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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctctcgaaagttaatctccagcacctacattgcttcaaaattctaataaattttttgctctccagGATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCACAAACTCCATCCTACTTGAAGGGAGAGTTTCCTGGCGATTATGGCTGGG

Basic information

species Selaginella moellendorffii
transcript EFJ32176
intron # 1
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|169059514|gb|FE468540.1|FE468540
EST:     AGAATGCTCTTCGCGATAGATCCGTCCAGTGCCAAGCAAAGGTTTCAATG                         GATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCA
genomic: AGAATGCTCTTCGCGATAGATCCGTCCAGTGCCAAGCAAAGGTTTCAATGgtaagctctc ... tgctctccagGATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCA
EST: gi|169059515|gb|FE468541.1|FE468541
EST:     AGAATGCTCTTCGCGATAGATCCGTCCAGTGCCAAGCAAAGGTTTCAATG                         GATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCA
genomic: AGAATGCTCTTCGCGATAGATCCGTCCAGTGCCAAGCAAAGGTTTCAATGgtaagctctc ... tgctctccagGATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCA
EST: gi|169051420|gb|FE457692.1|FE457692
EST:     AGAATGCTCTTCGCGGTAGATCCGTCCAGTGCCAAGCAAAGGTTTCAATG                         GATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCA
genomic: AGAATGCTCTTCGCGATAGATCCGTCCAGTGCCAAGCAAAGGTTTCAATGgtaagctctc ... tgctctccagGATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCA
EST: gi|169066315|gb|FE472991.1|FE472991
EST:     AGAATGCTCTTCGCGATAGATCCGTCCAGTGCCAAGCAAAGGTTTCAATG                         GATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCA
genomic: AGAATGCTCTTCGCGATAGATCCGTCCAGTGCCAAGCAAAGGTTTCAATGgtaagctctc ... tgctctccagGATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCA
EST: gi|169114834|gb|FE516095.1|FE516095
EST:     AGAATGCTCTTCGCGATAGATCCGTCCAGTGCCAAGCAAAGGTTTCAATG                         GATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCA
genomic: AGAATGCTCTTCGCGATAGATCCGTCCAGTGCCAAGCAAAGGTTTCAATGgtaagctctc ... tgctctccagGATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCA
EST: gi|169080816|gb|FE486648.1|FE486648
EST:     AGAATGCTCTTCGCGGTAGATCCGTCCAGTGCCAAGCAAAGGTTTCAATG                         GATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCA
genomic: AGAATGCTCTTCGCGATAGATCCGTCCAGTGCCAAGCAAAGGTTTCAATGgtaagctctc ... tgctctccagGATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCA
EST: gi|169096663|gb|FE496793.1|FE496793
EST:     AGAATGCTCTTCGCGGTAGATCCGTCCAGTGCCAAGCAAAGGTTTCAATG                         GATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCA
genomic: AGAATGCTCTTCGCGATAGATCCGTCCAGTGCCAAGCAAAGGTTTCAATGgtaagctctc ... tgctctccagGATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCA
EST: gi|169051421|gb|FE457693.1|FE457693
EST:     AGAATGCTCTTCGCGGTAGATCCGTCCAGTGCCAAGCAAAGGTTTCAATG                         GATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCA
genomic: AGAATGCTCTTCGCGATAGATCCGTCCAGTGCCAAGCAAAGGTTTCAATGgtaagctctc ... tgctctccagGATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCA
EST: gi|169108630|gb|FE512041.1|FE512041
EST:     AGAATGCTCTTCGCGATAGATCCGTCCAGTGCCAAGCAAAGGTTTCAATG                         GATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCA
genomic: AGAATGCTCTTCGCGATAGATCCGTCCAGTGCCAAGCAAAGGTTTCAATGgtaagctctc ... tgctctccagGATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCA
EST: gi|169108629|gb|FE512040.1|FE512040
EST:     TGCTCTTCGCGATAGATCCGTCCAGTGCCAAGCAAAGGTTTCAATG                         GATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCA
genomic: TGCTCTTCGCGATAGATCCGTCCAGTGCCAAGCAAAGGTTTCAATGgtaagctctc ... tgctctccagGATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCA
EST: gi|169060049|gb|FE468659.1|FE468659
EST:     AGAATGCTCTTCGCGGTAGATCCGTCCAGTGCCAAGCAAAGGTTTCAATG                         GATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCA
genomic: AGAATGCTCTTCGCGATAGATCCGTCCAGTGCCAAGCAAAGGTTTCAATGgtaagctctc ... tgctctccagGATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCA
EST: gi|169043794|gb|FE453486.1|FE453486
EST:     AGAATGCTCTTCGCGATAGATCCGTCCAGTGCCAAGCAAAGGTTTCAATG                         GATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCA
genomic: AGAATGCTCTTCGCGATAGATCCGTCCAGTGCCAAGCAAAGGTTTCAATGgtaagctctc ... tgctctccagGATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCA
EST: gi|169096664|gb|FE496794.1|FE496794
EST:     AGAATGCTCTTCGCGGTAGATCCGTCCAGTGCCAAGCAAAGGTTTCAATG                         GATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCA
genomic: AGAATGCTCTTCGCGATAGATCCGTCCAGTGCCAAGCAAAGGTTTCAATGgtaagctctc ... tgctctccagGATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCA
EST: gi|169101520|gb|FE501493.1|FE501493
EST:     AGAATGCTCTTCGCGGTAGATCCGTCCAGTGCCAAGCAAAGGTTTCAATG                         GATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCA
genomic: AGAATGCTCTTCGCGATAGATCCGTCCAGTGCCAAGCAAAGGTTTCAATGgtaagctctc ... tgctctccagGATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCA
EST: gi|169060050|gb|FE468660.1|FE468660
EST:     AGAATGCTCTTCGCGGTAGATCCGTCCAGTGCCAAGCAAAGGTTTCAATG                         GATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCA
genomic: AGAATGCTCTTCGCGATAGATCCGTCCAGTGCCAAGCAAAGGTTTCAATGgtaagctctc ... tgctctccagGATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCA

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), 35 (downstream exon)
Score: 81

CACCGCGGCTGCGTCAGGCAGCTCCTTCTTGCGGGGATCCGGGTCCAGGAAGAATGCTCTTCGCGATAGATCCGTCCAGTGCCAAGCAAAGGTTTCAATGgtaagctctc ... tgctctccagGATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCACAAACTCCATCCTACTTGAAGGGAGAGTTTCCTGGCGATTATGGCTGGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaatctccagcacctacattgcttcaaaattctaataaattttttgctctccagGATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCACAAACTCCATCCTACTTGAAGGGAGAGTTTCCTGGCGATTATGGCTGGG
                              ttctaat  putative branch site (score: 81)
                                        ttttttgctctcc  putative PPT
                  attgcttcaaaattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctctcgaaagttaatctccagcacctacattgcttcaaaattctaataaattttttgctctccagGATCTCTGGTATGGACCAGACCGTGTCAAGTTCCTGGGTCCTTTCTCCGCACAAACTCCATCCTACTTGAAGGGAGAGTTTCCTGGCGATTATGGCTGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG