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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatcttacaaatctattaaagctgtggctcatgcatgacatgcttttcagGTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGATCGATTACTCCAAGGCAAACTCTCCCCTGCAAAGAGATCTCGAAGCTG

Basic information

species Selaginella moellendorffii
transcript EFJ10940
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ10940 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: LOC_Os08g23810.2 (Oryza sativa), 3'ss of exon 11
---------------------------------------------gtaaaatcttacaaatctattaaagctgtggctcatgcatgacatgc-ttttcagGTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGATCGATTACTCCAAGGCAAACTCTCCCCTGCAAAGAGATCTCGAAGCTG
                                              |||     ||  |||   |   || |    || ||  || | ||    |   |||||| |||  |||| |||||||||||||||| |||||||||||||||||||| || |||||  | |  ||  | ||  |||| | ||| ||    || |
atttcccttggatatgatttgcataattatttaggatctcttactttaacgatgtaggaataattgtgagttcattctgatttattaaatttactcatagGTCCTTTGGGAAGCCGAGCTGCCAAGGCAATTGGATTCATTGAGAAGATGATAGAATACTCTTATGTTAATGCACCGTTGCAGAAAGAACTGTTGGCAG

upper sequence: EFJ10940 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GRMZM2G070422_T03 (Zea mays), 3'ss of exon 10
---------------------------------------------gtaaaatcttacaaat---ctatta----aagctgtggc--tcatgcatgacatgc-ttttcagGTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGATCGATTACTCCAAGGCAAACTCTCCCCTGCAAAGAGATCTCGAAGCTG
                                             ||| | | ||     |   |||||     | ||  || |  | |  |   || ||    |  ||| ||  |    ||| ||||||| |||||||| ||||| |||||||||||||| || |||||  | |  ||  | ||  |||| |  || ||    ||||
gtacttttatcacgtaatactgttgaagtaaaaggaatattagcagtatattttttttggtgagctattcctctatgccttgacaattaacctacacctgtacctatagGCCCTCTTGGGAGCCGAGCTGCTAAGGCAATTGGATTTATTGAGAAGATGATAGAGTACTCATATGTTAATGCACCATTGCAGAAGGAGCTGTTGGCTG
















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|169109266|gb|FE514068.1|FE514068
EST:     GTTCGAAGCCGGAAGGAAATACAAGATCAGGGTCAACACAATCTCAGCAG                         GTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGA
genomic: GTTCGAAGCCGGAAGGAAATACAAGATCAGGGTCAACACAATCTCAGCAGgtaaaatctt ... tgcttttcagGTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGA
EST: gi|169029497|gb|FE438897.1|FE438897
EST:     GTTCGAAGCCGGAAGGAAATACAAGATCAGGGTCAACACAATCTCAGCAG                         GTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGA
genomic: GTTCGAAGCCGGAAGGAAATACAAGATCAGGGTCAACACAATCTCAGCAGgtaaaatctt ... tgcttttcagGTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGA
EST: gi|169041054|gb|FE450354.1|FE450354
EST:     GTTCGAAGCCGGAAGGAAATACAAGATCAGGGTCAACACAATCTCAGCAG                         GTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGA
genomic: GTTCGAAGCCGGAAGGAAATACAAGATCAGGGTCAACACAATCTCAGCAGgtaaaatctt ... tgcttttcagGTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGA
EST: gi|169024460|gb|FE434385.1|FE434385
EST:     GTTCGAAGCCGGAAGGAAATACAAGATCAGGGTCAACACAATCTCAGCAG                         GTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGA
genomic: GTTCGAAGCCGGAAGGAAATACAAGATCAGGGTCAACACAATCTCAGCAGgtaaaatctt ... tgcttttcagGTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGA
EST: gi|169106433|gb|FE507445.1|FE507445
EST:     GTTCGAAGCCGGAAGGAAATACAAGATCAGGGTCAACACAATCTCAGCAG                         GTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGA
genomic: GTTCGAAGCCGGAAGGAAATACAAGATCAGGGTCAACACAATCTCAGCAGgtaaaatctt ... tgcttttcagGTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGA
EST: gi|169069401|gb|FE480524.1|FE480524
EST:     GTTCGAAGCCGGAAGGAAATACAAGATCAGGGTCAACACAATCTCAGCAG                         GTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGA
genomic: GTTCGAAGCCGGAAGGAAATACAAGATCAGGGTCAACACAATCTCAGCAGgtaaaatctt ... tgcttttcagGTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGA
EST: gi|169083532|gb|FE495876.1|FE495876
EST:     GTTCGAAGCCGGAAGGAAATACAAGATCAGGGTCAACACAATCTCAGCAG                         GTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGA
genomic: GTTCGAAGCCGGAAGGAAATACAAGATCAGGGTCAACACAATCTCAGCAGgtaaaatctt ... tgcttttcagGTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGA
EST: gi|169069400|gb|FE480523.1|FE480523
EST:     GTTCGAAGCCGGAAGGAAATACAAGATCAGGGTCAACACAATCTCAGCAG                         GTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGA
genomic: GTTCGAAGCCGGAAGGAAATACAAGATCAGGGTCAACACAATCTCAGCAGgtaaaatctt ... tgcttttcagGTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGA
EST: gi|169035072|gb|FE444881.1|FE444881
EST:     GTTCGAAGCCGGAAGGAAATACAAGATCAGGGTCAACACAATCTCAGCAG                         GTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGA
genomic: GTTCGAAGCCGGAAGGAAATACAAGATCAGGGTCAACACAATCTCAGCAGgtaaaatctt ... tgcttttcagGTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGA
EST: gi|169113335|gb|FE515286.1|FE515286
EST:     GTTCGAAGCCGGAAGGAAATACAAGATCAGGGTCAACACAATCTCAGCAG                         GTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGA
genomic: GTTCGAAGCCGGAAGGAAATACAAGATCAGGGTCAACACAATCTCAGCAGgtaaaatctt ... tgcttttcagGTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGA

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: 35 (upstream exon), 29 (downstream exon)
Score: 26

GGGATGAGCTCGGCCAAGGCAGCTCTAGAAAGTGACACACGGGTTCTCGCGTTCGAAGCCGGAAGGAAATACAAGATCAGGGTCAACACAATCTCAGCAGgtaaaatctt ... tgcttttcagGTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGATCGATTACTCCAAGGCAAACTCTCCCCTGCAAAGAGATCTCGAAGCTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaaatcttacaaatctattaaagctgtggctcatgcatgacatgcttttcagGTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGATCGATTACTCCAAGGCAAACTCTCCCCTGCAAAGAGATCTCGAAGCTG
      atcttac  putative branch site (score: 26)
                                             tgcttttc  putative PPT
         ttacaaatctattaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaatcttacaaatctattaaagctgtggctcatgcatgacatgcttttcagGTCCCTTGAAAAGCAGAGCTGCCAAGGCAATCGGATTCATTGAGAAGATGATCGATTACTCCAAGGCAAACTCTCCCCTGCAAAGAGATCTCGAAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG