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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAACAGCATGATCAATTTCTCATATTTGCTTCTGATGGTCTTTGGGAACACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAATgtaagataaatgtactatatggttgtttctattttgttttatattttgcattttttattgcttggttactgtagttttgtccagtcataatttacatgcc...

Basic information

species Glycine max
transcript GLYMA16G23090.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G23090.1 (Glycine max), 5'ss of exon 8
lower sequence: LOC_Os06g50380.1 (Oryza sativa), 5'ss of exon 5
TCAACAGCATGATCAATTTCTCATATTTGCTTCTGATGGTCTTTGGGAACACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAATgtaagataaatgtactatatggttgtttctattttgttttatattt-tgcattttttattgcttggttactgtagttttgtccagtcataatttacatgcc-
 ||||  ||||||||||||||||||||||| ||||||||||| ||||| ||| | | |||||| || || ||||| || ||||| |  | ||| | |||||||||       | ||  |    |   | ||   ||    |||    | ||||  ||     ||    | || |    ||        |  || ||||    
ACAACCACATGATCAATTTCTCATATTTGCATCTGATGGTCTATGGGAGCACTTAACCAATCAAGAGGCCGTTGACATTGTTCACAGTAGCCCTCGCAATgtaagtgcttgctcctgcacaaataaat-taacatgaaacatacagatacattggttggcatttt-ccattgcaaccatgcatgtcattggttgacatatat

upper sequence: GLYMA16G23090.1 (Glycine max), 5'ss of exon 8
lower sequence: GRMZM2G069970_T02 (Zea mays), 5'ss of exon 4
TCAACAGCATGATCAATTTCTCATATTTGCTTCTGATGGTCTTTGGGAACACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAATgtaagataaatgtactatatggttgtttctattttgttttatattttgcattttttattgcttggttactgtagttttgtccagtcataatttacatgcc---
 ||||  || || || |||||||||||||| |||||||| |||||||| ||| | | ||| || || ||||||||||| ||||| |  | ||| | || |||||| ||    | |    || || |      |||   |  |  |||| |||  |   |  | |  | |       |   | | ||  |   |||   |    
ACAACCACACGACCAGTTTCTCATATTTGCATCTGATGGACTTTGGGAGCACTTAACCAACCAAGAAGCTGTTGATATTGTTCACAGTAGCCCCCGCAGTgtaagttagtctttcccc-tgtttttgatgggtttccctattcatttgaattaatg--tattcgtcttccaacaaatgaacaaatcgaaggatactcactgtc
















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|208091060|gb|GD889231.1|GD889231
EST:     ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
genomic: ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tgtcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
EST: gi|193453337|gb|FK418105.1|FK418105
EST:     GCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
genomic: GCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tgtcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
EST: gi|208075001|gb|GD875498.1|GD875498
EST:     ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCA
genomic: ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tgtcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCA
EST: gi|208334240|gb|GE132493.1|GE132493
EST:     ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
genomic: ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tgtcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
EST: gi|208197221|gb|GE001495.1|GE001495
EST:     ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
genomic: ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tgtcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
EST: gi|208095717|gb|GD894519.1|GD894519
EST:     ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
genomic: ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tgtcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
EST: gi|207801487|gb|GD773865.1|GD773865
EST:     ATGCTGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
genomic: ATGCTGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tgtcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
EST: gi|193530369|gb|FK486568.1|FK486568
EST:     TAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
genomic: TAGTTCAAAACAACCCACACAATgtaagataaa ... tgtcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
EST: gi|208168743|gb|GD968299.1|GD968299
EST:     ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
genomic: ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tgtcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
EST: gi|193364523|gb|FK333564.1|FK333564
EST:     ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
genomic: ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tgtcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
EST: gi|208265015|gb|GE065343.1|GE065343
EST:     ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
genomic: ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tgtcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
EST: gi|207773636|gb|GD746160.1|GD746160
EST:     ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
genomic: ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tgtcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
EST: gi|193399268|gb|FK361774.1|FK361774
EST:     ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAG-CTCATCAAAG
genomic: ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tgtcttgcagGGAATTGCTCGGAGGCTCATCAAAG
EST: gi|208302994|gb|GE100927.1|GE100927
EST:     ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAAGAAGCAGCAAA
genomic: ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tgtcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAA-GAAGCAGCAAA
EST: gi|208335894|gb|GE138473.1|GE138473
EST:     TTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
genomic: TTCAAAACAACCCACACAATgtaagataaa ... tgtcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
EST: gi|193606868|gb|FK556543.1|FK556543
EST:     ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAG
genomic: ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tgtcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAG
EST: gi|193319694|gb|FK283507.1|FK283507
EST:     ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAA-G
genomic: ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tgtcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
EST: gi|193558654|gb|FK516229.1|FK516229
EST:     ACCTTAGTAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
genomic: ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tgtcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
EST: gi|193341857|gb|FK307587.1|FK307587
EST:     ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
genomic: ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tgtcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
EST: gi|207687226|gb|GD667912.1|GD667912
EST:     ACCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAAT                         AGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
genomic: ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tgtcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
EST: gi|208299991|gb|GE098104.1|GE098104
EST:     ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGA
genomic: ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tgtcttgcagGGAATTGCTCGGA
EST: gi|208317360|gb|GE117513.1|GE117513
EST:     TTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
genomic: TTCAAAACAACCCACACAATgtaagataaa ... tgtcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
EST: gi|208303692|gb|GE105217.1|GE105217
EST:     ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAG
genomic: ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tgtcttgcagGGAATTGCTCGGAGGCTCATCAAAG
EST: gi|207774283|gb|GD743741.1|GD743741
EST:     TATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
genomic: TATAGTTCAAAACAACCCACACAATgtaagataaa ... tgtcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
EST: gi|208063484|gb|GD863318.1|GD863318
EST:     ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
genomic: ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tgtcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
EST: gi|208256446|gb|GE051787.1|GE051787
EST:     ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAA
genomic: ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tgtcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAA
EST: gi|209697720|gb|BW655621.1|BW655621
EST:     ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
genomic: ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tgtcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
EST: gi|208106580|gb|GD906047.1|GD906047
EST:     ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGGGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
genomic: ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tgtcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
EST: gi|193326210|gb|FK288213.1|FK288213
EST:     CCTTAGCAATCAGGATGCCGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCGTTGCAAGAAGCAGCAAAAAAG
genomic: CCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tgtcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
EST: gi|208333992|gb|GE129977.1|GE129977
EST:     ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAAT                         GGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG
genomic: ACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAATgtaagataaa ... tgtcttgcagGGAATTGCTCGGAGGCTCATCAAAGCTGCTTTGCAAGAAGCAGCAAAAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAACAGCATGATCAATTTCTCATATTTGCTTCTGATGGTCTTTGGGAACACCTTAGCAATCAGGATGCTGTTGATATAGTTCAAAACAACCCACACAATgtaagataaatgtactatatggttgtttctattttgttttatattttgcattttttattgcttggttactgtagttttgtccagtcataatttacatgcc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT