chr24_2

cmsearch-Rfam

Family :

HOXA11-AS1_6

Id:

RF02142

Type:

Gene; lncRNA;

Taxonomy:

Eukaryota;

Ontology:

GO:0010629 negative regulation of gene expression

Description:

not description

Score:

19.8

E-value:

0.0076

From sequence:

702234

To sequence:

702127

Alignments:

                 ::::::::::::::::::::::::::::::::::::::::::::::::::..:::..::::::::::::::::::::::::::::::::::::::: CS
  RF02142     44 GAgGCCAAAAAUGUUUuGGAGGAAGAAAAACAAAGGCAGGAAGUGGCgGC..gGc..CUGACGGUGCGUGUGUGUCUgcGgaGAAGGGAGGGAGcc 135   
                 GA   CA AAA G      AGGA GAAAAACA  GG AG  AGUGGC  C   G   CUGAC   GC UGUGUGU Ug+Gg G  GGG GGG    
    chr24 702234 GAAUACACAAACGAGC-UAAGGAUGAAAAACACUGGAAG--AGUGGCACCacCGUcuCUGACA-CGCAUGUGUGUGUGUGGGGGGGGGGGGGGAGG 702143
                 4444455566665555.468999*********9998887..5666655441134312567776.45566666666666666666655555555555 PP

                 :::::::::::::::: CS
  RF02142    136 guUuCAaUCUCuuCUU 151   
                 g+Uu  aU  C uCUU
    chr24 702142 GGUUGUAUGGCAUCUU 702127
                 5555555655655533 PP



Internal HMM-only pipeline statistics summary: (run for model(s) with zero basepairs)
--------------------------------------------------------------------------------------
Query model(s):                                          1  (179 consensus positions)
Target sequences:                                       34  (57702516 residues searched)
Windows passing local HMM SSV      filter:           25862  (0.1952); expected (0.02)
Windows passing local HMM MSV bias filter:           22295  (0.1693); expected (0.02)
Windows passing local HMM Viterbi  filter:            1952  (0.01613); expected (0.001)
Windows passing local HMM Forward  filter:            1240  (0.01094); expected (1e-05)
Total HMM hits reported:                                 8  (1.506e-05)

# CPU time: 9.99u 0.01s 00:00:10.00 Elapsed: 00:00:02.50
//

RNAfold
>chr24_2
GGCUGCCCCAUGGCACGGAUGCGGACUCCCCAACAAAGAUGCCAUACAAC
CCCUCCCCCCCCCCCCCCACACACACACAUGCGUGUCAGAGACGGUGGUG
CCACUCUUCCAGUGUUUUUCAUCCUUAGCUCGUUUGUGUAUUCGUGUGCU
UGUUGGGUGAACGGCGGACUUGACCCGCC
..((((.((.......))..))))..((((((((((...((.....)).....................((((((((((.(((.((.(((((((.(((..........))).)))))))........)).))).)))))....))))).)))))))).))..(((((.......))))) (-43.80)

Length sequence

: 179

Length match:

106