NONHSAT119676

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HOXA-AS2, which is located between the HOXA3 and HOXA4 genes in the HOXA cluster, is expressed in both human peripheral blood PMN and in the human promyelocytic leukemia cell line NB4 and plays important roles in the mediation of inflammatory disorders, where apoptosis plays a major role in the resolution of inflammation and prevention of tissue damage.

Annotated Information

Name

HOXA-AS2: HOXA cluster antisense RNA 2

HOXA3as: HOXA cluster antisense RNA 2 (non-protein coding)

Characteristics

HOXA cluster antisense RNA 2 (HOXA-AS2) is a long non-coding RNA located between the HOXA3 and HOXA4 genes in the HOXA cluster. [1]

Function

Effect of HOXA-AS2 knockdown on NB4 cell proliferation. [1].


HOXA-AS2 functions as an apoptosis repressor in ATRA-treated NB4 cells, through mechanisms mediated in part by TRAIL.[1]

Expression

Its transcript is expressed in NB4 promyelocytic leukemia cells and human peripheral blood neutrophils, and expression is increased in NB4 cells treated with all trans retinoic acid (ATRA). [1]

Primer Forward primer Reverse primer
RT-PCR 5'-AACCCATCTTTGCCTTCTGC-3' 5'-CGGAGGAGTTTGGAGTTGG-3'[1]
Knockdown HOXA-AS2 shRNA A acacaccgttagccaatattt [1]
HOXA-AS2 shRNA B ctgttggcagattagatatat [1]
HOXA-AS2 shRNA C ttgtcccattacttaaatcta [1]

Transcriptomic Nomeclature

Please input transcriptomic nomeclature information here.

Regulation

Please input regulation information here.


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Labs working on this lncRNA

  • Department of Pediatrics, University of Massachusetts Medical School, Worcester, MA 01655, USA. [1]

References

  1. 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 Zhao H, Zhang X, Frazao JB, Condino-Neto A, Newburger PE. HOX antisense lincRNA HOXA-AS2 is an apoptosis repressor in all trans retinoic acid treated NB4 promyelocytic leukemia cells[J]. Journal of cellular biochemistry. 2013,114(10):2375-83.

Basic Information

Transcript ID

NONHSAT119676

Source

NONCODE4.0

Same with

,

Classification

antisense

Length

2074 nt

Genomic location

chr7+:27161536..27168379

Exon number

4

Exons

27161536..27161645,27162086..27162285,27163079..27164229,27167819..27168379

Genome context

Sequence
000001 GGAAAAGGAA ACGCCAAGAC ATAGAAAACC ACGCTTTTCC CGTAGGAAGA ACCGATGATG AGCCCTGATG AAAGAAGGAA 000080
000081 GAAGACCCGC TGTCTGCGAA GGCCTAAAGG CCGCGGTTGC CAGGAACCGT GGAGGGCCAA CTCCTCCCAA CCGCCCTGGT 000160
000161 GCAAAGTCCC ACGCGGCGAA GAGTTTTGGA GCAGCGCTTA CCTAGAAAGA TGTTTAAATT CTGAACCAGG AATTGTCTCC 000240
000241 AACTCCAGGC GCTCAGGGAA TCGCCTTTTC CGGTGTCCAG GCGCTCTGCA GACAAATAAA CAGCAGAAGC AAATGGTCAC 000320
000321 CGAGCCGGCA GTCAGCTTTC TGGGAGTGGG AGATGATGGG GAAAGAGGAA AGAATCGTCC GCTCGCCGGA CCCTGGCTTG 000400
000401 GAGAAGTTCT GCGCTCCGCT GGGACTCTGC GGGCCCTTTG CGTCTACAGA CCTATCCCTG CCCCGACTAC CCCTTCACTC 000480
000481 AGACCCAGGT AACCTCTTAC CCCAGCCTGC CCCAAACCAG CCCTCCGCTG TCTGTCTGCC TTCACGCAAT TCTGTAGATA 000560
000561 GCGCTAAGAG GGGATATCAA ATAGCTGAGG AGTCCCCTGA CCCCTGGCTT CGGAGCCCCC TAGCACGTGG AACAAGTGGC 000640
000641 CGCACACCGG TAGCTGCGCT CTGCCACAGT TCGACCCGTA GCCCCCACAA ACCAAAGGAA AAGGACCCAG GATCCACGCT 000720
000721 GCGCGCTGCG CCCCCTTTCT CTTGTTCAAA CTTGCTTTCT GTGTCCCCAA AGGGAGTGCC CCCTGGTCTT GGGGCTCCTG 000800
000801 GCATGACCAT GAGCAAGGTG GACTCAGCCA TCCTGCACTT TGCCTCTCAA TTTCATTCCA GAAAGATCCG CTATGCCGCC 000880
000881 ACCCACCACT CCCCTGCGTG ACACTTAGGA GTATGTAATT ATTATGGTTA TTATTTTTGC TGTTTCCTTA TCTCCAAGTC 000960
000961 TAATATTCAT GGCTGCTGTA CCCCATAAAT CGTTCAGACT AATGAGTCAC AGAGAGATGC TGCCCAGGTC TCTCACTTTA 001040
001041 CAATGGCTGC CGCCGCCGCC GTGGCCTCTC TCTCCGCGTT TTTGGCGCTC GCTTGCTCCC TCGCTCGCCC GGCGCGGGTG 001120
001121 ATTTATGAAC GCCGGGAAAA TTGAACAAAG CCGCGCGCCC GTCCTGTGGT ATCTCTGCAG CCTTCCCCAG CGTGAATCAG 001200
001201 AACATTACCA ACTGTCTGCG CATCCGTCCC ACTTCATCAC CAAAGCCAGG ATGTGACCGC AGAAAACCCA AGCCCGAACT 001280
001281 CACGTTTCCC CGGACGCGGC GCGCTCCCTG GACTCGCAGA AACCCTGCGG AAAAGGCCCC AAGATCTGGT GAGGGCCTGC 001360
001361 CAGCTCCGTC CTCCCTGCCG AGGGCTCTCT CCTGCCTTCC TGAAGGAGTT AAAAGCCTTT GGAGATAAAT CTGAGGGTGT 001440
001441 GTGTTTTTAA AAATCAAATG GGAAGGACAC GTTTCTATGC CTTACAGAGA CTTGAATCCT GAAAGCCTGG CCAAGTTTGG 001520
001521 GAAGAAGAGG AGCCCTCTCA GAGCTCAAGA GCCTTCCTAC TCTTTGGAAC TTTTCCACAG TAGGCCAAGC TTGACAAGAG 001600
001601 TTCAGCTCAA GTTGAACATA CATACACACA CTCTCACACA CAAATTATGT GAGCCGTCAG AATCCAAGTG AATCCATCTC 001680
001681 AAGCTATCTA CAAGGTTTTT ACATGCAAGG TCAAGTATCT CAATCCAGAG GACTTTTGTT TTCTTAATGA AAAGCTTAGA 001760
001761 AAACACATGA ATCTTAGATT TTTAATGTTT TTTAAATGGA GTTTATTCTT AGCACATGGC TTTCTATGTA GCCACATCAC 001840
001841 AATTTGTACA GTTCCACATA AGTCTAAATG CACTCCCCTC TCCCCAAAGA CCGTGCCCCA GAAGGTGACA ACAGTATCTC 001920
001921 TGTAACAGTG TCTTAAATAA ATGCAAGTAA GAAAAACTAA CATGTCACAC CTACCATCAA GGTCTACACA TCTTAAGAAT 002000
002001 TAAATAATCT TGTGAGGTCC AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAAAAAAAA AAAA
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Predicted Small Protein

Name NONHSAT119676_smProtein_923:1120
Length 66
Molecular weight 7479.9524
Aromaticity 0.107692307692
Instability index 87.5123076923
Isoelectric point 12.3991088867
Runs 12
Runs residual 0.0343269230769
Runs probability 0.0216760878526
Amino acid sequence MVIIFAVSLSPSLIFMAAVPHKSFRLMSHREMLPRSLTLQWLPPPPWPLSPRFWRSLAPS
LARRG
Secondary structure LEEEEEELLLHHHHEEEELLLLLEEELLHHHLLLLLLLLLLLLLLLLLLLHHHHHHHHHH
HHLLL
PRMN HHHHHHHHHHHHHHHHHHLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL
LLLLL
PiMo i???????????????????????????????????????????????????????????
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