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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGCGTGGGAAGACGGGGACGAGGTAGTTCTCGTTGCTTGCCGCATGCCAAAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCTgtaagttcttttctttttcaagtctctcttttcctcacaaaatccttggacacag

Basic information

species Selaginella moellendorffii
transcript EFJ09546
intron # 10
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|169045510|gb|FE450703.1|FE450703
EST:     AAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCT                         CTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
genomic: AAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCTgtaagttctt ... ttggacacagCTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
EST: gi|70669704|gb|DN838281.1|DN838281
EST:     AAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCT                         CTACGAATTTCGGTTCAATATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
genomic: AAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCTgtaagttctt ... ttggacacagCTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
EST: gi|169041728|gb|FE449299.1|FE449299
EST:     AAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCT                         CTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
genomic: AAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCTgtaagttctt ... ttggacacagCTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
EST: gi|169115409|gb|FE516150.1|FE516150
EST:     AAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCT                         CTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
genomic: AAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCTgtaagttctt ... ttggacacagCTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
EST: gi|70669547|gb|DN838124.1|DN838124
EST:     AAGTTCGACATGGAGCTCATGAAAGACACTAACGATCATGTTCTCGAGCT                         CTACGAATTTCGGGTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
genomic: AAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCTgtaagttctt ... ttggacacagCTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
EST: gi|169060191|gb|FE467553.1|FE467553
EST:     AAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCT                         CTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
genomic: AAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCTgtaagttctt ... ttggacacagCTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
EST: gi|169054032|gb|FE461331.1|FE461331
EST:     AAGTTCGACATGGAGCTCATGAAAGACACTAACGATCATGTTCTCGAGCT                         CTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
genomic: AAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCTgtaagttctt ... ttggacacagCTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
EST: gi|169060192|gb|FE467554.1|FE467554
EST:     AAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCT                         CTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
genomic: AAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCTgtaagttctt ... ttggacacagCTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
EST: gi|169052819|gb|FE461197.1|FE461197
EST:     AAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCT                         CTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
genomic: AAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCTgtaagttctt ... ttggacacagCTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
EST: gi|169081597|gb|FE491251.1|FE491251
EST:     AAGTTCGACATGGAGCTCATGAAAGACACTAACGATCATGTTCTCGAGCT                         CTGCGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
genomic: AAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCTgtaagttctt ... ttggacacagCTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
EST: gi|169052818|gb|FE461196.1|FE461196
EST:     AAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCT                         CTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
genomic: AAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCTgtaagttctt ... ttggacacagCTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
EST: gi|169099587|gb|FE502620.1|FE502620
EST:     AAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCT                         CTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
genomic: AAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCTgtaagttctt ... ttggacacagCTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
EST: gi|169029568|gb|FE438929.1|FE438929
EST:     AAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCT                         CTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
genomic: AAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCTgtaagttctt ... ttggacacagCTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
EST: gi|169096935|gb|FE497065.1|FE497065
EST:     AAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCT                         CTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
genomic: AAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCTgtaagttctt ... ttggacacagCTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
EST: gi|169078720|gb|FE487555.1|FE487555
EST:     AAGTTCGACATGGAGCTCATGAAAGACACTAACGATCATGTTCTCGAGCT                         CTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
genomic: AAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCTgtaagttctt ... ttggacacagCTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
EST: gi|169054031|gb|FE461330.1|FE461330
EST:     NAGTTCGACATGGAGCTCATGAAAGACACTAACGATCATGTTCTCGAGCT                         CTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
genomic: AAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCTgtaagttctt ... ttggacacagCTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
EST: gi|169078771|gb|FE489621.1|FE489621
EST:     AAGTTCGACATGGAGCTCATGAAAGACACTAACGATCATGTTCTCGAGCT                         CTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
genomic: AAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCTgtaagttctt ... ttggacacagCTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
EST: gi|169088168|gb|FE493394.1|FE493394
EST:     AAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCT                         CTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
genomic: AAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCTgtaagttctt ... ttggacacagCTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
EST: gi|169075080|gb|FE481453.1|FE481453
EST:     AAGTTCGACATGGAGCTCATGAAAGACACTAACGATCATGTTCTCGAGCT                         CTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
genomic: AAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCTgtaagttctt ... ttggacacagCTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
EST: gi|169088396|gb|FE495442.1|FE495442
EST:     AAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCT                         CTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT
genomic: AAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCTgtaagttctt ... ttggacacagCTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACT

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: 31 (upstream exon), 31 (downstream exon)
Score: 17

ATGCGTGGGAAGACGGGGACGAGGTAGTTCTCGTTGCTTGCCGCATGCCAAAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCTgtaagttctt ... ttggacacagCTACGAATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACTCTCAAAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGCGTGGGAAGACGGGGACGAGGTAGTTCTCGTTGCTTGCCGCATGCCAAAGTTCGACATGGAGCTCATGAAAGACACTGACGATCATGTTCTCGAGCTgtaagttcttttctttttcaagtctctcttttcctcacaaaatccttggacacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA