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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttgtaatctctagcttcctgacattaccatagtttattggggctagaatatgcgcctggttattggtaatttttttttaatgggaatttatttggcagAGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGTATTGGGAGGATCAAGTTTAAAGCTTTTGATCTCGGGGGTCACCAGATTG

Basic information

species Glycine max
transcript GLYMA20G38360.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38360.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G122666_T01 (Zea mays), 3'ss of exon 1
--ctttgtaatctctagcttcctgacattaccatagtttattggggctagaatatgcgcctgg-ttattggtaatttttt-tttaatgggaatttatttg--gcagAGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGTATTGGGAGGATCAAGTTTAAAGCTTTTGATCTCGGGGGTCACCAGATTG
  | |    | |||   | |||   | ||  | | |   |||   |    | |||||    |  |||  ||  |||  |  | |  |  || |   ||    |||| | || || ||||| ||||| || ||||| ||||| ||||| |||||||| || || ||||||||||| || || || || || ||||| |||||||| |
gtcctctctacctccgacatccgccccttttccttgcgaattccagtctta-tatgctttcgacttaacggggattcctgatctggttcgattgggttcatcgcagCGGCTCGTACAGCACCAGCCGACGCAGTACCCCACGTCAGAAGAGTTGAGCATCGGCAGGATCAAGTTCAAGGCGTTCGACCTTGGGGGCCACCAGATCG

upper sequence: GLYMA20G38360.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S7_338V6.1 (Physcomitrella patens), 3'ss of exon 1
ctttgtaatctctagcttcctgacattaccatagtttattggggctagaatatgcgcctggttattggtaatttttttttaatgggaatttatt-tgg-----cagAGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGTATTGGGAGGATCAAGTTTAAAGCTTTTGATCTCGGGGGTCACCAGATTG
    ||||      ||      |     |  | | | | ||  || |     ||   | |||| ||  |   | |   | ||| | |   || | |||     |||||  | |  |||||||| || || || ||||| ||||| ||||||||||| ||||| |  || ||||| ||||| ||||| || || ||||||||||| |
----gtaaggaagtgcgatg-aatggagcggttggtgagtgatgcaatgccgtgaaaccggttgttt-ttcctgtcactaaattgcatcctactatggtgatacagAGGTTGGCCCAGCATCAACCGACGCAATATCCTACATCGGAGGAGTTGAGCATTGGAAAAATTAAGTTCAAAGCGTTTGACCTGGGTGGTCACCAGATCG

upper sequence: GLYMA20G38360.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S183_17V6.1 (Physcomitrella patens), 3'ss of exon 1
ctttgtaatctctagcttcctgac-attaccatagtttattggggctagaatatgcgcctggttattggtaatttttttttaa-tgggaatttatt-tgg-----cagAGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGTATTGGGAGGATCAAGTTTAAAGCTTTTGATCTCGGGGGTCACCAGATTG
         ||  |||    | |    | | || || ||  ||  | |  |  ||     |||  ||  |   ||||   ||| | | |   |||| |||     |||||  | |  || ||||| || || || ||||| || || |||||||||||||| || |  |||||||| ||||| |||||||| || ||||||||||| |
--------gctgaagcgcgataattggtgcgattgtgtagcggctcgatcaagtggaatcggtggttcttttcttttcactaaattgcatcctattgtggtgacacagAGGTTGGCCCAACATCAACCGACGCAATATCCTACTTCGGAGGAGTTGAGTATCGGAAAAATCAAGTTCAAAGCATTTGATCTGGGTGGTCACCAGATCG

upper sequence: GLYMA20G38360.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ12822 (Selaginella moellendorffii), 3'ss of exon 1
ctttgtaatctctagcttcctgacattaccatagtttattggggctagaatatgcgcctggttattggtaatttttttttaatgggaatttatttg-gcagAGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGTATTGGGAGGATCAAGTTTAAAGCTTTTGATCTCGGGGGTCACCAGATTG
                         | | |  | ||| ||||   |    |   | ||| | |  |||  || |         |||| |     || ||||||||| || ||||| ||||| || ||||| || || || |||||| |||| || || | ||||||||| ||||| |||||||| || ||||||||||| |
------------------------gtaagcg-aatttcttggaatt----tcctcccctaggtcatgg--atctg--------gggattgcgcctgcgcagAGACTCGTCCAGCACCAGCCGACGCAGTACCCGACCTCGGAGGAGCTGAGCATAGGCAAGATCAAGTTCAAAGCGTTTGATCTGGGCGGTCACCAGATCG

upper sequence: GLYMA20G38360.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ16976 (Selaginella moellendorffii), 3'ss of exon 1
ctttgtaatctctagcttcctgacattaccatagtttattggggctagaatatgcgcctggttattggtaatttttttttaatgggaatttatttg-gcagAGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGTATTGGGAGGATCAAGTTTAAAGCTTTTGATCTCGGGGGTCACCAGATTG
                         | | |  | ||| ||||      ||| | | ||    | | ||| ||   | |     |||| |     || ||||||||| || ||||| ||||| || ||||| || || || |||||| |||| || || | ||||||||| ||||| |||||| | || ||||||||||| |
------------------------gtaagcg-aatttcttgg------aatttcctcc----tctaggtcatggatctg----gggattgcgcctgcgcagAGACTCGTCCAGCACCAGCCGACGCAGTACCCGACCTCGGAGGAGCTGAGCATCGGCAAGATCAAGTTCAAAGCGTTTGATTTGGGAGGTCACCAGATCG

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|298184483|gb|HO029696.1|HO029696
EST:     GTCTCGATAATGCCGGAAAGACCACCTTGCTTCACATGCTCAAAGACGAG                         AGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGT
genomic: GTCTCGATAATGCCGGAAAGACCACCTTGCTTCACATGCTCAAAGACGAGgtttcccttt ... tatttggcagAGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGT
EST: gi|151395352|gb|EV265223.1|EV265223
EST:     GTCTCGATAATGCCGGAAAGACCACCTTGCTTCACATGCTCAAAGACGAG                         AGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGT
genomic: GTCTCGATAATGCCGGAAAGACCACCTTGCTTCACATGCTCAAAGACGAGgtttcccttt ... tatttggcagAGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGT
EST: gi|151404323|gb|EV274133.1|EV274133
EST:     GTCTCGATAATGCCGGAAAGACCACCTTGCTTCACATGCTCAAAGACGAG                         AGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGT
genomic: GTCTCGATAATGCCGGAAAGACCACCTTGCTTCACATGCTCAAAGACGAGgtttcccttt ... tatttggcagAGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGT
EST: gi|38193512|gb|CF922718.1|CF922718
EST:     GTCTCGATAATGCCGGAAAGACCACCTTGCTTCACATGCTCAAAGACGAG                         AGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGT
genomic: GTCTCGATAATGCCGGAAAGACCACCTTGCTTCACATGCTCAAAGACGAGgtttcccttt ... tatttggcagAGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGT
EST: gi|298172634|gb|HO019674.1|HO019674
EST:     GTCTCGATAATGCCGGAAAGACCACCTTGCTTCACATGCTCAAAGACGAG                         AGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGT
genomic: GTCTCGATAATGCCGGAAAGACCACCTTGCTTCACATGCTCAAAGACGAGgtttcccttt ... tatttggcagAGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGT
EST: gi|213594908|gb|DB971781.1|DB971781
EST:     GTCTCGATAATGCCGGANAGACCACCTTGCTTCACATGCTCAAAGACGAG                         AGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGT
genomic: GTCTCGATAATGCCGGAAAGACCACCTTGCTTCACATGCTCAAAGACGAGgtttcccttt ... tatttggcagAGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGT
EST: gi|192312909|gb|FK004051.1|FK004051
EST:     GTCTCGATAATACCGGAAAGACCACCTTGCTTCACATGCTCAAAGACGAG                         AGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGT
genomic: GTCTCGATAATGCCGGAAAGACCACCTTGCTTCACATGCTCAAAGACGAGgtttcccttt ... tatttggcagAGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGT
EST: gi|192312908|gb|FK004050.1|FK004050
EST:     GTCTCGATAATACCGGAAAGACCACCTTGCTTCACATGCTCAAAGACGAG                         AGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGT
genomic: GTCTCGATAATGCCGGAAAGACCACCTTGCTTCACATGCTCAAAGACGAGgtttcccttt ... tatttggcagAGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGT
EST: gi|298181703|gb|HO025878.1|HO025878
EST:     GTCTCGATAATGCCGGAAAGACCACCTTGCTTCACATGCTCAAAGACGAG                         AGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGT
genomic: GTCTCGATAATGCCGGAAAGACCACCTTGCTTCACATGCTCAAAGACGAGgtttcccttt ... tatttggcagAGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGT
EST: gi|298198297|gb|HO039836.1|HO039836
EST:     GTCTCGATAATGCCGGAAAGACCACCTTGCTTCACATGCTCAAAGACGAG                         AGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGT
genomic: GTCTCGATAATGCCGGAAAGACCACCTTGCTTCACATGCTCAAAGACGAGgtttcccttt ... tatttggcagAGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGT
EST: gi|151401289|gb|EV271103.1|EV271103
EST:     GTCTCGATAATGCCGGAAAGACCACCTTGCTTCACATGCTCAAAGACGAG                         AGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGT
genomic: GTCTCGATAATGCCGGAAAGACCACCTTGCTTCACATGCTCAAAGACGAGgtttcccttt ... tatttggcagAGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGT
EST: gi|151403505|gb|EV273315.1|EV273315
EST:     GTCTCGATAATGCCGGAAAGACCACCTTGCTTCACATGCTCAAAGACGAG                         AGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGT
genomic: GTCTCGATAATGCCGGAAAGACCACCTTGCTTCACATGCTCAAAGACGAGgtttcccttt ... tatttggcagAGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGT
EST: gi|192306733|gb|FG998873.1|FG998873
EST:     GTCTCGATAATGCCGGAAAGACCACCTTGCTTCACATGCTCAAAGACGAG                         AGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGT
genomic: GTCTCGATAATGCCGGAAAGACCACCTTGCTTCACATGCTCAAAGACGAGgtttcccttt ... tatttggcagAGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagaatatgcgcctggttattggtaatttttttttaatgggaatttatttggcagAGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGTATTGGGAGGATCAAGTTTAAAGCTTTTGATCTCGGGGGTCACCAGATTG
                               ttttaat  putative branch site (score: 3)
                                           tttattt  putative PPT
                ttattggtaatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttgtaatctctagcttcctgacattaccatagtttattggggctagaatatgcgcctggttattggtaatttttttttaatgggaatttatttggcagAGACTAGTTCAGCATCAGCCTACACAGTATCCCACATCAGAGGAGTTGAGTATTGGGAGGATCAAGTTTAAAGCTTTTGATCTCGGGGGTCACCAGATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - cctgaca
- - - - - - - - - - - - - - - - - - -attgggg
- - - - - - - - - - - - - - - - - - - - - - - - - - -gcgcctg