ENST00000427391.1

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

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

↑ ^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 TC

[ref1-1] 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.

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