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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCTGGATACAAACCTGGAAGAATCATCTTCTACAGAGATGGTGTGAGCGAAGGACAGTTCTACCAAGTTCTCCTTCACGAGCTGGATGCAATTAGAAAGgtatagtatggaaagacttggcacattgactgattcagctcttcgttttggacag

Basic information

species Selaginella moellendorffii
transcript EFJ14095
intron # 16
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ14095 (Selaginella moellendorffii), 5'ss of exon 16
lower sequence: GLYMA02G00510.1 (Glycine max), 5'ss of exon 17
CTCTGGATACAAACCTGGAAGAATCATCTTCTACAGAGATGGTGTGAGCGAAGGACAGTTCTACCAAGTTCTCCTTCACGAGCTGGATGCAATTAGAAAGgtatagtatggaaagacttggcacattgactgattcagctcttcgttttg-gacag------------------------------
                                     |||||||| || ||||| ||||| ||||||||||| ||| | ||| ||||||||||| | |||||  || || ||     |   | |||     | |  ||    || ||||   |||                               
------------------------------------GGATGGTGTAAGTGAAGGGCAGTTTTACCAAGTTCTACTTTATGAGTTGGATGCAATTCGGAAGgt-cagaattgattacttattcccatcataagttctagtaggtcattttataacacatgttctcacaagaatatatttatttgcag
















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|169025753|gb|FE433663.1|FE433663
EST:     AAGGACAGTTCTACCAAGTTCTCCTTCACGAGCTGGATGCAATTAGAAAG                         GCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTG
genomic: AAGGACAGTTCTACCAAGTTCTCCTTCACGAGCTGGATGCAATTAGAAAGgtatagtatg ... ttttggacagGCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTG
EST: gi|169052412|gb|FE462246.1|FE462246
EST:     AAGGACAGTTCTACCAAGTTCTCCTTCACGAGCTGGATGCAATTAGAAAG                         GCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTG
genomic: AAGGACAGTTCTACCAAGTTCTCCTTCACGAGCTGGATGCAATTAGAAAGgtatagtatg ... ttttggacagGCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTG
EST: gi|169110846|gb|FE509329.1|FE509329
EST:     AAGGACAGTTCTACCAAGTTCTCCTTCACGAGCTGGATGCAATTAGAAAG                         GCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTG
genomic: AAGGACAGTTCTACCAAGTTCTCCTTCACGAGCTGGATGCAATTAGAAAGgtatagtatg ... ttttggacagGCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTG
EST: gi|169053756|gb|FE461523.1|FE461523
EST:     AAGGACAGTTCTACCAAGTTCTCCTTCACGAGTTGGATGCAATTAGAAAG                         GCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTG
genomic: AAGGACAGTTCTACCAAGTTCTCCTTCACGAGCTGGATGCAATTAGAAAGgtatagtatg ... ttttggacagGCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTG
EST: gi|169076999|gb|FE485340.1|FE485340
EST:     AAGGACAGTTCTACCAAGTTCTCCTTCACGAGCTGGATGCAATTAGAAAG                         GCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTG
genomic: AAGGACAGTTCTACCAAGTTCTCCTTCACGAGCTGGATGCAATTAGAAAGgtatagtatg ... ttttggacagGCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTG
EST: gi|169081815|gb|FE486414.1|FE486414
EST:     AAGGACAGTTCTACCAAGTTCTCCTTCACGAGTTGGATGCAATTAGAAAG                         GCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTG
genomic: AAGGACAGTTCTACCAAGTTCTCCTTCACGAGCTGGATGCAATTAGAAAGgtatagtatg ... ttttggacagGCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTG
EST: gi|169026881|gb|FE432386.1|FE432386
EST:     AAGGACAGTTCTACCAAGTTCTCCTTCACGAGCTGGATGCAATTAGAAAG                         GCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTG
genomic: AAGGACAGTTCTACCAAGTTCTCCTTCACGAGCTGGATGCAATTAGAAAGgtatagtatg ... ttttggacagGCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTG
EST: gi|169078633|gb|FE487065.1|FE487065
EST:     AAGGACAGTTCTACCAAGTTCTCCTTCACGAGCTGGATGCAATTAGAAAG                         GCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTG
genomic: AAGGACAGTTCTACCAAGTTCTCCTTCACGAGCTGGATGCAATTAGAAAGgtatagtatg ... ttttggacagGCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTG
EST: gi|169108088|gb|FE511031.1|FE511031
EST:     AAGGACAGTTCTACCAAGTTCTCCTTCACGAGTTGGATGCAATTAGAAAG                         GCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTG
genomic: AAGGACAGTTCTACCAAGTTCTCCTTCACGAGCTGGATGCAATTAGAAAGgtatagtatg ... ttttggacagGCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTG
EST: gi|169026857|gb|FE434221.1|FE434221
EST:     AAGGACAGTTCTACCAAGTTCTCCTTCACGAGTTGGATGCAATTAGAAAG                         GCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTG
genomic: AAGGACAGTTCTACCAAGTTCTCCTTCACGAGCTGGATGCAATTAGAAAGgtatagtatg ... ttttggacagGCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTG
EST: gi|169076998|gb|FE485339.1|FE485339
EST:     AAGGACAGTTCTACCAAGTTCTCCTTCACGAGCTGGATGCAATTAGAAAG                         GCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTG
genomic: AAGGACAGTTCTACCAAGTTCTCCTTCACGAGCTGGATGCAATTAGAAAGgtatagtatg ... ttttggacagGCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTG
EST: gi|169027233|gb|FE435091.1|FE435091
EST:     TCACGAGCTGGATGCAATTAGAAAG                         GCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTG
genomic: TCACGAGCTGGATGCAATTAGAAAGgtatagtatg ... ttttggacagGCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTG
EST: gi|169026895|gb|FE432387.1|FE432387
EST:     AAGGACAGTTCTACCAAGTTCTCCTTCACGAGCTGGATGCAATTAGAAAG                         GCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTG
genomic: AAGGACAGTTCTACCAAGTTCTCCTTCACGAGCTGGATGCAATTAGAAAGgtatagtatg ... ttttggacagGCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTG
EST: gi|169092972|gb|FE495266.1|FE495266
EST:     AAGGACAGTTCTACCAAGTTCTCCTTCACGAGCTGGATGCAATTAGAAAG                         GCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTG
genomic: AAGGACAGTTCTACCAAGTTCTCCTTCACGAGCTGGATGCAATTAGAAAGgtatagtatg ... ttttggacagGCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTG
EST: gi|169021773|gb|FE430420.1|FE430420
EST:     AAGGACAGTTCTACCAAGTTCTCCTTCACGAGCTGGATGCAATTAGAAAG                         GCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTG
genomic: AAGGACAGTTCTACCAAGTTCTCCTTCACGAGCTGGATGCAATTAGAAAGgtatagtatg ... ttttggacagGCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTG
EST: gi|169077159|gb|FE484538.1|FE484538
EST:     AAGGACAGTTCTACCAAGTTCTCCTTCACGAGCTGGATGCAATTAGAAAG                         GCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTG
genomic: AAGGACAGTTCTACCAAGTTCTCCTTCACGAGCTGGATGCAATTAGAAAGgtatagtatg ... ttttggacagGCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTG

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: 33 (upstream exon), 35 (downstream exon)
Score: 32

CTCTGGATACAAACCTGGAAGAATCATCTTCTACAGAGATGGTGTGAGCGAAGGACAGTTCTACCAAGTTCTCCTTCACGAGCTGGATGCAATTAGAAAGgtatagtatg ... ttttggacagGCTTGCGCGTCACTCGAGCCGAACTATCAGCCTCTCGTGACGTTCGTTGTGGTCCAGAAACGGCACCACACCCGGCTATTTGCTAACGATCACGACGATA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCTGGATACAAACCTGGAAGAATCATCTTCTACAGAGATGGTGTGAGCGAAGGACAGTTCTACCAAGTTCTCCTTCACGAGCTGGATGCAATTAGAAAGgtatagtatggaaagacttggcacattgactgattcagctcttcgttttggacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA