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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtcaccatactcacttatcctatgttcaaagaaaattattatcttatcttacataaaattgtttatttctaattcacagCGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGAAGTGATTTCATCTGCGTCACAAGGAAGCAAATTGACTCGAGCAAGATCGAGTCTAATAT

Basic information

species Glycine max
transcript GLYMA20G36790.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G36790.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G138268_T01 (Zea mays), 3'ss of exon 4
--------------------------gttagtcaccatactcacttatcctatgttcaaagaaaattattatcttatct--tacataaaattgtttatttctaa--ttcacagCGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGAAGTGATTTCATCTGCGTCACAAGGAAGCAAATTGACTCGAGCAAGATCGAGTCTAATAT-----
                           ||| | | |  |   ||  |    |  ||| | |  | | |  | |   | |  | |||    |  | ||| ||| |  ||  |||||||||| ||| |||| || |||||||||||||||||| ||   ||   |    | | |  |||   |||  |   | | | || |   |  |   ||       
gtgagttgacatatatgattattattattactaatctcaacaacaaaagagactttctagggtagtaagcagcccgtttgtttcatctggtc-tctatctctgaattttccagCGCCAAGGGCCATGGAGAAATGCAAGAACAGAAGCTGAGGAGAAGA---CGGACG-GACGGAAGCTTGCATCTCAGCACCACCAGGGGTGGATG-GATGCAAGAA

upper sequence: GLYMA20G36790.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0081g00010.t01 (Vitis vinifera), 3'ss of exon 4
-----------------gttagtcaccatactcacttatcctatgttcaaag--------aaaattattatctta---tcttacataaaattgtttatttc-taattcacagCGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGAAGTGATTTCATCTGCGTCACAAGGAAGCAAATTGACTCGAGCAAGATCGAGTCTAATAT--
                 | |      |||  ||| |     ||||||||||         |   ||  |  ||||   ||||  ||    ||| ||| |   |      |||| |||||||| ||||| |||||||||||||||||||  ||       | ||    |  | ||   ||| |||  | |   ||||     |  ||    ||  
gttagtcatatatacttgctgcaactcatgatcattatggttatgttcaaaattttcaccacttttgctgacttaatctcttgtatttgcttgattaatcaatggcatgcagCCCCAAGAGCAGTGGAGAAGTGCAAGAACAGAAGCTAGAGGCACCCATCCACAGTCTGCCCATCAAAGGAAA--GCCAGAAGCAGCTGAGGATCATGGATGG
















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|21594765|gb|BQ610259.1|BQ610259
EST:     ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTG                         CGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGAAGTGATTTCA
genomic: ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTGgttagtcacc ... taattcacagCGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGAAGTGATTTCA
EST: gi|254339868|gb|GR857993.1|GR857993
EST:     ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTG                         CGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGAAGTGATTTCA
genomic: ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTGgttagtcacc ... taattcacagCGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGAAGTGATTTCA
EST: gi|254339867|gb|GR857992.1|GR857992
EST:     ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTG                         CGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGAAGTGATTTCA
genomic: ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTGgttagtcacc ... taattcacagCGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGAAGTGATTTCA
EST: gi|21600987|gb|BQ611327.1|BQ611327
EST:     ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTG                         CGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAA
genomic: ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTGgttagtcacc ... taattcacagCGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAA
EST: gi|26057410|gb|CA800324.1|CA800324
EST:     ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTG                         CGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGC
genomic: ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTGgttagtcacc ... taattcacagCGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGC
EST: gi|151396677|gb|EV266550.1|EV266550
EST:     ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTG                         CGCCAAGAGCCGTGGAAA-GTGCA-GA-CAGA-GCTGAAGA-GTGATTTCA
genomic: ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTGgttagtcacc ... taattcacagCGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGAAGTGATTTCA
EST: gi|151398070|gb|EV267948.1|EV267948
EST:     ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTG                         CGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGAAGTGATTTCA
genomic: ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTGgttagtcacc ... taattcacagCGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGAAGTGATTTCA
EST: gi|192317984|gb|FK009464.1|FK009464
EST:     ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTG                         CGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGAAGTGATTTCA
genomic: ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTGgttagtcacc ... taattcacagCGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGAAGTGATTTCA
EST: gi|21602083|gb|BQ612414.1|BQ612414
EST:     ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTG                         CGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGAAGTGATTTCA
genomic: ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTGgttagtcacc ... taattcacagCGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGAAGTGATTTCA
EST: gi|51335090|gb|CO978956.1|CO978956
EST:     ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTG                         CGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGAAGTGATTTCA
genomic: ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTGgttagtcacc ... taattcacagCGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGAAGTGATTTCA
EST: gi|58024615|gb|CX711356.1|CX711356
EST:     ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTG                         CGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGAAGTGATTTCA
genomic: ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTGgttagtcacc ... taattcacagCGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGAAGTGATTTCA
EST: gi|192317983|gb|FK009463.1|FK009463
EST:     ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTG                         CGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGAAGTGATTTCA
genomic: ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTGgttagtcacc ... taattcacagCGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGAAGTGATTTCA
EST: gi|42722983|gb|CK768882.1|CK768882
EST:     ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTG                         CGCCAAGAGCCGTGGATAAGTGCAAGAACAGAAGCTGATGAAGTGATTTCA
genomic: ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTGgttagtcacc ... taattcacagCGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGAAGTGATTTCA
EST: gi|208178460|gb|GD977797.1|GD977797
EST:     ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTG                         CGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGAAGTGATTTCA
genomic: ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTGgttagtcacc ... taattcacagCGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGAAGTGATTTCA
EST: gi|192297650|gb|FG992758.1|FG992758
EST:     ATCATGCAAGCGTTTTCGCATAATGAAAGGTTCCGAGGCAATCGGTCTTG                         CGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGAAGTGATTTCA
genomic: ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTGgttagtcacc ... taattcacagCGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGAAGTGATTTCA
EST: gi|214008573|gb|DB986750.1|DB986750
EST:     ATCATGCAAGATTCAACGCATAATGAAAGGCTCCGAGGCAATCGGTCTTG                         CGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGAAGTGATTTCA
genomic: ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTGgttagtcacc ... taattcacagCGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGAAGTGATTTCA
EST: gi|57576038|gb|CX549009.1|CX549009
EST:     ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTG                         CGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGAAGTGATTTCA
genomic: ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTGgttagtcacc ... taattcacagCGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGAAGTGATTTCA
EST: gi|26058652|gb|CA801566.1|CA801566
EST:     ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTG                         CGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAA
genomic: ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTGgttagtcacc ... taattcacagCGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAA
EST: gi|10236738|gb|BE805626.1|BE805626
EST:     ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTG                         CGCCAAGAGCCGTGGAAAAGTGGCAA-AACAGAAGC
genomic: ATCATGCAAGCGTCTTCGCATAATGAAAGGCTCCGAGGCAATCGGTCTTGgttagtcacc ... taattcacagCGCCAAGAGCCGTGGAAAAGTG-CAAGAACAGAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaaagaaaattattatcttatcttacataaaattgtttatttctaattcacagCGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGAAGTGATTTCATCTGCGTCACAAGGAAGCAAATTGACTCGAGCAAGATCGAGTCTAATAT
                                          ttctaat  putative branch site (score: 2)
                                     tttatttct  CT-rich tract
     agaaaattattatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtcaccatactcacttatcctatgttcaaagaaaattattatcttatcttacataaaattgtttatttctaattcacagCGCCAAGAGCCGTGGAAAAGTGCAAGAACAGAAGCTGAAGAAGTGATTTCATCTGCGTCACAAGGAAGCAAATTGACTCGAGCAAGATCGAGTCTAATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA