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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAGTCACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaacacgctttaatattttaccctctcaatttcgttgtggatacttctatttctctgttttggttgctatgatttttgtttggttttgctgatt...

Basic information

species Glycine max
transcript GLYMA14G17930.4
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G17930.4 (Glycine max), 5'ss of exon 2
lower sequence: GRMZM2G080930_T01 (Zea mays), 5'ss of exon 2
-CTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAGTCACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaacacgctttaatattttaccctctcaatttcgttgtggatacttctatttctctgttttggttg--ctatgatttttgtttggttttgctgatt--------
  || |    | ||| | |||||||||||||| |||||||||||||| || ||     | || |||||||| || |||||||| || |||||| | || |||| | ||       ||| | | ||||     |||  ||   | | ||||| | |  |  | | ||   ||||  |   ||   |||  || ||  ||   ||        
AATTGTTCTCA-ATGGCCCGCGTGTATGTTGGCAACTTGGATTCACGGGTGACTTCTGGGGAACTCGAAGATGAGTTCCGCGTGTTTGGAGTTCTGCGAAGgtcacttt-----ttttcaaactttat----tcaggttttgtatagatacatttcatagttttttcatgttgtccctcgagccttgaatgattg-gcaagttaactaaga
















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|298170870|gb|HO015846.1|HO015846
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|213589771|gb|DB969592.1|DB969592
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|13790205|gb|BG652796.1|BG652796
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCTTTGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|192324562|gb|FK016453.1|FK016453
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|298179401|gb|HO027872.1|HO027872
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|151395696|gb|EV265573.1|EV265573
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|298185492|gb|HO030705.1|HO030705
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|7285723|gb|AW598210.1|AW598210
EST:     AGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: AGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|9983911|gb|BE658019.1|BE658019
EST:     CGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: CGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|207702915|gb|GD686149.1|GD686149
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|192299813|gb|FG993333.1|FG993333
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACTTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|192295485|gb|FG987099.1|FG987099
EST:     GCCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|8669525|gb|BE190632.1|BE190632
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|209700148|gb|BW652992.1|BW652992
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|298198145|gb|HO039684.1|HO039684
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|298164978|gb|HO011027.1|HO011027
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|6070422|gb|AW099809.1|AW099809
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAG                         TGTTGTGGGTTGCACGTACACCACCTGGTTATGCTTTTATTGACTTTGATG
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTT-TGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATG
EST: gi|192300160|gb|FG989282.1|FG989282
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|298178379|gb|HO024114.1|HO024114
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|7591104|gb|AW706844.1|AW706844
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|298179203|gb|HO027674.1|HO027674
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGTGTTTTCGGAGTTATTCGGAG                         TGTTTGGATTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA
EST: gi|298165150|gb|HO011199.1|HO011199
EST:     ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAG                         TGTTTGGGTTGCACGTAGACCACCTGGTTATGCCTTTATTGACTTTGATGA
genomic: ACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaac ... atgtttgcagTGTTTGGGTTGCACGTAGACCACCTGGTTATGCTTTTATTGACTTTGATGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCTGAAAAGATGTCTCGCGTGTATGTTGGTAACTTGGATTCACGAGTCACCGAGAGAGATCTCGAAGACGAATTCCGCGTTTTCGGAGTTATTCGGAGgtaaattaacacgctttaatattttaccctctcaatttcgttgtggatacttctatttctctgttttggttgctatgatttttgtttggttttgctgatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA