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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtgtgatgatttgaatctagaccttaccgatactgacactcatattgttcttacagGCAACTGCTAGTTTTCCACCACAACTATTCCAGCCATCAAGTGGGATTCTCATGACCAATGATACGACCGAGAACAATCCGGAAGAAGCTGTGCCTTGCA

Basic information

species Selaginella moellendorffii
transcript EFJ37833
intron # 19
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|169031531|gb|FE438996.1|FE438996
EST:     CTAGTGCAGTTCACAAGGTTTGGAAATGGTCTCGCAATCCACTTGGAAAA                         GCAACTGCTAGTTTTCCACCACAACTATTCCAGCCATCAAGTGGGATTCTC
genomic: CTAGTGCAGTTCACAAGGTTTGGAAATGGTCTCGCAATCCACTTGGAAAAgtatgtgtga ... gttcttacagGCAACTGCTAGTTTTCCACCACAACTATTCCAGCCATCAAGTGGGATTCTC
EST: gi|169048259|gb|FE456246.1|FE456246
EST:     CTAGTGCAGTTCACAAGGTTTGGAAATGGTCTCGCAATCCACTTGGAAAA                         GCGACTGCTAGTTTTCCACCACAACTATTCCAGCCATCAAGTGGGATTCTC
genomic: CTAGTGCAGTTCACAAGGTTTGGAAATGGTCTCGCAATCCACTTGGAAAAgtatgtgtga ... gttcttacagGCAACTGCTAGTTTTCCACCACAACTATTCCAGCCATCAAGTGGGATTCTC
EST: gi|169026734|gb|FE436308.1|FE436308
EST:     CTAGTGCAGTTCACAAGGTTTGGAAATGGTCTCGCAATCCACTTGGAAAA                         GCAACTGCTAGTTTTCCACCACAACTATTCCAGCCATCAAGTGGGATTCTC
genomic: CTAGTGCAGTTCACAAGGTTTGGAAATGGTCTCGCAATCCACTTGGAAAAgtatgtgtga ... gttcttacagGCAACTGCTAGTTTTCCACCACAACTATTCCAGCCATCAAGTGGGATTCTC
EST: gi|169110734|gb|FE514183.1|FE514183
EST:     CTAGTGCAGTTCACAAGGTTTGGAAATGGTCTCGCAATCCACTTGGAAAA                         GCGACTGCTAGTTTTCCACCACAACTATTCCAGCCATCAAGTGGGATTCTC
genomic: CTAGTGCAGTTCACAAGGTTTGGAAATGGTCTCGCAATCCACTTGGAAAAgtatgtgtga ... gttcttacagGCAACTGCTAGTTTTCCACCACAACTATTCCAGCCATCAAGTGGGATTCTC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 34 (upstream exon), 30 (downstream exon)
Score: 6

ATCAAGACTTATCTTCACAAACAATGGTCTGGGCTTATTAGCGCTCGCTTCTAGTGCAGTTCACAAGGTTTGGAAATGGTCTCGCAATCCACTTGGAAAAgtatgtgtga ... gttcttacagGCAACTGCTAGTTTTCCACCACAACTATTCCAGCCATCAAGTGGGATTCTCATGACCAATGATACGACCGAGAACAATCCGGAAGAAGCTGTGCCTTGCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgatgatttgaatctagaccttaccgatactgacactcatattgttcttacagGCAACTGCTAGTTTTCCACCACAACTATTCCAGCCATCAAGTGGGATTCTCATGACCAATGATACGACCGAGAACAATCCGGAAGAAGCTGTGCCTTGCA
                             tactgac  putative branch site (score: 6)
                                           ttgttctt  putative PPT
       atttgaat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtgtgatgatttgaatctagaccttaccgatactgacactcatattgttcttacagGCAACTGCTAGTTTTCCACCACAACTATTCCAGCCATCAAGTGGGATTCTCATGACCAATGATACGACCGAGAACAATCCGGAAGAAGCTGTGCCTTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG