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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtactcacaaacttatttttgtcctatcctttggatctctgctaatgagtttggcctacacacttcagtacttgactaacaatcctataagatgtttgtggtgatttatagttgcacaaatagtatattttacttgttcatgggtgtaaatatggtgcgcagGCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGGAGCTGAAATTGGTGGTGCCTTTGGTGGAGAAAAGGCGACAGGTGGTGGC

Basic information

species Glycine max
transcript GLYMA09G08150.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G08150.2 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os09g26880.3 (Oryza sativa), 3'ss of exon 12
gtaagtactcacaaacttatttttgtcctatcctttggatctctgctaatgagtttggcctacacacttcagtacttgactaacaatcctataagatgtttgtggtgatttatagttgcacaaatagtatattttacttgttcatgggtgtaaatatggtgcgcagGCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGGAGCTGAAATTGGTGGTGCCTTTGGTGGAGAAAAGGCGACAGGTGGTGGC
                                                |    |||    ||||| ||     | ||   | ||   |       |||        ||  |  | |  |     ||||  || || |||| || |           || ||  |||||| |  |||||||| ||||| || || |||| ||| || || |||||||| |||||||||||||| || |||||||||||||| || || |||||||| 
------------------------------------------------acacctttcttttacacgctctcagatttcttttactgcc-------atgccccataagacatgaaatgactatggtagtg-atgtt-cttgctctt---------cttgctgtacagGCCTCATGGTAGTGACTGTGGCATTGTTAATGTAAATATTCCCACAAATGGTGCTGAAATTGGTGGAGCTTTTGGTGGAGAAAAAGCTACTGGTGGTGGA

upper sequence: GLYMA09G08150.2 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G130440_T02 (Zea mays), 3'ss of exon 12
gtaagtactcacaaacttatttttgtcctatcctttggatctctgctaatgagtttggcctacacacttcagtacttgactaacaatcctataagatgtttgtggtgatttatagttgcacaaatagtatattttacttgttcatgggtgtaaatatggtgcgcagGCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGGAGCTGAAATTGGTGGTGCCTTTGGTGGAGAAAAGGCGACAGGTGGTGGC
                                                       | |  |||  | | ||  | ||    |    || | |  |  ||   | | | | |||  ||  |     | ||    | ||| |||      |||     |  |  ||||||| |  |||||||||||||||||||||||||  ||||||||||| ||||| |||||||||||||| || |||||||||||||| || || |||||||| 
-------------------------------------------------------ttgaatacttattgcaaaaatttctca----tcttttgtggggtccttcgagttatattttttgattgccaataagcctcact-gtt------tgttctcttattatgcagGCCCCATGGTAGTGATTGTGGTATAGTGAATGTGAACATACCTACTAATGGTGCTGAAATTGGTGGAGCATTTGGTGGAGAAAAAGCAACTGGTGGTGGA

upper sequence: GLYMA09G08150.2 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM5G820733_T01 (Zea mays), 3'ss of exon 4
gtaagtactcacaaacttatttttgtcctatcctttggatctctgctaatgagtttggcctacacacttcagtacttgactaacaatcctataagatgtttgtggtgatttatagttgcacaaatagtatattttacttgttcatgggtgtaaatatggtgcgcagGCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGGAGCTGAAATTGGTGGTGCCTTTGGTGGAGAAAAGGCGACAGGTGGTGGC
                                                       | |  ||   | | ||  |    | |    ||| | |  |  ||   | | | | |||  ||  |     | ||  | | ||| |||      |||     |  |  ||||||| |  |||||||||||||||||||||||||  ||||||||||| ||||| |||||||||||||| || |||||||||||||| ||  | |||||||| 
-------------------------------------------------------ttgaatatttattgcaaaa----agttctcatcttttgtggggtcctttgggttatattttttgattgccaataagtctcact-gtt------tgttctcttattatgcagGCCCCATGGTAGTGATTGTGGTATAGTGAATGTGAACATACCTACTAATGGTGCTGAAATTGGTGGAGCATTTGGTGGAGAAAAAGCAGCTGGTGGTGGA

upper sequence: GLYMA09G08150.2 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G070514_T02 (Zea mays), 3'ss of exon 5
gtaagtactcacaaacttatttttgtcctatcctttggatctctgctaatgagtttggcctacacacttcagtacttgactaacaatcctataagatgtttgtggtgatttatagttgcacaaatagtatattttacttgttcatgggtgtaaatatggtgcgcagGCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGGAGCTGAAATTGGTGGTGCCTTTGGTGGAGAAAAGGCGACAGGTGGTGGC
                                                       | |  ||   | | ||  |    | |    ||| | |  |  ||   | | | | |||  ||  |     | ||    | ||| |||  |   ||| | ||||     |||||| |  |||||||||||||||||||||||||  ||||||||||| ||||| |||||||||||||| || |||||||||||||| ||  | |||||||| 
-------------------------------------------------------ttgaatatttattgcaaaa----agttctcatcttttgtggggtcctttgggttatattttttgattgccaataagcctcact-gtttgttc-tgttattatg-----cagGCCCCATGGTAGTGATTGTGGTATAGTGAATGTGAACATACCTACTAATGGTGCTGAAATTGGTGGAGCATTTGGTGGAGAAAAAGCAGCTGGTGGTGGA

upper sequence: GLYMA09G08150.2 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM5G828253_T01 (Zea mays), 3'ss of exon 1
gtaagtactcacaaacttatttttgtcctatcctttggatctctgctaatgagtttggcctacacacttcagtacttgactaacaatcctataagatgtttgtggtgatttatagttgcacaaatagtatattttacttgttcatgggtgtaaatatggtgcgcagGCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGGAGCTGAAATTGGTGGTGCCTTTGGTGGAGAAAAGGCGACAGGTGGTGGC
                                                       | |  ||   | | ||  |  |    | |  |  | |  | |  ||  ||| || | |  ||  |     | ||    | ||| |||      |||     |  |  ||||||| |  |||||||||||||||||||||||||  ||||||||||| ||||| |||||||||||||| || |||||||||||||| ||  | |||||||| 
-------------------------------------------------------ttgaatatttattgcaaaatgttctcatc--ttttgtggggtcctttcggttatattt--tttgattgccaataagcctcact-gtt------tgttctcttattatgcagGCCCCATGGTAGTGATTGTGGTATAGTGAATGTGAACATACCTACTAATGGTGCTGAAATTGGTGGAGCATTTGGTGGAGAAAAAGCAGCTGGTGGTGGA

upper sequence: GLYMA09G08150.2 (Glycine max), 3'ss of exon 11
lower sequence: GRMZM2G382159_T01 (Zea mays), 3'ss of exon 3
gtaagtactcacaaacttatttttgtcctatcctttggatctctgctaatgagtttggcctacacacttcagtacttgactaacaatcctataagatgtttgtggtgatttatagttgcacaaatagtatattttacttgttcatgggtgtaaatatggtgcgcagGCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGGAGCTGAAATTGGTGGTGCCTTTGGTGGAGAAAAGGCGACAGGTGGTGGC
                                                       | |  ||   | | ||  |    | |    ||| | |  |  ||   | | | | |||  ||  |     | ||    | ||| |||      |||     |  |  ||||||| |  |||||||||||||||||||||||||  ||||||||||| ||||| |||||||||||||| || |||||||||||||| ||  | |||||||| 
-------------------------------------------------------ttgaatatttattgcaaaa----agttctcatcttttgtggggtcctttgcgttatatttttttattgccaataagcctcact-gtt------tgttctcttattatgcagGCCCCATGGTAGTGATTGTGGTATAGTGAATGTGAACATACCTACTAATGGTGCTGAAATTGGTGGAGCATTTGGTGGAGAAAAAGCAGCTGGTGGTGGA

upper sequence: GLYMA09G08150.2 (Glycine max), 3'ss of exon 11
lower sequence: AT1G54100.2 (Arabidopsis thaliana), 3'ss of exon 12
gtaagtactcacaaacttatttttgtcctatcctttggatctctgctaatgagtttggcctacacacttcagtacttgactaacaatcctataagatgtttgtggtgatttata-gttgcacaaatagtatattttacttgttcatgggtgtaaatatggtgcgcagGCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGGAGCTGAAATTGGTGGTGCCTTTGGTGGAGAAAAGGCGACAGGTGGTGGC
                                                                    | ||| ||  |  |||||     |||     |  |   ||   |||   |  ||  | | ||  ||| |  || |    ||| | | ||        || ||||  || ||||| ||||| || |||||||  |||||||| || ||||||||||| |||||||| || ||||| || || || ||||| |||||||| 
-------------------------------------------------------------------gtaagtgctataaaaacaacaacttaactcaatctttccgaccaatataatctactgaaattaattttaatgtgat----ggttttactac------tagACCACTGGGAAGTGACTGTGGCATTGTGAATGTGAACATACCGACGAATGGAGCTGAGATTGGTGGAGCTTTTGGAGGCGAGAAAGCGACTGGTGGTGGT

upper sequence: GLYMA09G08150.2 (Glycine max), 3'ss of exon 11
lower sequence: Vv11s0016g00900.t01 (Vitis vinifera), 3'ss of exon 12
gtaagtactcacaaacttatttttgtcctatcctttggatctctgctaatgagtttggcctacacacttcagtacttgactaaca-atcctataagatgtttgtgg---tgatttatagttgcacaaatagtatattttacttgttcatgggtgtaaatatggtgcgcagGCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGGAGCTGAAATTGGTGGTGCCTTTGGTGGAGAAAAGGCGACAGGTGGTGGC
                                                               |     ||||  |||| |  ||   |  |||||   || ||||   |  |  ||   ||  |   |   |||||||  |  |  ||| || |        |   ||||||||  || ||||| |||||||| ||||||| ||| |||||||||||||||||||| |||||||| || ||||| ||||||||||| || |||||||| 
--------------------------------------------------------------gaagaggcagttgttgaatgtcatgacacataagggattggtggatctagtgcattaatgtccctgtgaaatattttgttcatatatgagtat--------tatacagGCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGGAGCTGAGATTGGTGGAGCTTTTGGGGGAGAAAAGGCAACTGGTGGTGGT

upper sequence: GLYMA09G08150.2 (Glycine max), 3'ss of exon 11
lower sequence: PP1S237_29V6.1 (Physcomitrella patens), 3'ss of exon 13
gtaagtactcacaaacttatttttgtcctatcctttggatctctgctaatgagtttggcctacacacttca-gtacttgactaacaatcctataagatgtttgtggtgatttatagttgcacaaatagtatattttacttgttcatgggtgtaaatatggtgcgcagGCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGGAGCTGAAATTGGTGGTGCCTTTGGTGGAGAAAAGGCGACAGGTGGTGGC
                                      ||   ||  ||||  |  |    |   |||||| | || | | | ||  || | |   || |||        || ||||   ||||  |  || |||  || |||                    |||| ||   ||| |||||||||||||| || ||||  |||||||| || |||||||| || ||||| || || || |||||||| ||||| ||||| || || 
--------------------------------------attagtgacaatg--tacgaggaagctacttcatgcacctcatttact-tcatttcgaatttttaca-----ttttagt--gacaagcaagatgtttctctcgttt-------------------gcagACCTACAGGCAGTGATTGTGGTATTGTCAATGTGAACATACCAACCAATGGAGCGGAGATTGGGGGAGCATTCGGTGGAGAGAAGGCAACAGGGGGCGGA

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|58019812|gb|CX706554.1|CX706554
EST:     AGTAGTTCAATCTTTACCCAAAGACCTGGAACTATATTCAAATGGATCGG                         GCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGG
genomic: AGTAGTTCAATCTTTACCCAAAGACCTGGAACTATATTCAAATGGATCGGgtaagtactc ... tggtgcgcagGCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGG
EST: gi|57575444|gb|CX548419.1|CX548419
EST:     AGTAGTTCAATCTTTACCCAAAGACCTGGAACTATATTCAAATGGATCGG                         GCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGG
genomic: AGTAGTTCAATCTTTACCCAAAGACCTGGAACTATATTCAAATGGATCGGgtaagtactc ... tggtgcgcagGCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGG
EST: gi|207747420|gb|GD719873.1|GD719873
EST:     AGTAGTTCAATCTTTACCCAAAGACCTGGAACTATATTCAAATGGATCGG                         GCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGG
genomic: AGTAGTTCAATCTTTACCCAAAGACCTGGAACTATATTCAAATGGATCGGgtaagtactc ... tggtgcgcagGCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGG
EST: gi|209713773|gb|BW681886.1|BW681886
EST:     AGTAGTTCAATCTTTACCCAAAGACCTGGAACTATATTCAAATGGATCGG                         GCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGG
genomic: AGTAGTTCAATCTTTACCCAAAGACCTGGAACTATATTCAAATGGATCGGgtaagtactc ... tggtgcgcagGCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGG
EST: gi|7590000|gb|AW705762.1|AW705762
EST:     TAGTTCAATCTTTACCCAAAGACCTGGAACTATATTCAAATGGATCGG                         GCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGG
genomic: TAGTTCAATCTTTACCCAAAGACCTGGAACTATATTCAAATGGATCGGgtaagtactc ... tggtgcgcagGCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGG
EST: gi|254336948|gb|GR843127.1|GR843127
EST:     AGTAGTTCAATCTTTACCCAAAGACCTGGAACTATATTCAAATGGATCGG                         GCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGG
genomic: AGTAGTTCAATCTTTACCCAAAGACCTGGAACTATATTCAAATGGATCGGgtaagtactc ... tggtgcgcagGCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGG
EST: gi|208261117|gb|GE060363.1|GE060363
EST:     AGTAGTTCAATCTTTACCCAAAGACCTGGAACTATATTCAAATGGATCGG                         GCCACGAGGTAGTGATTGT
genomic: AGTAGTTCAATCTTTACCCAAAGACCTGGAACTATATTCAAATGGATCGGgtaagtactc ... tggtgcgcagGCCACGAGGTAGTGATTGT
EST: gi|58022816|gb|CX709557.1|CX709557
EST:     AGTAGTTCAATCTTTACCCAAAGACCTGGAACTATATTCAAATGGATCGG                         GCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGG
genomic: AGTAGTTCAATCTTTACCCAAAGACCTGGAACTATATTCAAATGGATCGGgtaagtactc ... tggtgcgcagGCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGG
EST: gi|208163845|gb|GD961511.1|GD961511
EST:     AGTAGTTCAATCTTTACCCAAAGACCTGGAACTATATTCAAATGGATCGG                         GCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCT
genomic: AGTAGTTCAATCTTTACCCAAAGACCTGGAACTATATTCAAATGGATCGGgtaagtactc ... tggtgcgcagGCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCT
EST: gi|254336949|gb|GR843128.1|GR843128
EST:     AGTAGTTCAATCTTTACCCAAAGACCTGGAACTATATTCAAATGGATCGG                         GCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGG
genomic: AGTAGTTCAATCTTTACCCAAAGACCTGGAACTATATTCAAATGGATCGGgtaagtactc ... tggtgcgcagGCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGG
EST: gi|193475794|gb|FK442519.1|FK442519
EST:     AGTAGTTCAATCTTTACCCAAAGACCTGGAACTATATTCAAATGGATCGG                         GCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGG
genomic: AGTAGTTCAATCTTTACCCAAAGACCTGGAACTATATTCAAATGGATCGGgtaagtactc ... tggtgcgcagGCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGG
EST: gi|213598271|gb|DB979891.1|DB979891
EST:     CTATATTCAAATGGATCGG                         GCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGG
genomic: CTATATTCAAATGGATCGGgtaagtactc ... tggtgcgcagGCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGG
EST: gi|58022682|gb|CX709423.1|CX709423
EST:     AGTAGTTCAATCTTTACCCAAAGACCTGGAACTATATTCAAATGGATCGG                         GCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGG
genomic: AGTAGTTCAATCTTTACCCAAAGACCTGGAACTATATTCAAATGGATCGGgtaagtactc ... tggtgcgcagGCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atagttgcacaaatagtatattttacttgttcatgggtgtaaatatggtgcgcagGCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGGAGCTGAAATTGGTGGTGCCTTTGGTGGAGAAAAGGCGACAGGTGGTGGC
          aaatagtatattttac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtactcacaaacttatttttgtcctatcctttggatctctgctaatgagtttggcctacacacttcagtacttgactaacaatcctataagatgtttgtggtgatttatagttgcacaaatagtatattttacttgttcatgggtgtaaatatggtgcgcagGCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGGAGCTGAAATTGGTGGTGCCTTTGGTGGAGAAAAGGCGACAGGTGGTGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG