTCCCAAAGCGCTGGGATTATAGGCGTGAGCCACCGCCCCCGGCCTTGACCATATGTTTTATTTCTAGCTTTGATGTCTGGGCATCGATTTCCCTCGGTTAAACTATTTGCTCAATGTTAAGGCCACTCTGTAGAAATTTGTCTGTGTAACTGAGGTGCTATGCAGGCCTGCCTGTGTGACTGTCATGCAGGCCTGTCTGTGTGATTGTCAGGGAGAATTGGTCTGCCACAATCCTTTTCTAAGCATAGCCAATAGAGGTAGTTAGGCATAATTTGTATATTACAGAAATTGCCTTACAGAGAGTAACACATTTCTATACTCTCCTTCCATAACAGACACTTAAAAAAACAAAAAAAGTAATGTATGCTTGCTGTGGACCTCATTTAAGATTGCAACAGAAGCACTTTTCAATACTATTAAACAGCTTTTTACTTTCCA</dnaseq>| | sequence = <dnaseq>GACACGTGGTGCCTTCAGGCTCTGGGGCCTAGGACCTTTGTGGTAGCAGAGTCACTGCAGAGAACCAGACAATACCAGGTTGCTTATAAAAGGATGCCATGTGCTTGCTGGAGGTCCCAGGTGCAACCAAATTGCTTGCAGCTAGGAGGACCTTGAAGAGAAATGGGATCAGCCCGCCAAACCAAGAAGGGTTAGCACTTTTGCTAGGAGAGCTGACCACGCACAAACAGATGAGAACCAAAACCGAGTGAAGAGGATTGAAGATGAACCCACATTTTAAAAGTTCTTGTCTGCTGGAGGTGGCATTACCTGTGACCTCGCTTCACTTCTCCATACATGGCTGTTATAGCAGAAAATCCAGCTTTCTGAAGCATATTTCACGACATATGATGAGACTTATGTGATGTGAGACCTGAGAAAACTATGATAGAAAGAAGCAACTCAAGTTGCAAGGATATTCCTCATGTATCATGCAAGGATATTCCTCATATATCATGCTTTTTCTATCTTCTGCTCTTTGCCACCTGTGAGGTCCCTGAAAATGAAGGCCAATACTACCCAGATTTGAATATTCTAAGAGATTTCTCAAAAAGCTGATATTCATAATTTGAGAAGCAATCAAGAACAAACGTGTACTGAAACAGTTGGTGCAAAATCCTTATTGACCACAGATGGAATTCAGTAATTTATATTTCTTCGAAACATAGAAAAACGGAATACTGAGATCTGGTGGGGGGCCGGCGGCAGTCTGGGAGCGGCGCGCCATGTACACCATCATCAACGGGCCCAGCAAGTTGGTCGCGCAGCGCCGCACAGGTCTCACGCAGCAGCAGGTGAAGGGCCAGCTCCAGGAGCTCCTGAAAAGCCGGCAGCCCGCGCCGCCGACCTTGCAGCCCCAGCGGGCGCAGCCCTTCGCGCAGCCGCTGGGACCCTGGCCCCTGTCGAGTGCAGGGCCAAGGCTTGTGTTCAATCGTGTGAATCGCCGGCGGGACCCCTCCAAGTCCCCATCCCTCCAGGGGACCCAGGAGACCTACACACTGGCCCACAAGGAGAATGTCCGCTTTGTGTCCGAAGCCTGGCAGCAGAGACTAAGGTGTCAGTATGTTCTTCAAGCTGCTCTGCTCCTGGGCCCAAGCTATTCTCCTGCCTCAGCCTTCCAAGAAGCTGAAACTACAAGAACACAAGACTGTACCTGGCTTGCAAACACCATTGCTAATAAGAAGATATTACATGGATCCCTGAGGTCGGTCCCCAATACGACAAGACAATTTGATATCATAATAGAACACTGCAGAAACAATGCTGAGTGAAGAAGAGTAGAAATGGGAAGACTTGGTTGAGCGGAAACTGAGTTCTTGAAAAGAGGAGATGCTTGATGAGGGCATGGATCCCTGAGGTCTGCCCCAGTACTATAAGACAATTTGATGTAAGAAAACACAGCAGATATAATACTGAGTGAAGAAGAGTATAAATGAGAAGATTGGTTGTGCAGATACTGAGTTCATGAAAAGAGGAGATGATTGATGAGGCCAGGTGCGGTGACTCATGCCTGTAATCCCTGCACTTTGGGAGGCTGCGGCGGGCGGATCACCTGAGGTCAGGAGTTCGAGACCAGCCTGGGAGACAGAGCATGGAAACCTAAGGTCTGTACCCAAAACTACAGGACTATTTGACATCATAATAAAACACTGCAGATATGATGCTGAGTAAGAGTAGAAATGGGAAGACTTGGTTGTGCAGTAACTGAGTTCTTGAAAAGAGGAGATGCTTGATGAGGGCATGGATCACTAAGGTCTGTTCCCAATACAAGAAGACTCTTTGACATCATAATAAAATACTGCAGATACGATGCTGAGTGAAAAAGAGTAGAAATGGGAAGACTTGGTTGTGCAGAAACTGAGTTCTTAAAGAGAGGAGATACTTTATGAGGGCTGGAGTGCACTGGAGCAATCCTGGCTGGCCAATACTGAGTTCTTGAAAACAGGAGATGCTTGATGAGGATGGGATCATCTAGTTGCAGGAAAACAAGGCTCAGGGTGCCTACTGATTCTACATTATGCTTGGTCCGGAGAGCTGCCTTGGACTCTCCAATGCAGCTGCCTCTGTTACCTTGACTCGTCTCAGATTTCATTGACCCAAGATGGGTCCTGGCACTAGGAATGTAAGACTGTCTCCATTCTTTTGGCTTGTTCCAGAGAAGCCCATGCAAGGTTCCTACTGACCATATGTTTCTTTCTTTTCTTTTGTTTTTTGAGACGGAGTTTCGCTGTTGTTGCCCAGGCTGGAGTGCAATGGCGCGATCTCCGCTCACTGCAACATCCGCCTCCCGGACTCAAGCGATTCTCCTGCCTCAGCCTCCCGAGTAGCTGGGATTACAGGCATGCGCCACCACGCCCGGCTAATTTTGTATTTCTAGTAGAGTTAGAGTTTCTCCATATTGGTCAGGCTGGTTTCGAACTCCTGGCCTCAGGTGATCTGCCCTCCTTGGCCTCCCAAAGCGCTGGGATTATAGGCGTGAGCCACCGCCCCCGGCCTTGACCATATGTTTTATTTCTAGCTTTGATGTCTGGGCATCGATTTCCCTCGGTTAAACTATTTGCTCAATGTTAAGGCCACTCTGTAGAAATTTGTCTGTGTAACTGAGGTGCTATGCAGGCCTGCCTGTGTGACTGTCATGCAGGCCTGTCTGTGTGATTGTCAGGGAGAATTGGTCTGCCACAATCCTTTTCTAAGCATAGCCAATAGAGGTAGTTAGGCATAATTTGTATATTACAGAAATTGCCTTACAGAGAGTAACACATTTCTATACTCTCCTTCCATAACAGACACTTAAAAAAACAAAAAAAGTAATGTATGCTTGCTGTGGACCTCATTTAAGATTGCAACAGAAGCACTTTTCAATACTATTAAACAGCTTTTTACTTTCCA</dnaseq>| | ||
}} | }} | ||
| − | [[Category:Intergenic]] | + | [[Category:Intergenic]][[Category:ENSG00000213468.3]][[Category:lnc-FRMD7-1]][[Category:Transcripts]] |
Latest revision as of 13:09, 11 August 2019
FIRRE, through a 156 bp repeating sequence and interacting with the nuclear matrix factor hnRNPU, localized across a ~5 Mb domain on the X-chromosome and modulate the topological organization of multiple chromosomes.
Contents
Annotated Information
Name
FIRRE, firre intergenic repeating RNA element (HGNC nomenclature)
"functional intergenic repeating RNA element", LINC01200[1]
LncBook ID: HSALNT0288976
Function
Firre forms cis and several trans chromosomal contacts[1]
Firre has important roles in both cell physiology and nuclear architecture. It may serve to interface with and modulate the topological organization of multiple chromosomes [1].
Expression
Firre localization across at least five distinct trans-chromosomal loci, which reside in spatial proximity to the Firre genomic locus on the X-chromosome [1].
Cellular Localization
Firre is nuclear-localized and forms expression foci on both X-chromosomes prior to, and after X-chromosome inactivation [1].
Labs working on this lncRNA
Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts, USA [1].
References
Basic Information
| Transcript ID |
ENST00000427391.1 |
| Source |
Gencode19 |
| Same with |
lnc-FRMD7-1:1,FIRRE |
| Classification |
intergenic |
| Length |
2928 nt |
| Genomic location |
chrX-:130836678..130964671 |
| Exon number |
13 |
| Exons |
130836678..130837546,130843526..130843584,130845679..130845748,130883334..130883486,130889626..130889774,130890639..130890737,130902577..130902724,130917915..130918067,130928352..130928494,130929837..130930359,130939000..130939065,130959250..130959393,130964320..130964671 |
| Genome context |
|
| Sequence |
000001 GACACGTGGT GCCTTCAGGC TCTGGGGCCT AGGACCTTTG TGGTAGCAGA GTCACTGCAG AGAACCAGAC AATACCAGGT 000080
000081 TGCTTATAAA AGGATGCCAT GTGCTTGCTG GAGGTCCCAG GTGCAACCAA ATTGCTTGCA GCTAGGAGGA CCTTGAAGAG 000160 000161 AAATGGGATC AGCCCGCCAA ACCAAGAAGG GTTAGCACTT TTGCTAGGAG AGCTGACCAC GCACAAACAG ATGAGAACCA 000240 000241 AAACCGAGTG AAGAGGATTG AAGATGAACC CACATTTTAA AAGTTCTTGT CTGCTGGAGG TGGCATTACC TGTGACCTCG 000320 000321 CTTCACTTCT CCATACATGG CTGTTATAGC AGAAAATCCA GCTTTCTGAA GCATATTTCA CGACATATGA TGAGACTTAT 000400 000401 GTGATGTGAG ACCTGAGAAA ACTATGATAG AAAGAAGCAA CTCAAGTTGC AAGGATATTC CTCATGTATC ATGCAAGGAT 000480 000481 ATTCCTCATA TATCATGCTT TTTCTATCTT CTGCTCTTTG CCACCTGTGA GGTCCCTGAA AATGAAGGCC AATACTACCC 000560 000561 AGATTTGAAT ATTCTAAGAG ATTTCTCAAA AAGCTGATAT TCATAATTTG AGAAGCAATC AAGAACAAAC GTGTACTGAA 000640 000641 ACAGTTGGTG CAAAATCCTT ATTGACCACA GATGGAATTC AGTAATTTAT ATTTCTTCGA AACATAGAAA AACGGAATAC 000720 000721 TGAGATCTGG TGGGGGGCCG GCGGCAGTCT GGGAGCGGCG CGCCATGTAC ACCATCATCA ACGGGCCCAG CAAGTTGGTC 000800 000801 GCGCAGCGCC GCACAGGTCT CACGCAGCAG CAGGTGAAGG GCCAGCTCCA GGAGCTCCTG AAAAGCCGGC AGCCCGCGCC 000880 000881 GCCGACCTTG CAGCCCCAGC GGGCGCAGCC CTTCGCGCAG CCGCTGGGAC CCTGGCCCCT GTCGAGTGCA GGGCCAAGGC 000960 000961 TTGTGTTCAA TCGTGTGAAT CGCCGGCGGG ACCCCTCCAA GTCCCCATCC CTCCAGGGGA CCCAGGAGAC CTACACACTG 001040 001041 GCCCACAAGG AGAATGTCCG CTTTGTGTCC GAAGCCTGGC AGCAGAGACT AAGGTGTCAG TATGTTCTTC AAGCTGCTCT 001120 001121 GCTCCTGGGC CCAAGCTATT CTCCTGCCTC AGCCTTCCAA GAAGCTGAAA CTACAAGAAC ACAAGACTGT ACCTGGCTTG 001200 001201 CAAACACCAT TGCTAATAAG AAGATATTAC ATGGATCCCT GAGGTCGGTC CCCAATACGA CAAGACAATT TGATATCATA 001280 001281 ATAGAACACT GCAGAAACAA TGCTGAGTGA AGAAGAGTAG AAATGGGAAG ACTTGGTTGA GCGGAAACTG AGTTCTTGAA 001360 001361 AAGAGGAGAT GCTTGATGAG GGCATGGATC CCTGAGGTCT GCCCCAGTAC TATAAGACAA TTTGATGTAA GAAAACACAG 001440 001441 CAGATATAAT ACTGAGTGAA GAAGAGTATA AATGAGAAGA TTGGTTGTGC AGATACTGAG TTCATGAAAA GAGGAGATGA 001520 001521 TTGATGAGGC CAGGTGCGGT GACTCATGCC TGTAATCCCT GCACTTTGGG AGGCTGCGGC GGGCGGATCA CCTGAGGTCA 001600 001601 GGAGTTCGAG ACCAGCCTGG GAGACAGAGC ATGGAAACCT AAGGTCTGTA CCCAAAACTA CAGGACTATT TGACATCATA 001680 001681 ATAAAACACT GCAGATATGA TGCTGAGTAA GAGTAGAAAT GGGAAGACTT GGTTGTGCAG TAACTGAGTT CTTGAAAAGA 001760 001761 GGAGATGCTT GATGAGGGCA TGGATCACTA AGGTCTGTTC CCAATACAAG AAGACTCTTT GACATCATAA TAAAATACTG 001840 001841 CAGATACGAT GCTGAGTGAA AAAGAGTAGA AATGGGAAGA CTTGGTTGTG CAGAAACTGA GTTCTTAAAG AGAGGAGATA 001920 001921 CTTTATGAGG GCTGGAGTGC ACTGGAGCAA TCCTGGCTGG CCAATACTGA GTTCTTGAAA ACAGGAGATG CTTGATGAGG 002000 002001 ATGGGATCAT CTAGTTGCAG GAAAACAAGG CTCAGGGTGC CTACTGATTC TACATTATGC TTGGTCCGGA GAGCTGCCTT 002080 002081 GGACTCTCCA ATGCAGCTGC CTCTGTTACC TTGACTCGTC TCAGATTTCA TTGACCCAAG ATGGGTCCTG GCACTAGGAA 002160 002161 TGTAAGACTG TCTCCATTCT TTTGGCTTGT TCCAGAGAAG CCCATGCAAG GTTCCTACTG ACCATATGTT TCTTTCTTTT 002240 002241 CTTTTGTTTT TTGAGACGGA GTTTCGCTGT TGTTGCCCAG GCTGGAGTGC AATGGCGCGA TCTCCGCTCA CTGCAACATC 002320 002321 CGCCTCCCGG ACTCAAGCGA TTCTCCTGCC TCAGCCTCCC GAGTAGCTGG GATTACAGGC ATGCGCCACC ACGCCCGGCT 002400 002401 AATTTTGTAT TTCTAGTAGA GTTAGAGTTT CTCCATATTG GTCAGGCTGG TTTCGAACTC CTGGCCTCAG GTGATCTGCC 002480 002481 CTCCTTGGCC TCCCAAAGCG CTGGGATTAT AGGCGTGAGC CACCGCCCCC GGCCTTGACC ATATGTTTTA TTTCTAGCTT 002560 002561 TGATGTCTGG GCATCGATTT CCCTCGGTTA AACTATTTGC TCAATGTTAA GGCCACTCTG TAGAAATTTG TCTGTGTAAC 002640 002641 TGAGGTGCTA TGCAGGCCTG CCTGTGTGAC TGTCATGCAG GCCTGTCTGT GTGATTGTCA GGGAGAATTG GTCTGCCACA 002720 002721 ATCCTTTTCT AAGCATAGCC AATAGAGGTA GTTAGGCATA ATTTGTATAT TACAGAAATT GCCTTACAGA GAGTAACACA 002800 002801 TTTCTATACT CTCCTTCCAT AACAGACACT TAAAAAAACA AAAAAAGTAA TGTATGCTTG CTGTGGACCT CATTTAAGAT 002880 002881 TGCAACAGAA GCACTTTTCA ATACTATTAA ACAGCTTTTT ACTTTCCA |
