ENST00000427391.1

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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.

Contents

Annotated Information

Name

FIRRE, firre intergenic repeating RNA element (HGNC nomenclature)

"functional intergenic repeating RNA element", LINC01200[1]

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

  1. 1.0 1.1 1.2 1.3 1.4 1.5 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.

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
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