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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acatattgggtgtgacatatagcctaagatctttgagcttttgtgaaggattttgtaaagcaaattatagtaatgaataataagttttgcccatttgcagGAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATATACCAAGAAAGGACTGGAATGGGTGAATACAACTGAGAGCCTAAAGGAT

Basic information

species Glycine max
transcript GLYMA19G01470.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G01470.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv14s0066g01670.t01 (Vitis vinifera), 3'ss of exon 9
acatattgggtgtgacatatagcctaagatctttgagcttttgtgaaggattttg--taaagcaaattatagtaatgaataataagttttgcc---catt---tgcagGAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATATACCAAGAAAGGACTGGAATGGGTGAATACAACTGAGAGCCTAAAGGAT
                | | |    || ||  | ||   ||     ||   |||   | ||     |  |     |   |  |  |||| |||   | |    ||||||||| |||  || |||||||||||||||||||| || || || |||||||| || ||||| ||||| ||||||||||| || || ||||| || || |||
--------------gtaaacaaaacaaaataatggaatattaaaatagacctttaattgaattggttattgaccgtatttggtgggtttggccatgcgtggaatgcagGAGGCTAGGGGCAGACAGGTTCTTCACAAGCAATTTCAACGAGGAGACATACACAAAGAAGGGACTTGAATGGGTGAACACCACGGAGAGTCTGAAAGAT
















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|15000829|gb|BI321643.1|BI321643
EST:     TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAG                         GAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
genomic: TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAGgtaagagcaa ... ccatttgcagGAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
EST: gi|254348900|gb|GR852579.1|GR852579
EST:     TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAG                         GAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
genomic: TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAGgtaagagcaa ... ccatttgcagGAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
EST: gi|254332514|gb|GR846452.1|GR846452
EST:     TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAG                         GAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
genomic: TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAGgtaagagcaa ... ccatttgcagGAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
EST: gi|16341633|gb|BI967228.1|BI967228
EST:     TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAG                         GAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
genomic: TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAGgtaagagcaa ... ccatttgcagGAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
EST: gi|120531316|gb|EH259449.1|EH259449
EST:     TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAG                         GAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
genomic: TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAGgtaagagcaa ... ccatttgcagGAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
EST: gi|254336836|gb|GR843015.1|GR843015
EST:     TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAG                         GAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
genomic: TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAGgtaagagcaa ... ccatttgcagGAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
EST: gi|15000650|gb|BI321464.1|BI321464
EST:     TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAG                         GAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
genomic: TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAGgtaagagcaa ... ccatttgcagGAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
EST: gi|7926022|gb|AW832048.1|AW832048
EST:     TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAG                         GAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
genomic: TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAGgtaagagcaa ... ccatttgcagGAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
EST: gi|6719817|gb|AW307464.1|AW307464
EST:     TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAG                         GAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
genomic: TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAGgtaagagcaa ... ccatttgcagGAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
EST: gi|120492176|gb|EH220343.1|EH220343
EST:     TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAG                         GAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
genomic: TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAGgtaagagcaa ... ccatttgcagGAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
EST: gi|120531173|gb|EH259306.1|EH259306
EST:     TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAG                         GAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
genomic: TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAGgtaagagcaa ... ccatttgcagGAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
EST: gi|254317376|gb|GR826321.1|GR826321
EST:     TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAG                         GAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
genomic: TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAGgtaagagcaa ... ccatttgcagGAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
EST: gi|254348901|gb|GR852580.1|GR852580
EST:     TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAG                         GAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
genomic: TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAGgtaagagcaa ... ccatttgcagGAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
EST: gi|254319857|gb|GR830881.1|GR830881
EST:     TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAG                         GAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
genomic: TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAGgtaagagcaa ... ccatttgcagGAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
EST: gi|17401344|gb|BM178126.1|BM178126
EST:     TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAG                         GAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
genomic: TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAGgtaagagcaa ... ccatttgcagGAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
EST: gi|13479194|gb|BG508537.1|BG508537
EST:     TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAG                         GAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
genomic: TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAGgtaagagcaa ... ccatttgcagGAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
EST: gi|254339407|gb|GR848124.1|GR848124
EST:     TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAG                         GAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGA-GAGACATA
genomic: TTTGCAATCAGTGAGACAGCTTTTGTTATATTCCTACTCATGGCAACCAGgtaagagcaa ... ccatttgcagGAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
EST: gi|254344326|gb|GR855304.1|GR855304
EST:     CTCATGGCAACCAG                         GAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA
genomic: CTCATGGCAACCAGgtaagagcaa ... ccatttgcagGAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggattttgtaaagcaaattatagtaatgaataataagttttgcccatttgcagGAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATATACCAAGAAAGGACTGGAATGGGTGAATACAACTGAGAGCCTAAAGGAT
                                       ttttgccc  CT-rich tract
                aaattatagtaatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acatattgggtgtgacatatagcctaagatctttgagcttttgtgaaggattttgtaaagcaaattatagtaatgaataataagttttgcccatttgcagGAGGTTAGAAGCTGACAGGTTCTTCACAAGCAACTTTAATGAAGAGACATATACCAAGAAAGGACTGGAATGGGTGAATACAACTGAGAGCCTAAAGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - -gggtgtg
- - - - - - - - - - - - - - - - - - - - - gtgaagg