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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGTTGAAAGTTCTTCTAGCGGACGGTGCAAACAAGGATGAGAAAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAGgtaagcaaatagattgagttgatttcctcctccacgactcatctgtcatctctttccag

Basic information

species Selaginella moellendorffii
transcript EFJ08399
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ08399 (Selaginella moellendorffii), 5'ss of exon 6
lower sequence: AT4G35450.5 (Arabidopsis thaliana), 5'ss of exon 7
GGGTTGAAAGTTCTTCTAGCGGACGGTGCAAACAAGGATGAGAAAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAGgtaagcaa-------atagattga-gttgatttcctcctccacgactcatctgtcatctctttccag---------------------------------
|| ||||||| |    | ||    ||||  ||||| |||||  |||| || ||||| || |||||| | |||||||||||||||||||| |||||| ||||       ||  ||| | |   |||   |  ||        ||   ||   | ||| |||                                 
GGTTTGAAAGCTGCCTTGGCATCTGGTGGTAACAAAGATGAAGAAGATTCTGAAGGAAGGACAGCATTGCATTTTGCTTGTGGATACGGCGAGgtatgcaattctcttatcaattcacggcaattaaatattcggatttagatggttctctttttttcagtagctgtgaagttaagaatctttataatcattc
















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|169115001|gb|FE516366.1|FE516366
EST:     AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAG                         TTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
genomic: AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAGgtaagcaaat ... ctctttccagTTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
EST: gi|169087065|gb|FE495157.1|FE495157
EST:     AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAG                         TTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
genomic: AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAGgtaagcaaat ... ctctttccagTTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
EST: gi|169115002|gb|FE516367.1|FE516367
EST:     AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAG                         TTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
genomic: AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAGgtaagcaaat ... ctctttccagTTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
EST: gi|169065055|gb|FE474503.1|FE474503
EST:     AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAG                         TTTGAA-TGCGC
genomic: AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAGgtaagcaaat ... ctctttccagTT-GAAATGCGC
EST: gi|169023042|gb|FE431590.1|FE431590
EST:     AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAG                         TTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
genomic: AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAGgtaagcaaat ... ctctttccagTTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
EST: gi|169108039|gb|FE511021.1|FE511021
EST:     AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAG                         TTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
genomic: AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAGgtaagcaaat ... ctctttccagTTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
EST: gi|169072467|gb|FE483863.1|FE483863
EST:     AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAG                         TTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
genomic: AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAGgtaagcaaat ... ctctttccagTTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
EST: gi|169072466|gb|FE483862.1|FE483862
EST:     AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAG                         TTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
genomic: AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAGgtaagcaaat ... ctctttccagTTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
EST: gi|169106626|gb|FE504648.1|FE504648
EST:     AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAG                         TTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
genomic: AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAGgtaagcaaat ... ctctttccagTTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
EST: gi|169065054|gb|FE474502.1|FE474502
EST:     AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAG                         TTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
genomic: AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAGgtaagcaaat ... ctctttccagTTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
EST: gi|169067484|gb|FE475239.1|FE475239
EST:     AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAG                         TTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
genomic: AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAGgtaagcaaat ... ctctttccagTTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
EST: gi|169072328|gb|FE479408.1|FE479408
EST:     AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAG                         TTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
genomic: AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAGgtaagcaaat ... ctctttccagTTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
EST: gi|169063745|gb|FE472475.1|FE472475
EST:     AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAG                         TTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
genomic: AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAGgtaagcaaat ... ctctttccagTTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
EST: gi|169062455|gb|FE469514.1|FE469514
EST:     AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAG                         TTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
genomic: AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAGgtaagcaaat ... ctctttccagTTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
EST: gi|169101054|gb|FE500642.1|FE500642
EST:     AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAG                         TTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
genomic: AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAGgtaagcaaat ... ctctttccagTTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
EST: gi|169066140|gb|FE475146.1|FE475146
EST:     AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAG                         TTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
genomic: AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAGgtaagcaaat ... ctctttccagTTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
EST: gi|169048080|gb|FE456795.1|FE456795
EST:     AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAG                         TTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
genomic: AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAGgtaagcaaat ... ctctttccagTTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
EST: gi|169054112|gb|FE462347.1|FE462347
EST:     AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAG                         TTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
genomic: AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAGgtaagcaaat ... ctctttccagTTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
EST: gi|169099404|gb|FE500487.1|FE500487
EST:     AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAG                         TTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
genomic: AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAGgtaagcaaat ... ctctttccagTTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
EST: gi|169058747|gb|FE464785.1|FE464785
EST:     AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAG                         TTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG
genomic: AAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAGgtaagcaaat ... ctctttccagTTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTG

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: 173

GGGTTGAAAGTTCTTCTAGCGGACGGTGCAAACAAGGATGAGAAAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAGgtaagcaaat ... ctctttccagTTGAAATGCGCGGAAGCTCTTCTCGAGGCTGGGGCGTTCGTGGACTCGGTGGACAAGAACAACAACACTCCATTGCATTACGCTGGTGGCTACGGCCGGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGTTGAAAGTTCTTCTAGCGGACGGTGCAAACAAGGATGAGAAAGACTCGGAAGGGAGAACAGCACTTCATTTTGCTTGTGGATACGGAGAGgtaagcaaatagattgagttgatttcctcctccacgactcatctgtcatctctttccag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA