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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcacgatttgattcgaaagctttccgatacatgatttgtatcccgattcaactgccgtggctaataactttggcaaccttgttttctttatttaatgcagTTTCTAGAAACAGGACCTGAACTGGGAAGTCACTATAATGACGTAATTGCACCTCAAGATGTTGCAACATATGGAGGACTTTGTGCACTTGCAACATTTG

Basic information

species Glycine max
transcript GLYMA03G01880.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G01880.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv15s0048g01980.t01 (Vitis vinifera), 3'ss of exon 2
tcacgatttgattcgaaagctttccgatacatgatttg--tatcccgattcaactgccgtggctaataactttggcaaccttgttttctttatttaat-gcagTTTCTAGAAACAGGACCTGAACTGGGAAGTCACTATAATGACGTAATTGCACCTCAAGATGTTGCAACATATGGAGGACTTTGTGCACTTGCAACATTTG
     | |||  | | ||  |    || | ||  |  |  |||   |   ||  |    | | | ||  | |     |  |  | |   |  |||| |  |||||  | ||||||||  |||||||||| |   |||| |  || || ||||| || ||||||||||| || ||||| || ||||||||||||||||  ||||
--gttacttggat-gcaacatagaagagaaattttcagattattatgcgccatattgaattgatcattccatcaatgaattaatgtctctggtttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCTCCACAAGATGTTGCTACCTATGGTGGTCTTTGTGCACTTGCAAGCTTTG

upper sequence: GLYMA03G01880.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S311_49V6.1 (Physcomitrella patens), 3'ss of exon 2
tcacgatttgattcgaaagctttccgatacatg-atttgtatcccgattcaactgccgtggctaataactttggcaaccttgttttctttatttaatgcagTTTCTAGAAACAGGACCTGAACTGGGAAGTCACTATAATGACGTAATTGCACCTCAAGATGTTGCAACATATGGAGGACTTTGTGCACTTGCAACATTTG
 |  | |  | | |   ||   | |||   | | | ||| ||   | | ||    |    |  | |  | | |     | | |  |   | ||| | ||||||| | || ||      |||  |||||||  |||||   || ||||  || |||||||||||||||||||||||||| ||||| || |||||| |||| |
ccgtgttcaggtccttgagagatgcgagtgacgtagttggattaagttccagacacttctga-agtggcgtagcagctcatatcatgggttttttacgcagTTTGTTGACACGAACTTTGAGTTGGGAAGCAACTATTCAGATGTAACAGCTCCTCAAGATGTTGCAACATATGGAGGTCTTTGCGCTCTTGCATCATTCG

upper sequence: GLYMA03G01880.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S31_338V6.1 (Physcomitrella patens), 3'ss of exon 2
tcacgatttgattcgaaagctttccgatacatgatttgtatcccgattcaactgccgtggctaataactttggcaaccttgttttctttatttaatgcagTTTCTAGAAACAGGACCTGAACTGGGAAGTCACTATAATGACGTAATTGCACCTCAAGATGTTGCAACATATGGAGGACTTTGTGCACTTGCAACATTTG
    | | ||||     || | |||  |      ||    |    | |        |    |||   | ||      | || | |   | |   | ||||||| | || ||       ||  |||| ||  ||||    || || || || || ||||||||||||||||||||||| ||||| || |||||| | ||||
attggttgtgatagacgagatgtcccttgaggagttaaagtgggaagttcggattagcatataaaggcgttacagctcatgctattggtttggtacgcagTTTGTTGACACGAACTTCGAGTTGGGTAGCAACTACTCAGATGTTATAGCTCCCCAAGATGTTGCAACATATGGAGGTCTTTGCGCGCTTGCATCGTTTG

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|57574802|gb|CX547777.1|CX547777
EST:     CAGGATT-GCTAATCTAGAAGCCAAAAAGTACAAGCTTGCTGCCNGAAAG                         TTTCTAGAAACAGGACCTGAACTGGGAAGTCACTATAATGACGTAATTGCA
genomic: CAGGATTGGCTAATCTAGAAGCCAAAAAGTACAAGCTTGCTGCCCGAAAGgtctgttcct ... tttaatgcagTTTCTAGAAACAGGACCTGAACTGGGAAGTCACTATAATGACGTAATTGCA
EST: gi|27427398|gb|CA938918.1|CA938918
EST:     CAGGATTGGCTAATCTAGAAGCCAAAAAGTACAAGCTTGCTGCCCGAAAG                         TTTCTAGAAACAGGACCTGAACTGGGAAGTCACTATAATGACGTAATTGCA
genomic: CAGGATTGGCTAATCTAGAAGCCAAAAAGTACAAGCTTGCTGCCCGAAAGgtctgttcct ... tttaatgcagTTTCTAGAAACAGGACCTGAACTGGGAAGTCACTATAATGACGTAATTGCA
EST: gi|37997756|gb|CF809345.1|CF809345
EST:     CAGGATTGGCTAATCTAGAAGCCAAAAAGTACAAGCTTGCTGCCCGAAAG                         TTTCTAGAAACAGGACCTGAACTGGGAAGTCACTATAATGACGTAATTGCA
genomic: CAGGATTGGCTAATCTAGAAGCCAAAAAGTACAAGCTTGCTGCCCGAAAGgtctgttcct ... tttaatgcagTTTCTAGAAACAGGACCTGAACTGGGAAGTCACTATAATGACGTAATTGCA
EST: gi|298172715|gb|HO019755.1|HO019755
EST:     CAGGATTGGCTAATCTAGAAGCCAAAAAGTACAAGCTTGCTGCCCGAAAG                         TTTCTAGAAACAGGACCTGAACTGGGAAGTCACTATAACGACGTAATTGCA
genomic: CAGGATTGGCTAATCTAGAAGCCAAAAAGTACAAGCTTGCTGCCCGAAAGgtctgttcct ... tttaatgcagTTTCTAGAAACAGGACCTGAACTGGGAAGTCACTATAATGACGTAATTGCA
EST: gi|151408473|gb|EV278281.1|EV278281
EST:     CAGGATTGGCTAATCTAGAAGCCAAAAAGTACAAGCTTGCTGCCCGAAAG                         TTTCTAGAAACAGGGCCTGAACTGGGAAGTCACTATAATGACGTAATTGCA
genomic: CAGGATTGGCTAATCTAGAAGCCAAAAAGTACAAGCTTGCTGCCCGAAAGgtctgttcct ... tttaatgcagTTTCTAGAAACAGGACCTGAACTGGGAAGTCACTATAATGACGTAATTGCA
EST: gi|58015910|gb|CX702652.1|CX702652
EST:     CAGGATTGG-TAATCTAGAAGCCAAAAAGTACAAGCTTGCTGCCCGAAAG                         TTTCTAGAAACAGGACNTGAACTGGGAAGTCACTATAATGACGTAATTGCA
genomic: CAGGATTGGCTAATCTAGAAGCCAAAAAGTACAAGCTTGCTGCCCGAAAGgtctgttcct ... tttaatgcagTTTCTAGAAACAGGACCTGAACTGGGAAGTCACTATAATGACGTAATTGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcaactgccgtggctaataactttggcaaccttgttttctttatttaatgcagTTTCTAGAAACAGGACCTGAACTGGGAAGTCACTATAATGACGTAATTGCACCTCAAGATGTTGCAACATATGGAGGACTTTGTGCACTTGCAACATTTG
                               ccttgttttctttatt  CT-rich tract
                                 ttgttttctttattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcacgatttgattcgaaagctttccgatacatgatttgtatcccgattcaactgccgtggctaataactttggcaaccttgttttctttatttaatgcagTTTCTAGAAACAGGACCTGAACTGGGAAGTCACTATAATGACGTAATTGCACCTCAAGATGTTGCAACATATGGAGGACTTTGTGCACTTGCAACATTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA