Difference between revisions of "ENST00000499008.3"
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===Characteristics=== | ===Characteristics=== | ||
| − | [[File:Genomic organization of the human BDNF locus showing.jpg|right|thumb| | + | [[File:Genomic organization of the human BDNF locus showing.jpg|right|thumb|800px'''Genomic organization of the human BDNF locus showing'''<ref name="ref1" />]] |
''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 . <ref name="ref1" /> | ''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 . <ref name="ref1" /> | ||
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| − | ===Diseases== | + | ===Diseases=== |
* Alzheimer’s disease, Parkinson’s disease and Fragile X syndrome<ref name="ref1" />. | * Alzheimer’s disease, Parkinson’s disease and Fragile X syndrome<ref name="ref1" />. | ||
| − | ==Labs working on this lncRNA== | + | ===Labs working on this lncRNA=== |
* Department of Psychiatry and Behavioral Sciences and Center for Therapeutic Innovation <ref name="ref1" />. | * Department of Psychiatry and Behavioral Sciences and Center for Therapeutic Innovation <ref name="ref1" />. | ||
| − | ==References== | + | ===References=== |
<references> | <references> | ||
<ref name="ref1"> 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 | <ref name="ref1"> 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 | ||
Revision as of 05:17, 9 April 2015
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
Transcriptomic Nomenclature
BDNF-AS:BDNF antisense RNA 1 (HGNC nomenclature)
BDNF-AS1, BT2A, BT2B, BT2C, BT2D, NCRNA00049, "non-protein coding RNA 49" [1]
Characteristics
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
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
- ↑ 1.00 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 |
