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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttggcatattcctgattgacatttcagtcccctgggacatactatctgaaattcaaaattttattgggtaattttcattgtttcagCTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT

Basic information

species Glycine max
transcript GLYMA03G38520.1
intron # 9
splice site 3'
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|193635003|gb|FK579752.1|FK579752
EST:     CAGTAAAGCTAATTGGGTGGGGAACAACTGATGATGGGGAGGACTATTGG                         CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
genomic: CAGTAAAGCTAATTGGGTGGGGAACAACTGATGATGGGGAGGACTATTGGgtatgttggc ... attgtttcagCTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT
EST: gi|13252459|gb|BG363370.1|BG363370
EST:     CAGTAAAGCTAATTGGGTGGGGAACAACTGATGATGGGGAGGACTATTGG                         CTTCTTGCAAATCAGTGGAACAGAGAATGGG-AGAT
genomic: CAGTAAAGCTAATTGGGTGGGGAACAACTGATGATGGGGAGGACTATTGGgtatgttggc ... attgtttcagCTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT
EST: gi|31312156|gb|CD397359.1|CD397359
EST:     CAGTAAAGCTAATTGGGTGGGGAACAACTGATGATGGGGAGGACTATTGG                         CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
genomic: CAGTAAAGCTAATTGGGTGGGGAACAACTGATGATGGGGAGGACTATTGGgtatgttggc ... attgtttcagCTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT
EST: gi|11273992|gb|BF324368.1|BF324368
EST:     CAGTAAAGCTAATTGGGTGGGGAACAACTGATGATGGGGAGGACTATTGG                         CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT
genomic: CAGTAAAGCTAATTGGGTGGGGAACAACTGATGATGGGGAGGACTATTGGgtatgttggc ... attgtttcagCTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT
EST: gi|18716048|gb|BM522863.1|BM522863
EST:     CAGTAAAGCTAATTGGGTGGGGAACAACTGATGATGGGGAGGACTATTGG                         CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT
genomic: CAGTAAAGCTAATTGGGTGGGGAACAACTGATGATGGGGAGGACTATTGGgtatgttggc ... attgtttcagCTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT
EST: gi|9899704|gb|BE608672.1|BE608672
EST:     CAGTAAAGCTAATTGGGTGGGGAACAACTGATGATGGGGAGGACTATTGG                         CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT
genomic: CAGTAAAGCTAATTGGGTGGGGAACAACTGATGATGGGGAGGACTATTGGgtatgttggc ... attgtttcagCTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT
EST: gi|41145378|gb|CK605589.1|CK605589
EST:     GGGGAACAACTGATGATGGGGAGGACTATTGG                         CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT
genomic: GGGGAACAACTGATGATGGGGAGGACTATTGGgtatgttggc ... attgtttcagCTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT
EST: gi|58018606|gb|CX705348.1|CX705348
EST:     CAGTAAAGCTAATTGGGTGGGGAACAACTGATGATGGGGAGGACTATTGG                         CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT
genomic: CAGTAAAGCTAATTGGGTGGGGAACAACTGATGATGGGGAGGACTATTGGgtatgttggc ... attgtttcagCTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT
EST: gi|298182905|gb|HO028118.1|HO028118
EST:     CAGTAAAGCTAATTGGGTGGGGAACAACTGATGATGGGGAGGACTATTGG                         CTTCTTGCAAATCGGTGGAACAGAGAATGGGGAGAT
genomic: CAGTAAAGCTAATTGGGTGGGGAACAACTGATGATGGGGAGGACTATTGGgtatgttggc ... attgtttcagCTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT
EST: gi|208272210|gb|GE067452.1|GE067452
EST:     ACTGATGATGGGGAGGACTATTGG                         CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
genomic: ACTGATGATGGGGAGGACTATTGGgtatgttggc ... attgtttcagCTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT
EST: gi|151400974|gb|EV270788.1|EV270788
EST:     CAGTAAAGCTAATTGGGTGGGGAACAACTGATGATGGGGAGGACTATTGG                         CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT
genomic: CAGTAAAGCTAATTGGGTGGGGAACAACTGATGATGGGGAGGACTATTGGgtatgttggc ... attgtttcagCTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT
EST: gi|18719713|gb|BM523220.1|BM523220
EST:     CAGTAAAGCTAATTGGGTGGGGAACAACTGATGATGGGGAGGACTATTGG                         CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT
genomic: CAGTAAAGCTAATTGGGTGGGGAACAACTGATGATGGGGAGGACTATTGGgtatgttggc ... attgtttcagCTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT
EST: gi|17402160|gb|BM178942.1|BM178942
EST:     CAGTAAAGCTAATTGGGTGGGGAACAACTGATGATGGGGAGGACTATTGG                         CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
genomic: CAGTAAAGCTAATTGGGTGGGGAACAACTGATGATGGGGAGGACTATTGGgtatgttggc ... attgtttcagCTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT
EST: gi|193619181|gb|FK569425.1|FK569425
EST:     CAGTAAAGCTAATTGGGTGGGGAACAACTGATGATGGGGAGGACTATTGG                         CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
genomic: CAGTAAAGCTAATTGGGTGGGGAACAACTGATGATGGGGAGGACTATTGGgtatgttggc ... attgtttcagCTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT
EST: gi|10235663|gb|BE804551.1|BE804551
EST:     CAGTAAAGCTAATTGGGTGGGGAACAACTGATGATGGGGAGGACTATTGG                         CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT
genomic: CAGTAAAGCTAATTGGGTGGGGAACAACTGATGATGGGGAGGACTATTGGgtatgttggc ... attgtttcagCTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT
EST: gi|10235891|gb|BE804779.1|BE804779
EST:     CAGTAAAGCTAATTGGGTGGGGAACAACTGATGATGGGGAGGACTATTGG                         CTTCTTGCAAATCAGTGGAACAGAGAATGGGGAGAT
genomic: CAGTAAAGCTAATTGGGTGGGGAACAACTGATGATGGGGAGGACTATTGGgtatgttggc ... attgtttcagCTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT
EST: gi|8670417|gb|BE191524.1|BE191524
EST:     CAGTAAAGCTAATTGGGTGGGGAACAACTGATGATGAGGAGGACTATTGG                         CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT
genomic: CAGTAAAGCTAATTGGGTGGGGAACAACTGATGATGGGGAGGACTATTGGgtatgttggc ... attgtttcagCTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT
EST: gi|254336334|gb|GR842513.1|GR842513
EST:     CAGTAAAGCTAATTGGGTGGGGAACAACTGATGATGGGGAGGACTATTGG                         CTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT
genomic: CAGTAAAGCTAATTGGGTGGGGAACAACTGATGATGGGGAGGACTATTGGgtatgttggc ... attgtttcagCTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgggacatactatctgaaattcaaaattttattgggtaattttcattgtttcagCTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT
                                        ttttcatt  CT-rich tract
       atactatctgaaattc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttggcatattcctgattgacatttcagtcccctgggacatactatctgaaattcaaaattttattgggtaattttcattgtttcagCTTCTCGCAAATCAGTGGAACAGAGAATGGGGAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT