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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTGGTGATGAAAAGCCTTCAGGTGAGGATGATGTTGCGGCAATTGGAAACAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAGgtgattgttcaagtgttctgattttatctttatctgcttctgtaagtgtcttatttttactttatcactagacaagtagaagatttgtcacttataactg...

Basic information

species Glycine max
transcript GLYMA20G39080.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G39080.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv15s0021g01420.t01 (Vitis vinifera), 5'ss of exon 4
---TTTTGGTGATGAAAAGCCTTCAGGTGAGGATGATGTTGCGGCAATTGGAAACAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAGgtgattgttcaagtgttctgattttatctttatctgcttctgtaagtgtcttatttttactttatcacta-gacaagtagaagatttgtcacttataactg
   ||| || | ||| ||||||  ||| || || |||||   ||||  ||| ||||||||||||||||  |||||| |||||||||| || |||||||| ||||||| ||      || | |   | | | | |  ||||    ||  |  ||| ||  |    | ||    | |||   |     |      |   |    | 
GAATTTGGGGGCTGAGAAGCCTGTAGGGGAAGAAGATGT---GGCAGATGGCAACAAGGAGAATCCTGTGAATGAACCTGAAGAAAAGGAACCTGAGGAAAAGgtgaatggctccatgatttagatgtttttat-cctgccaaagttggcatctcatcctataatcatattcatgactcttgatccacagcaaaagcaaggttt
















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|193395392|gb|FK357885.1|FK357885
EST:     ACAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAG                         GAGATGACTCTCGA
genomic: ACAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAGgtgattgttc ... tgttggatagGAGATGACTCTCGA
EST: gi|208287458|gb|GE084870.1|GE084870
EST:     ACAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAG                         GAGATGACTCTCGAGG
genomic: ACAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAGgtgattgttc ... tgttggatagGAGATGACTCTCGAGG
EST: gi|120491229|gb|EH219396.1|EH219396
EST:     ACAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAG                         GAGATGACTCTCGAGGAATATGAAAAAGTACTAGAAGAGAGAAGGAAGGCT
genomic: ACAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAGgtgattgttc ... tgttggatagGAGATGACTCTCGAGGAATATGAAAAAGTACTAGAAGAGAGAAGGAAGGCT
EST: gi|193313514|gb|FK280071.1|FK280071
EST:     ACAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAG                         GAGATGACTCTCGAGGAATAT
genomic: ACAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAGgtgattgttc ... tgttggatagGAGATGACTCTCGAGGAATAT
EST: gi|208128978|gb|GD927578.1|GD927578
EST:     ACAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAG                         GAGATGACTCTCGAGGAATATG
genomic: ACAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAGgtgattgttc ... tgttggatagGAGATGACTCTCGAGGAATATG
EST: gi|208316811|gb|GE115845.1|GE115845
EST:     ACAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAG                         GAGATGACTCTCGAGGAATAT
genomic: ACAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAGgtgattgttc ... tgttggatagGAGATGACTCTCGAGGAATAT
EST: gi|6481724|gb|AW200995.1|AW200995
EST:     AGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAG                         GAGATGACTCTCGAGGAATATGAAAAAGTACTAGAAGAGAGAAGGAAGGCT
genomic: AGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAGgtgattgttc ... tgttggatagGAGATGACTCTCGAGGAATATGAAAAAGTACTAGAAGAGAGAAGGAAGGCT
EST: gi|192325319|gb|FK017135.1|FK017135
EST:     ACAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAA                         GAGATGACTCTCGAGGAATATGAAAAAGTACTAGAAGAGAGAACGAAG-CT
genomic: ACAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAGgtgattgttc ... tgttggatagGAGATGACTCTCGAGGAATATGAAAAAGTACTAGAAGAGAGAAGGAAGGCT
EST: gi|192322787|gb|FK014478.1|FK014478
EST:     ACAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAG                         GAGATGACTCTCGAGGAATATGAAAAAGTACTAGAAGAGAGAAGGAAGGCT
genomic: ACAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAGgtgattgttc ... tgttggatagGAGATGACTCTCGAGGAATATGAAAAAGTACTAGAAGAGAGAAGGAAGGCT
EST: gi|193645898|gb|FK593883.1|FK593883
EST:     ACAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAG                         GAGATGACTCTCGAGGAATATGAAAAAGTACTAGAAGAGAGAAGGAAGGCT
genomic: ACAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAGgtgattgttc ... tgttggatagGAGATGACTCTCGAGGAATATGAAAAAGTACTAGAAGAGAGAAGGAAGGCT
EST: gi|193630216|gb|FK581773.1|FK581773
EST:     ACAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAG                         GAGATGACTCTCGAGG
genomic: ACAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAGgtgattgttc ... tgttggatagGAGATGACTCTCGAGG
EST: gi|31307409|gb|CD392612.1|CD392612
EST:     CAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAG                         GAGATGACTCTCGAGGAATATGAAAAAGTACTAGAAGAGAGAAGGAAGGCT
genomic: CAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAGgtgattgttc ... tgttggatagGAGATGACTCTCGAGGAATATGAAAAAGTACTAGAAGAGAGAAGGAAGGCT
EST: gi|193445746|gb|FK414027.1|FK414027
EST:     ACAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAG                         GAGATGACTCTCGAGGAATATG
genomic: ACAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAGgtgattgttc ... tgttggatagGAGATGACTCTCGAGGAATATG
EST: gi|24136573|gb|BU927083.1|BU927083
EST:     ACAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAG                         GAGATGACTCTCGAGGAATATGAAAAAGTACTAGAAGAGAGAAGGAAGGCT
genomic: ACAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAGgtgattgttc ... tgttggatagGAGATGACTCTCGAGGAATATGAAAAAGTACTAGAAGAGAGAAGGAAGGCT
EST: gi|208284294|gb|GE082826.1|GE082826
EST:     ACAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAG                         GAGATGACTCTCGAGGAATATG
genomic: ACAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAGgtgattgttc ... tgttggatagGAGATGACTCTCGAGGAATATG
EST: gi|10843741|gb|BF067004.1|BF067004
EST:     ACAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAG                         GAGATGACTCTCGAGGAATATGAAAAAGTACTAGAAGAGAGAAGGAAGGCT
genomic: ACAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAGgtgattgttc ... tgttggatagGAGATGACTCTCGAGGAATATGAAAAAGTACTAGAAGAGAGAAGGAAGGCT
EST: gi|193336011|gb|FK298037.1|FK298037
EST:     ACAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAG                         GAGATGACTCTCGA
genomic: ACAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAGgtgattgttc ... tgttggatagGAGATGACTCTCGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTTGGTGATGAAAAGCCTTCAGGTGAGGATGATGTTGCGGCAATTGGAAACAAGGAGAATCCTGCTAATGAAGCTGAAGAAAAAGAGCCTGAGGATAAGgtgattgttcaagtgttctgattttatctttatctgcttctgtaagtgtcttatttttactttatcactagacaagtagaagatttgtcacttataactg

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT