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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCCGACGTGCTCGACTCTGCTCTCTTGAGACCTGGCCGATTTGATCGGCAAGTGACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAGgtaaagctgaagttttgataacgttcttacttacgtttttcttttcttttcttttcag

Basic information

species Selaginella moellendorffii
transcript EFJ31931
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|169071578|gb|FE479139.1|FE479139
EST:     AAGTGACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAG                         GTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTGAGAAGATC
genomic: AAGTGACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAGgtaaagctga ... ttcttttcagGTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTGAGAAGATC
EST: gi|169113345|gb|FE514672.1|FE514672
EST:     AAGTCACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAG                         GTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTGAGAAGATC
genomic: AAGTGACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAGgtaaagctga ... ttcttttcagGTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTGAGAAGATC
EST: gi|169073439|gb|FE482087.1|FE482087
EST:     AAGTCACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAG                         GTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTGAGAAGATC
genomic: AAGTGACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAGgtaaagctga ... ttcttttcagGTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTGAGAAGATC
EST: gi|169032231|gb|FE438812.1|FE438812
EST:     AAGTCACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAG                         GTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTGAGAAGATC
genomic: AAGTGACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAGgtaaagctga ... ttcttttcagGTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTGAGAAGATC
EST: gi|169069495|gb|FE480566.1|FE480566
EST:     AAGTCACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAG                         GTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTGAGAAGATC
genomic: AAGTGACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAGgtaaagctga ... ttcttttcagGTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTGAGAAGATC
EST: gi|169049266|gb|FE459542.1|FE459542
EST:     AAGTGACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAG                         GTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTGAGAAGATC
genomic: AAGTGACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAGgtaaagctga ... ttcttttcagGTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTGAGAAGATC
EST: gi|169068738|gb|FE478431.1|FE478431
EST:     AAGTCACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAG                         GTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTGAGAAGATC
genomic: AAGTGACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAGgtaaagctga ... ttcttttcagGTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTGAGAAGATC
EST: gi|169067886|gb|FE474757.1|FE474757
EST:     AAGTGACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAG                         GTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTGAGAAGATC
genomic: AAGTGACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAGgtaaagctga ... ttcttttcagGTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTGAGAAGATC
EST: gi|169040759|gb|FE447394.1|FE447394
EST:     AAGTCACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAG                         GTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTGAGAAGATC
genomic: AAGTGACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAGgtaaagctga ... ttcttttcagGTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTGAGAAGATC
EST: gi|169066449|gb|FE474672.1|FE474672
EST:     AAGTGACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAG                         GTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTGAGAAGATC
genomic: AAGTGACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAGgtaaagctga ... ttcttttcagGTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTGAGAAGATC
EST: gi|169044423|gb|FE451060.1|FE451060
EST:     AAGTGACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAG                         GTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTG
genomic: AAGTGACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAGgtaaagctga ... ttcttttcagGTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTG
EST: gi|169082832|gb|FE486261.1|FE486261
EST:     AAGTGACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAG                         GTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTGAGAAGATC
genomic: AAGTGACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAGgtaaagctga ... ttcttttcagGTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTGAGAAGATC
EST: gi|169078968|gb|FE489688.1|FE489688
EST:     AAGTCACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAG                         GTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTGAGAAGATC
genomic: AAGTGACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAGgtaaagctga ... ttcttttcagGTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTGAGAAGATC
EST: gi|169029308|gb|FE439436.1|FE439436
EST:     AAGTGACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAG                         GTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTGAGAAGATC
genomic: AAGTGACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAGgtaaagctga ... ttcttttcagGTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTGAGAAGATC
EST: gi|169040867|gb|FE447918.1|FE447918
EST:     AAGTGACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAG                         GTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTGAGAAGATC
genomic: AAGTGACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAGgtaaagctga ... ttcttttcagGTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTGAGAAGATC
EST: gi|169050496|gb|FE459603.1|FE459603
EST:     AAGTGACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAG                         GTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTGAGAAGATC
genomic: AAGTGACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAGgtaaagctga ... ttcttttcagGTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTGAGAAGATC

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), 34 (downstream exon)
Score: 54

GCCCGACGTGCTCGACTCTGCTCTCTTGAGACCTGGCCGATTTGATCGGCAAGTGACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAGgtaaagctga ... ttcttttcagGTCCATTCTAAAGGAAAATCCCTGGGCAAGGATGTCGACTTTGAGAAGATCGCAAGAAGAACTCCAGGCTTTACCGGCGCGGACTTGCAAAACCTCATGA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCCGACGTGCTCGACTCTGCTCTCTTGAGACCTGGCCGATTTGATCGGCAAGTGACGGTTGACAGACCTGATGTGGCTGGACGAGTGAGGATTTTGGAGgtaaagctgaagttttgataacgttcttacttacgtttttcttttcttttcttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG