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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatcaccagagcactaccgtctaatgctactaagaatctctctgtgatttttgccgctacagCCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCATCCTGGTGGATGCTCTAGCTTATCTCGAGTGCACAGTGGTGACTCGAAT

Basic information

species Selaginella moellendorffii
transcript EFJ07706
intron # 9
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|169065499|gb|FE475857.1|FE475857
EST:     AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGG                         CCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
genomic: AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGGgtaagcatca ... gccgctacagCCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
EST: gi|169070025|gb|FE476494.1|FE476494
EST:     AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGG                         CCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
genomic: AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGGgtaagcatca ... gccgctacagCCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
EST: gi|169057396|gb|FE465700.1|FE465700
EST:     AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGG                         CCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
genomic: AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGGgtaagcatca ... gccgctacagCCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
EST: gi|169059367|gb|FE467509.1|FE467509
EST:     AAACTCCACAAAACTAATGAAACACTTTTTAAAACGTTTTCCTCCTGGGG                         CCGATCGCTTCGAGGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
genomic: AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGGgtaagcatca ... gccgctacagCCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
EST: gi|169070026|gb|FE476495.1|FE476495
EST:     AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGG                         CCGATCGCTTCGAAGGAGTGGAATGGACTGTTGG
genomic: AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGGgtaagcatca ... gccgctacagCCGATCGCTTCGAAGGAGTGGAATGGACTGTTGG
EST: gi|169019340|gb|FE427650.1|FE427650
EST:     AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGG                         CCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
genomic: AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGGgtaagcatca ... gccgctacagCCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
EST: gi|169050567|gb|FE459635.1|FE459635
EST:     AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGG                         CCGATCGCTTCGAGGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
genomic: AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGGgtaagcatca ... gccgctacagCCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
EST: gi|169067246|gb|FE473051.1|FE473051
EST:     AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGG                         CCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
genomic: AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGGgtaagcatca ... gccgctacagCCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
EST: gi|169038570|gb|FE446895.1|FE446895
EST:     AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGG                         CCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
genomic: AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGGgtaagcatca ... gccgctacagCCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
EST: gi|169098316|gb|FE499633.1|FE499633
EST:     AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGG                         CCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
genomic: AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGGgtaagcatca ... gccgctacagCCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
EST: gi|169044934|gb|FE450856.1|FE450856
EST:     AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGG                         CCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
genomic: AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGGgtaagcatca ... gccgctacagCCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
EST: gi|169029313|gb|FE439441.1|FE439441
EST:     AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGG                         CCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
genomic: AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGGgtaagcatca ... gccgctacagCCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
EST: gi|169102150|gb|FE505776.1|FE505776
EST:     AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGG                         CCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
genomic: AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGGgtaagcatca ... gccgctacagCCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
EST: gi|169036582|gb|FE444140.1|FE444140
EST:     AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGG                         CCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
genomic: AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGGgtaagcatca ... gccgctacagCCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
EST: gi|169111537|gb|FE510397.1|FE510397
EST:     AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGG                         CCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
genomic: AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGGgtaagcatca ... gccgctacagCCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
EST: gi|169035367|gb|FE444305.1|FE444305
EST:     AAACTCCACAAAAGTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGG                         CCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
genomic: AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGGgtaagcatca ... gccgctacagCCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
EST: gi|169114972|gb|FE516337.1|FE516337
EST:     AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGG                         CCGATCGCTTCGAGGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
genomic: AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGGgtaagcatca ... gccgctacagCCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
EST: gi|169113900|gb|FE515955.1|FE515955
EST:     AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGG                         CCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
genomic: AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGGgtaagcatca ... gccgctacagCCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
EST: gi|169099896|gb|FE503384.1|FE503384
EST:     AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGG                         CCGATCGCTTCGAGGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
genomic: AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGGgtaagcatca ... gccgctacagCCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
EST: gi|169030941|gb|FE436844.1|FE436844
EST:     AAACTCCCCAAAACTAATGAAACACTTTTTAAAACGTTTTCCTCCTGGGG                         CCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
genomic: AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGGgtaagcatca ... gccgctacagCCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
EST: gi|169061129|gb|FE470135.1|FE470135
EST:     AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGG                         CCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA
genomic: AAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGGgtaagcatca ... gccgctacagCCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCA

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), 33 (downstream exon)
Score: 26

GTTGGTGACAACTTCGTCCTCAACTGTTTGGAAGAAGGAAACTCCACAAAACTAATGAAACACTTTCTAAAACGTTTTCCTCCTGGGGgtaagcatca ... gccgctacagCCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCATCCTGGTGGATGCTCTAGCTTATCTCGAGTGCACAGTGGTGACTCGAAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagcactaccgtctaatgctactaagaatctctctgtgatttttgccgctacagCCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCATCCTGGTGGATGCTCTAGCTTATCTCGAGTGCACAGTGGTGACTCGAAT
           gtctaat  putative branch site (score: 26)
                                        tttttgcc  putative PPT
                                     tgattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcatcaccagagcactaccgtctaatgctactaagaatctctctgtgatttttgccgctacagCCGATCGCTTCGAAGGAGTGGAATGGACTGTTGGAAAAAATTCGTGTCCCATCCTGGTGGATGCTCTAGCTTATCTCGAGTGCACAGTGGTGACTCGAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA