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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgtttggttgacagtattggtagtagatgacaattaaattctaattatattactttgttttgctaaaacttatgaattttgtatacatgatggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTCAGACCAATTCTTCACCACTACGACGGCCCTAAGTTCCGTCTTGAGCTGA

Basic information

species Glycine max
transcript GLYMA13G10640.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G10640.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G42050.1 (Arabidopsis thaliana), 3'ss of exon 2
ctgtttggttgacagtattggtagtagatgacaattaaattctaattatattactttgttttgctaaaa--cttatgaattttgtata-catgatggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTCAGACCAATTCTTCACCACTACGACGGCCCTAAGTTCCGTCTTGAGCTGA
              ||| |  ||     | ||  |       |  ||  |   |||  |||||   |||  || |  |||||| |     |  |    || ||||    |  || || |||||||| |||  |||||| || |||||||| ||| |||| ||| | |||||||||||||| ||||||||||| || || || |
--------------gtactactatgtacttactttcttgcgtttctttgagctcttgcttttgtctaaatgctaacaaattttttggggtaataaaaataaagGTGAGGGCCATAACGAGGAAAGTATGTTTGCCACTGGAAGAAGATTCTTTCCGACCCATTTTGCACCACTACGACGGTCCTAAGTTCCGACTCGAACTCA
















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|308098890|gb|HO760731.1|HO760731
EST:     CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
genomic: CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
EST: gi|254331893|gb|GR846203.1|GR846203
EST:     CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
genomic: CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
EST: gi|151402959|gb|EV272772.1|EV272772
EST:     CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
genomic: CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
EST: gi|58024390|gb|CX711131.1|CX711131
EST:     CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
genomic: CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
EST: gi|5057954|gb|AI736430.1|AI736430
EST:     CGGCTTGGGAGGATNAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
genomic: CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
EST: gi|151395760|gb|EV265637.1|EV265637
EST:     CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
genomic: CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
EST: gi|4396241|gb|AI495238.1|AI495238
EST:     CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
genomic: CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
EST: gi|15000771|gb|BI321585.1|BI321585
EST:     CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
genomic: CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
EST: gi|14990506|gb|BI316179.1|BI316179
EST:     CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGC
genomic: CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGC
EST: gi|254321753|gb|GR825070.1|GR825070
EST:     GTGAATCTCGTTT-CCTGCTCAG                         G-TCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
genomic: GTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
EST: gi|213611124|gb|DB974998.1|DB974998
EST:     CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
genomic: CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
EST: gi|11274747|gb|BF325082.1|BF325082
EST:     CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
genomic: CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
EST: gi|21600694|gb|BQ611025.1|BQ611025
EST:     CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
genomic: CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
EST: gi|213594925|gb|DB977239.1|DB977239
EST:     CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
genomic: CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
EST: gi|9204543|gb|BE330767.1|BE330767
EST:     CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
genomic: CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
EST: gi|120494939|gb|EH223106.1|EH223106
EST:     CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
genomic: CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
EST: gi|4313652|gb|AI460771.1|AI460771
EST:     CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
genomic: CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
EST: gi|254331894|gb|GR846204.1|GR846204
EST:     CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
genomic: CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
EST: gi|11413917|gb|BF425928.1|BF425928
EST:     CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTANGAAAGTTTGTGAGCCACTAGAGGAAGAT
genomic: CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGAT
EST: gi|9204544|gb|BE330768.1|BE330768
EST:     TGGCTCGGAAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
genomic: -GGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
EST: gi|10843221|gb|BF066529.1|BF066529
EST:     CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTATGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
genomic: CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
EST: gi|4301736|gb|AI443233.1|AI443233
EST:     CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
genomic: CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
EST: gi|58017712|gb|CX704454.1|CX704454
EST:     CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
genomic: CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
EST: gi|7588504|gb|AW704360.1|AW704360
EST:     CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
genomic: CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
EST: gi|214006357|gb|DB985747.1|DB985747
EST:     CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
genomic: CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
EST: gi|58018450|gb|CX705192.1|CX705192
EST:     CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAG                         GTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC
genomic: CGGCTTGGGAGGATAAGAAGTGCCCTGGTGAATCTCGTTTCCCTGCTCAGgtatatatca ... atggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatattactttgttttgctaaaacttatgaattttgtatacatgatggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTCAGACCAATTCTTCACCACTACGACGGCCCTAAGTTCCGTCTTGAGCTGA
                tgctaaa  putative branch site (score: 2)
                   taaaacttatgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgtttggttgacagtattggtagtagatgacaattaaattctaattatattactttgttttgctaaaacttatgaattttgtatacatgatggttacagGTTCAAGTGATTACTAGGAAAGTTTGTGAGCCACTAGAGGAAGATTCCTTCAGACCAATTCTTCACCACTACGACGGCCCTAAGTTCCGTCTTGAGCTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
ctgtttg