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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatctaacagctaattaagaactaggcattcaaactccactaattaagtaactggatcacaggctaagttaattgtgcttgttattcaatattcattagGTGCAAAGAAGTGTGGATGATCAATCTGTTCTGGTTGCAACTTATGAAGGAGAGCACAATCATCCTCACCCTTCTCAAATGGAGGTAACAACAGGCTCCA

Basic information

species Glycine max
transcript GLYMA13G44730.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G44730.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0018g00240.t01 (Vitis vinifera), 3'ss of exon 4
----------------------------------gtaaatctaacagctaattaagaactaggcattcaaactccactaattaagtaactggatcacaggctaagttaattgtgcttgttattcaatattcattagGTGCAAAGAAGTGTGGATGATCAATCTGTTCTGGTTGCAACTTATGAAGGAGAGCACAATCATCCTCACCCTTCTCAAATGGAGGTAACAACAGGCTCCA
                                  ||   | ||  | ||  |    |  |  | ||| ||| |   |  ||| |||   ||  |  ||  ||||| |  ||       ||  |     ||| | |||||||||||||||| || ||||||||| |  |||| ||||| || ||||| ||||| |||||||| ||||||  || ||| |||   ||| ||||  | |
gtgagcctaaacttgacaatcccacctgtgattcgtctttttaggaacttgtgtcaaggtccggattgaaattgtcc--attgagtt-ttgcttagcattctaagctgttttctgcaatttgtttcctttcttcagGTGCAAAGAAGTGTTGAAGATCAATCTATATTGGTAGCAACCTACGAAGGCGAGCATAATCATCCACACCCTGGTCGAATTGAGCCCACATCAGGTGCAA
















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|5760480|gb|AI965843.1|AI965843
EST:     GAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCGGTCAAAAAGAAG                         GTGC--ATAAGTGTGGATGATCAATCTGTTCTGGTTGCAACTTATGAAGGA
genomic: GAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCGGTCAAAAAGAAGgtaaatctaa ... tattcattagGTGCAAAGAAGTGTGGATGATCAATCTGTTCTGGTTGCAACTTATGAAGGA
EST: gi|5761174|gb|AI966537.1|AI966537
EST:     GAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCGGTCAAATAGAAT                         GTGCAAAGAAGTGTGGATGATCAATCTGTTCTGGCTGCAACTTATGAAGGA
genomic: GAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCGGTCAAAAAGAAGgtaaatctaa ... tattcattagGTGCAAAGAAGTGTGGATGATCAATCTGTTCTGGTTGCAACTTATGAAGGA
EST: gi|5666936|gb|AI930972.1|AI930972
EST:     GAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCGGTCAAAAAGAAG                         GTGCAAAGAAGTGTGGATGATCAATCTGTTCTGGTTGCAACTTATGAAGGA
genomic: GAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCGGTCAAAAAGAAGgtaaatctaa ... tattcattagGTGCAAAGAAGTGTGGATGATCAATCTGTTCTGGTTGCAACTTATGAAGGA
EST: gi|17400389|gb|BM177171.1|BM177171
EST:     GAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCGGTCAAAAAGAAG                         GTGCAAAGAAGTGTGGATGATCAATCTGTTCTGGTTGCAACTTATGAAGGA
genomic: GAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCGGTCAAAAAGAAGgtaaatctaa ... tattcattagGTGCAAAGAAGTGTGGATGATCAATCTGTTCTGGTTGCAACTTATGAAGGA
EST: gi|13252596|gb|BG363499.1|BG363499
EST:     GAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCGGTCAAAAAGAAG                         GTGCAAAGAAGTGTGGATGATCAATCTGTTCTGGTTGCAACTTATGAAGGA
genomic: GAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCGGTCAAAAAGAAGgtaaatctaa ... tattcattagGTGCAAAGAAGTGTGGATGATCAATCTGTTCTGGTTGCAACTTATGAAGGA
EST: gi|18732716|gb|BM527205.1|BM527205
EST:     GAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCGGTCAAAAAGAAG                         GTGCAAAGAAGTGTGGATGATCAATCTGTTCTGGTTGCAACTTATGAAGGA
genomic: GAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCGGTCAAAAAGAAGgtaaatctaa ... tattcattagGTGCAAAGAAGTGTGGATGATCAATCTGTTCTGGTTGCAACTTATGAAGGA
EST: gi|151403380|gb|EV273190.1|EV273190
EST:     GAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCGGTCAAAAAGAAG                         GTGCAAAGAAGTGTGGATGATCAATCTGTTCTGGTTGCAACTTATGAAGGA
genomic: GAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCGGTCAAAAAGAAGgtaaatctaa ... tattcattagGTGCAAAGAAGTGTGGATGATCAATCTGTTCTGGTTGCAACTTATGAAGGA
EST: gi|5820418|gb|AI988624.1|AI988624
EST:     GAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCGGTCAAAAAGAAG                         GTGCANAGAAGTGTGGATGATCAATCTGTTCTG
genomic: GAGCATATTTCAAGTGCTCTTTTGCTCCAAGCTGCCCGGTCAAAAAGAAGgtaaatctaa ... tattcattagGTGCAAAGAAGTGTGGATGATCAATCTGTTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagtaactggatcacaggctaagttaattgtgcttgttattcaatattcattagGTGCAAAGAAGTGTGGATGATCAATCTGTTCTGGTTGCAACTTATGAAGGAGAGCACAATCATCCTCACCCTTCTCAAATGGAGGTAACAACAGGCTCCA
                                     ttattcaatattcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatctaacagctaattaagaactaggcattcaaactccactaattaagtaactggatcacaggctaagttaattgtgcttgttattcaatattcattagGTGCAAAGAAGTGTGGATGATCAATCTGTTCTGGTTGCAACTTATGAAGGAGAGCACAATCATCCTCACCCTTCTCAAATGGAGGTAACAACAGGCTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG