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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGTATTGCGATTTGCTTGCTGCCGCGGCCATGGCGTCCAAGAGAATCCTCAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAGgtgagcgcgcgccacaaaatccatgggattttggtgtcgggattttccttctttgccttgatttctagctgacgatctcgtcgatctatcgatctcactgctttgcgcgattcgcag

Basic information

species Selaginella moellendorffii
transcript EFJ35297
intron # 1
splice site 5'
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|169025632|gb|FE436545.1|FE436545
EST:     GGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAG                         GTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
genomic: GGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAGgtgagcgcgc ... cgattcgcagGTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
EST: gi|169078304|gb|FE490337.1|FE490337
EST:     CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAG                         GTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
genomic: CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAGgtgagcgcgc ... cgattcgcagGTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
EST: gi|169105950|gb|FE504310.1|FE504310
EST:     CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAG                         GTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
genomic: CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAGgtgagcgcgc ... cgattcgcagGTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
EST: gi|169038738|gb|FE446959.1|FE446959
EST:     CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAG                         GTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
genomic: CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAGgtgagcgcgc ... cgattcgcagGTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
EST: gi|70670995|gb|DN839572.1|DN839572
EST:     CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAG                         GTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
genomic: CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAGgtgagcgcgc ... cgattcgcagGTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
EST: gi|70670805|gb|DN839382.1|DN839382
EST:     CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAT                         GTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATTATGGGTCCGC
genomic: CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAGgtgagcgcgc ... cgattcgcagGTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
EST: gi|70670872|gb|DN839449.1|DN839449
EST:     CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAG                         GTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
genomic: CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAGgtgagcgcgc ... cgattcgcagGTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
EST: gi|169022096|gb|FE429105.1|FE429105
EST:     CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAG                         GTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
genomic: CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAGgtgagcgcgc ... cgattcgcagGTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
EST: gi|169112483|gb|FE512760.1|FE512760
EST:     CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAG                         GTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
genomic: CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAGgtgagcgcgc ... cgattcgcagGTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
EST: gi|169039764|gb|FE449426.1|FE449426
EST:     CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAG                         GTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
genomic: CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAGgtgagcgcgc ... cgattcgcagGTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
EST: gi|169079016|gb|FE488579.1|FE488579
EST:     CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAG                         GTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
genomic: CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAGgtgagcgcgc ... cgattcgcagGTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
EST: gi|70670087|gb|DN838664.1|DN838664
EST:     CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAG                         GTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
genomic: CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAGgtgagcgcgc ... cgattcgcagGTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
EST: gi|169086731|gb|FE494368.1|FE494368
EST:     CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAG                         GTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
genomic: CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAGgtgagcgcgc ... cgattcgcagGTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
EST: gi|169020751|gb|FE430152.1|FE430152
EST:     CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAG                         GTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
genomic: CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAGgtgagcgcgc ... cgattcgcagGTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
EST: gi|169079924|gb|FE487368.1|FE487368
EST:     CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAG                         GTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
genomic: CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAGgtgagcgcgc ... cgattcgcagGTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
EST: gi|169095814|gb|FE498895.1|FE498895
EST:     CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAG                         GTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
genomic: CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAGgtgagcgcgc ... cgattcgcagGTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
EST: gi|169020893|gb|FE429306.1|FE429306
EST:     CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAG                         GTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
genomic: CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAGgtgagcgcgc ... cgattcgcagGTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
EST: gi|169046060|gb|FE453957.1|FE453957
EST:     CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAG                         GTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
genomic: CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAGgtgagcgcgc ... cgattcgcagGTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
EST: gi|169026535|gb|FE434796.1|FE434796
EST:     CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAG                         GTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
genomic: CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAGgtgagcgcgc ... cgattcgcagGTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
EST: gi|169032175|gb|FE439289.1|FE439289
EST:     CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAG                         GTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
genomic: CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAGgtgagcgcgc ... cgattcgcagGTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
EST: gi|169082868|gb|FE491120.1|FE491120
EST:     CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAG                         GTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
genomic: CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAGgtgagcgcgc ... cgattcgcagGTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
EST: gi|169032189|gb|FE439290.1|FE439290
EST:     CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAG                         GTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
genomic: CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAGgtgagcgcgc ... cgattcgcagGTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
EST: gi|169046059|gb|FE453956.1|FE453956
EST:     CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAG                         GTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
genomic: CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAGgtgagcgcgc ... cgattcgcagGTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
EST: gi|169061380|gb|FE470428.1|FE470428
EST:     CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAG                         GTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
genomic: CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAGgtgagcgcgc ... cgattcgcagGTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
EST: gi|70669831|gb|DN838408.1|DN838408
EST:     CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAG                         GTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
genomic: CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAGgtgagcgcgc ... cgattcgcagGTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
EST: gi|169081704|gb|FE488162.1|FE488162
EST:     CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAG                         GTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
genomic: CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAGgtgagcgcgc ... cgattcgcagGTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
EST: gi|169078305|gb|FE490338.1|FE490338
EST:     CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAG                         GTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
genomic: CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAGgtgagcgcgc ... cgattcgcagGTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
EST: gi|70669414|gb|DN837991.1|DN837991
EST:     CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAG                         GTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
genomic: CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAGgtgagcgcgc ... cgattcgcagGTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
EST: gi|169092996|gb|FE495290.1|FE495290
EST:     CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAG                         GTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC
genomic: CAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAGgtgagcgcgc ... cgattcgcagGTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGC

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), 35 (downstream exon)
Score: 147

GGGTATTGCGATTTGCTTGCTGCCGCGGCCATGGCGTCCAAGAGAATCCTCAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAGgtgagcgcgc ... cgattcgcagGTCCCGTGGCGGAAGATATGTTTCATTGGCAAGCGACGATAATGGGTCCGCCCGATAGCCCCTACGCGGGCGGTGTGTTCCTGGTCACTATTCATTTCCC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGTATTGCGATTTGCTTGCTGCCGCGGCCATGGCGTCCAAGAGAATCCTCAAGGAATTGAAGGACTTGCAGAAGGATCCGCCCACGTCGTGCAGCGCAGgtgagcgcgcgccacaaaatccatgggattttggtgtcgggattttccttctttgccttgatttctagctgacgatctcgtcgatctatcgatctcactgctttgcgcgattcgcag

- - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG