ENST00000499008.3

From LncRNAWiki
Jump to: navigation, search

BDNF-AS which is approximately 200 kb downstream from the BDNF promoter and is located on the positive strand of chromosome-11,represses BDNF sense RNA transcription.

Contents

Annotated Information

Name

BDNF-AS:BDNF antisense RNA 1 (HGNC nomenclature)

BDNF-AS1, BT2A, BT2B, BT2C, BT2D, NCRNA00049, "non-protein coding RNA 49" [1]

Characteristics

Genomic organization of the human BDNF locus showing[1]

BDNF-AS is approximately 200 kb downstream from the BDNF promoter and it is located on the positive strand of chromosome-11. Transcription from this site gives rise to 16–25 splice variant long ncRNAs with 6–8 exons8. Exon-5 of BDNF-AS, which contain 225-nucleotides of full complementarity to BDNF mRNA (overlapping) and exon-4 (non-overlapping) are common between all these variants . [1]

It belongs to the category of "Antisense" in lncRNA classification[1].

Function

Antisense-mediated regulation of sense mRNA and protein[1]

BDNF-AS tonically represses BDNF sense RNA transcription by altering chromatin structure at the BDNF locus, which in turn reduces endogenous BDNF protein and function[1].

BDNF-AS represses chromatin by recruiting Polycomb Repressive Complex 2 (PRC2) to the BDNF promoter region[1].

Expression

BDNF mRNA levels are generally 10–100 fold higher than BDNF-AS transcript, except in testis, kidney and heart, which contain equal or higher levels of BDNF-AS. Both transcripts are expressed in brain, muscle and embryonic tissues. BDNF mRNA levels were relatively low in all post-natal tissues examined except in brain, bladder, heart and skeletal muscle.In rhesus monkey and mouse tissues, both transcripts are co-expressed in many tissues, which suggest BDNF-AS potential for regulation of BDNF mRNA[1].

Primer name Sequence Application
Human BDNF-AS siRNA-1 GGCTCACCAGTTGTTTGTT siRNA[1]
Scramble siRNA-1 AGCTCGCCAGTCGTTTATT Scrambled control[1]
Human BDNF-AS siRNA-2 GCAATGTATCTTAGGCTCA siRNA[1]
Human BDNF-AS siRNA-3 GCTAATCTTACAACAGCAC siRNA[1]
Scramble siRNA-3 ACTAAGCTTACAGCAGCGC Scrambled control[1]
Human BDNF-AS siRNA-4 TCCCTACAAACATGTCAT siRNA[1]
Scramble siRNA-4 GCCCGACAAACAAGTCAAT Scrambled control[1]
Control siRNA CCUCUCCACGCGCAGUACATT Non-targeting control[1]
Human BDNF-AS primer-F AGTGGCTAATATTACAACAGCACAA Real time PCR[1]
Human BDNF-AS primer-R CTCAGTAGTCAAGTGCCTTTGGA Real time PCR[1]
Human BDNF-AS probe CCTCCTCTTCTCTTTCTGGTTAG Real time PCR[1]

Diseases

  • Alzheimer’s disease, Parkinson’s disease and Fragile X syndrome[1].

Labs working on this lncRNA

  • Department of Psychiatry and Behavioral Sciences and Center for Therapeutic Innovation [1].

References

  1. 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 1.14 1.15 1.16 1.17 1.18 1.19 1.20 Modarresi F, Faghihi MA, Lopez-Toledano MA, Fatemi RP, Magistri M, Brothers SP, et al. Inhibition of natural antisense transcripts in vivo results in gene-specific transcriptional upregulation[J]. Nature biotechnology. 2012,30(5):453-9

Basic Information

Transcript ID

ENST00000499008.3

Source

Gencode19

Same with

lnc-METTL15-4:4,NONHSAT018493,BDNF-AS

Classification

intergenic

Length

2324 nt

Genomic location

chr11+:27528399..27699354

Exon number

8

Exons

27528399..27528445,27561567..27561663,27605816..27605884,27661392..27661552,27679788..27680009,27680718..27680775,27696844..27697687,27698529..27699354

Genome context

Sequence
000001 ATCGCGAGAT CAGGAAGGTG GCCGAGTGTG TCGCCGCGGC CATCAGGCAC TTCTCCTTCC TGCCCTTGTA TGAAGAAGGA 000080
000081 TGTGTTTGCT TCCCCTTGTG CCATGATTGT AAATTTCCTG AGGCCTCCTC AGCCCTGCAG AACTGGGGTT ATAGCCATGT 000160
000161 GACTGATCTT CGTCCAAGAA TATGTAAAGA AAAAGTGTTG AGTTGGCTTT TAGGGCTAGA GCAATGTATC TTAGGCTCAC 000240
000241 TTAAGGAAGC TGTAGAGATG AGCCCAAGGA GGGAAACCAG AAGAGCCCCC CAGGCTCACC AGTTGTTTGT TGGCTCCCTA 000320
000321 CAAACATGTC ATTCAAGTGG CTAATCTTAC AACAGCACAA ATTCATCTAA CCAGAAAGAG AAGAGGAGGC TCCAAAGGCA 000400
000401 CTTGACTACT GAGCATCACC CTGGACGTGT ACAAGTCTGC GTCCTTATTG TTTTCTTCAT TGGGCCGAAC TTTCTGGTCC 000480
000481 TCATCCAACA GCTCTTCTAT CACGTGTTCG AAAGTGTCAG CCAATGATGT CAAGCCTCTT GAACCTGCCT TGGGCCCATT 000560
000561 CACGCTCTCC AGAGTCCCAT GGGTCCGCAC ACCTGGAGAT ACTCTATTAT AGCAAAGAAG AAAGATAATT TCATTGAGCC 000640
000641 ATCCTGTTTT ACAGTATTGA ATTATTACCA CAAGGTACCA ACCATATATG CATACTTAAT AGGGTATTTT GTCAAAACTA 000720
000721 TGCATGAAGG TCATTTGTTT GAGATGTCAG AACATTTTCC CGTGAGAAGA TCTCATTGGG CATTGAAACA GAACCACATG 000800
000801 CTCTTCAGAC CAGCAACCGC GACTACCAAA TACTCCTCTG TCAACTCTAC TTGAGTAAGA ACGCTTTCAA TTAAGGCCTA 000880
000881 AGTGTCAACA TGCCTTTAAA AAAAATCGTG GTGACACAAA ATCTTTCTTT TTAGCACCCA ACAGAATCCC TTCAAAGCCT 000960
000961 CGTGGTCTGA CACCCTATGC TACGTGACTT GTGACCCATC CATTTGTCAT GTTCTTCGGG AATGTGGCTA AGGGGCTAAG 001040
001041 ATGTGACTTG AAAAGAAAGG TAGAACAAGA TCATCTCAAA TTTATTATCA AGGAATAGTT CAGAAAACGA CTTCAGACCA 001120
001121 CAGAGACAGC AGAACAGATG GTCCGGCATG GATAGAGCAT CAGACACTCA CAGACTGTGC CAACAAGAGC CATCGAGTCA 001200
001201 AAACAGCCAA AGGAAGGAGG GTCATGGAAT GGGTTCTCTC ACACCAAACT GATGCCCAGA GGCCCTCAGC ATGAATAACA 001280
001281 AAGGCAACCA GACCCACAAG CCATACTGAG TGGATACAAA ACCTATACCT AGGCTGACAT CCCAAATGTG TGTGGCAAGT 001360
001361 TAGATGATGA TGGCACAAAA GACAGAACAC CTTGCTTCTG GCCATTGTCA GCTCTTGGAA GAGAGCACAC TTTTAGAGGA 001440
001441 GCAGCTGCAA GGAGCCTGAG AACAAAACTG GAAATGTCTG TTATGAAAGC CTTCACAGGA AATTCTGCAA GTGGCAACGT 001520
001521 GGGTCCATTC CGTGTGTGTC ACTAGAGCTG GCGCAAGCCC ATGGCCATGG TGAGGCAGCG TTTCCACTGG AACTAATCTG 001600
001601 ATACCTGCAC CAGCTCTTGC AACTGTGCAG TGTTCCCACT GCAAACTACG GATGGGGTAA AAGACTGCTC ACCTCCTATT 001680
001681 TCTCATCTAA TCTCACACAC TCTGTTTGAT GAGGCTATGG AGAAACAGGT CTTCTCATAC ACTAAAGGTG GGAGTACAAA 001760
001761 CAATTCAAGC CCTGTGCAGG ACAATTAGGC AATACCTATC AAAATTATAC ATGATTTTTC CTGCTGACCC AGCAATTCCA 001840
001841 CTTCTGGGAA TAATTGACAG ATATAGGTGC ATATGTACAA AATGATGGAA AGCTCTCTGG TATATATTAG TAAGTGATAA 001920
001921 AACAAGGTGT AAAATAGTGT ATATATGGCT ACTACCTTTT GTTTTAAAAA TGGGGGAAAA TGGTGGAGCT TGCGGTGAGC 002000
002001 CGAGATCGTG CCACTGCACT CCAGCCTGGG CGACAGAGCG AGACTCCGTC TCAAAAAAAA AACAGGGTGG GGTGGGGGGG 002080
002081 AAATAATAGT ACATACTCAT ATTTACCTGT ATCTATATAA AACACACTAT CAAGGATTCA CAAGAAACTA ATACAAATGA 002160
002161 TCACCTTATA GATGGTATGT ATTGGGGGAT ACTGAGGTGA GCAGGGTATA AGTGGGGCAA GACTTTTCAG TGTAAACTTC 002240
002241 TTTTAAATTT TATTTTGATT TTTGAATAAT GTAAATTAAC TGTCAAATAA TTAAATTAAA AATAACCAAT TTATTAACAA 002320
002321 AACA
[back to top]
Personal tools
Namespaces

Variants
Actions
Navigation
About
ScienceWikis
Toolbox