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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttgtgaaatctatcttctctgtgatagttctaatgtcctgcgttgtttagCTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATACTCGAAACGGTGTAACTCATACAGCATGCTCG

Basic information

species Selaginella moellendorffii
transcript EFJ22768
intron # 7
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|169022717|gb|FE428405.1|FE428405
EST:     CATTGTGCAGGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAG                         CTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
genomic: CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAGgtacttgtga ... cgttgtttagCTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
EST: gi|169028104|gb|FE435956.1|FE435956
EST:     CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAG                         CTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
genomic: CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAGgtacttgtga ... cgttgtttagCTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
EST: gi|169096681|gb|FE496811.1|FE496811
EST:     CATTGTGCAGGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAG                         CTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
genomic: CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAGgtacttgtga ... cgttgtttagCTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
EST: gi|169050285|gb|FE458352.1|FE458352
EST:     CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAG                         CTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
genomic: CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAGgtacttgtga ... cgttgtttagCTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
EST: gi|169019880|gb|FE426967.1|FE426967
EST:     CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAG                         CTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
genomic: CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAGgtacttgtga ... cgttgtttagCTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
EST: gi|169081666|gb|FE491320.1|FE491320
EST:     CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAG                         CTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
genomic: CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAGgtacttgtga ... cgttgtttagCTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
EST: gi|169109250|gb|FE510230.1|FE510230
EST:     CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAG                         CTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
genomic: CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAGgtacttgtga ... cgttgtttagCTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
EST: gi|169096537|gb|FE499449.1|FE499449
EST:     CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAG                         TTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
genomic: CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAGgtacttgtga ... cgttgtttagCTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
EST: gi|169082427|gb|FE488989.1|FE488989
EST:     CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAG                         CTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
genomic: CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAGgtacttgtga ... cgttgtttagCTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
EST: gi|169075666|gb|FE482052.1|FE482052
EST:     CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAG                         CTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
genomic: CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAGgtacttgtga ... cgttgtttagCTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
EST: gi|169031591|gb|FE439056.1|FE439056
EST:     CATTGTGCAGGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAG                         CTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
genomic: CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAGgtacttgtga ... cgttgtttagCTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
EST: gi|169080525|gb|FE488463.1|FE488463
EST:     CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAG                         CTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
genomic: CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAGgtacttgtga ... cgttgtttagCTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
EST: gi|169102388|gb|FE507080.1|FE507080
EST:     CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAG                         CTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
genomic: CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAGgtacttgtga ... cgttgtttagCTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
EST: gi|169028103|gb|FE435955.1|FE435955
EST:     CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAG                         CTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
genomic: CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAGgtacttgtga ... cgttgtttagCTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
EST: gi|169096682|gb|FE496812.1|FE496812
EST:     CATTGTGCAGGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAG                         CTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
genomic: CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAGgtacttgtga ... cgttgtttagCTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
EST: gi|169022716|gb|FE428404.1|FE428404
EST:     CATTGTGCAGGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAG                         CTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
genomic: CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAGgtacttgtga ... cgttgtttagCTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
EST: gi|169115682|gb|FE517268.1|FE517268
EST:     CATTGTGCAGGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAG                         CTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
genomic: CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAGgtacttgtga ... cgttgtttagCTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
EST: gi|169026482|gb|FE434769.1|FE434769
EST:     CATTGTGCAGGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAG                         CTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
genomic: CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAGgtacttgtga ... cgttgtttagCTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
EST: gi|169045242|gb|FE453555.1|FE453555
EST:     CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAG                         CTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
genomic: CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAGgtacttgtga ... cgttgtttagCTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
EST: gi|169107250|gb|FE508249.1|FE508249
EST:     CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAG                         CTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
genomic: CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAGgtacttgtga ... cgttgtttagCTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
EST: gi|169096538|gb|FE499450.1|FE499450
EST:     CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAG                         TTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
genomic: CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAGgtacttgtga ... cgttgtttagCTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
EST: gi|169083003|gb|FE488525.1|FE488525
EST:     CATTGTGCAGGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAG                         CTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
genomic: CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAGgtacttgtga ... cgttgtttagCTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
EST: gi|169050286|gb|FE458353.1|FE458353
EST:     CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAG                         CTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
genomic: CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAGgtacttgtga ... cgttgtttagCTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
EST: gi|169114821|gb|FE516082.1|FE516082
EST:     CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAG                         CTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
genomic: CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAGgtacttgtga ... cgttgtttagCTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
EST: gi|169080940|gb|FE486109.1|FE486109
EST:     CATTGTGCAGGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAG                         CTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA
genomic: CATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAGgtacttgtga ... cgttgtttagCTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATA

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: 157

GATACTTTCCGTGGAAGAGTGTGCGAGTGTCCCATTGTGCAAGGCGTGCAGTACAGCGGAGATGGATACAGTCACTGTGAAGgtacttgtga ... cgttgtttagCTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATACTCGAAACGGTGTAACTCATACAGCATGCTCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacttgtgaaatctatcttctctgtgatagttctaatgtcctgcgttgtttagCTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATACTCGAAACGGTGTAACTCATACAGCATGCTCG
                                ttctaat  putative branch site (score: 157)
 aaatctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttgtgaaatctatcttctctgtgatagttctaatgtcctgcgttgtttagCTCTCGGACCTGGGAGATGCAAACTTAATAATGGAGGATGCTGGCAGCATACTCGAAACGGTGTAACTCATACAGCATGCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG