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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtctcgggttgaaagagttcttttatgaactgatggaaaaaaaaaatttttttttttcagGCTTGCATTCAGGTTTGCCCCAGGAATCCAGAAAATTTCAATGTCGATAATGTTCGAGTTGCGAAGCTGCTTGGCGGTGGTCTTCGGGATTCTTGTGTCG

Basic information

species Selaginella moellendorffii
transcript EFJ21647
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ21647 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GRMZM2G083095_T03 (Zea mays), 3'ss of exon 3
-------------------------------gttagtctcgggttgaaagagttcttttatgaactgatggaaaaaaaaaattttttt-----ttttcagGCTTGCATTCAGGTTTGCCCCAGGAATCCAGAAAATTTCAATGTCGATAATGTTCGAGTTGCGAAGCTGCTTGGCGGTGGTCTTCGGGATTCTTGTGTCG
                               |   || |   |||     | |  ||  ||||    |   || |      || ||       |||| |||| |||||||| ||||||||||  ||||||| ||| ||||||||||| |||||| |||| || ||||||||||| |||||| | |   |||||| ||| |
gttctcaaatcaaactaaaaaggaaaaaaccgaaggttttatgttatgtaattatttagatgataccaactaatattgggtttgttgcatcgatttttagGCCTGCATTCAAGTTTGCCCCAAAAATCCAGCAAACTTCAATGTCGACAATGTTAGAGTGGCTAAGCTGCTTGGAGGTGGTTTGCACAATTCTTCTGTGG
















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|169036842|gb|FE443828.1|FE443828
EST:     CCAGTAAACAGTATGGCCAGGAGGATTTTCTGTGTCCTCTTATTGCTGAA                         GCTTGCATTCAGGTTTGCCCCAGGAAT
genomic: CCAGTAAACAGTATGGCCAGGAGGATTTTCTGTGTCCTCTTATTGCTGAGgttagtctcg ... tttttttcagGCTTGCATTCAGGTTTGCCCCAGGAAT
EST: gi|169023688|gb|FE429531.1|FE429531
EST:     GTAAACAGTATGGCCAGGAGGATTTTCTGTGTCCTCTTATTGCTGAG                         GCTTGCATTCAGGTTTGCCCCAGGAATCCAGAGAATTTCAATGTCGATAAT
genomic: GTAAACAGTATGGCCAGGAGGATTTTCTGTGTCCTCTTATTGCTGAGgttagtctcg ... tttttttcagGCTTGCATTCAGGTTTGCCCCAGGAATCCAGAAAATTTCAATGTCGATAAT
EST: gi|169072128|gb|FE479884.1|FE479884
EST:     CCAGTAAACAGTATGGCCAGGAGGATTTTCTGTGTCCTCTTATTGCTGAG                         GCTTGCATTCAGGTTTGCCCCAGGAATCCAGAGAATTTCAATGTCGATAAT
genomic: CCAGTAAACAGTATGGCCAGGAGGATTTTCTGTGTCCTCTTATTGCTGAGgttagtctcg ... tttttttcagGCTTGCATTCAGGTTTGCCCCAGGAATCCAGAAAATTTCAATGTCGATAAT
EST: gi|169034976|gb|FE444837.1|FE444837
EST:     CCAGTAAACAGTATGGCCAGGAGGATTTTCTGTGTCCTCTTATTGCTGAG                         GCTTGCATTCAGGTTTGCCCCAGGAATCCAGAAAATTTCAATGTCGATAAT
genomic: CCAGTAAACAGTATGGCCAGGAGGATTTTCTGTGTCCTCTTATTGCTGAGgttagtctcg ... tttttttcagGCTTGCATTCAGGTTTGCCCCAGGAATCCAGAAAATTTCAATGTCGATAAT
EST: gi|169070715|gb|FE477314.1|FE477314
EST:     CCAGTAAACAGTATGGCCAGGAGGATTTTCTGTGTCCTCTTATTGCTGAG                         GCTTGCATTCAGGTTTGCCCCAGGAATCCAGAGAATTTCAATGTCGATAAT
genomic: CCAGTAAACAGTATGGCCAGGAGGATTTTCTGTGTCCTCTTATTGCTGAGgttagtctcg ... tttttttcagGCTTGCATTCAGGTTTGCCCCAGGAATCCAGAAAATTTCAATGTCGATAAT
EST: gi|169071330|gb|FE479606.1|FE479606
EST:     CCAGTAAACAGTATGGCCAGGAGGATTTTCTGTGTCCTCTTATTGCTGAG                         GCTTGCATTCAGGTTTGCCCCAGGAATCCAGAAAATTTCAATGTCGATAAT
genomic: CCAGTAAACAGTATGGCCAGGAGGATTTTCTGTGTCCTCTTATTGCTGAGgttagtctcg ... tttttttcagGCTTGCATTCAGGTTTGCCCCAGGAATCCAGAAAATTTCAATGTCGATAAT
EST: gi|169034406|gb|FE446377.1|FE446377
EST:     CCAGTAAACAGTATGGCCAGGAGGATTTTCTGTGTCCTCTTATTGCTGAG                         GCTTGCATTCAGGTTTGCCCCAGGAATCCAGAAAATTTCAATGTCGATAAT
genomic: CCAGTAAACAGTATGGCCAGGAGGATTTTCTGTGTCCTCTTATTGCTGAGgttagtctcg ... tttttttcagGCTTGCATTCAGGTTTGCCCCAGGAATCCAGAAAATTTCAATGTCGATAAT

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: 29 (upstream exon), 25 (downstream exon)
Score: 9

GGACTGTCGCAACAAAGAGCAAGTTGTTTTGAGGATGAAAGCCGCTGTTGCCAGTAAACAGTATGGCCAGGAGGATTTTCTGTGTCCTCTTATTGCTGAGgttagtctcg ... tttttttcagGCTTGCATTCAGGTTTGCCCCAGGAATCCAGAAAATTTCAATGTCGATAATGTTCGAGTTGCGAAGCTGCTTGGCGGTGGTCTTCGGGATTCTTGTGTCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggttgaaagagttcttttatgaactgatggaaaaaaaaaatttttttttttcagGCTTGCATTCAGGTTTGCCCCAGGAATCCAGAAAATTTCAATGTCGATAATGTTCGAGTTGCGAAGCTGCTTGGCGGTGGTCTTCGGGATTCTTGTGTCG
                      aactgat  putative branch site (score: 9)
                                         tttttttttttc  putative PPT
               ttttatgaactgatgg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtctcgggttgaaagagttcttttatgaactgatggaaaaaaaaaatttttttttttcagGCTTGCATTCAGGTTTGCCCCAGGAATCCAGAAAATTTCAATGTCGATAATGTTCGAGTTGCGAAGCTGCTTGGCGGTGGTCTTCGGGATTCTTGTGTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT