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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAGgtatccttttctttcccaaagtttttagatttcttttgaattctgtttctgtaagctaatagtttgttgactttcag

Basic information

species Glycine max
transcript GLYMA15G40110.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 9
lower sequence: LOC_Os02g01280.1 (Oryza sativa), 5'ss of exon 10
GTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAGgt--atccttttctttcccaa--------agtttttagatttcttttgaattctgtttctgtaagctaatagtttgttgactttcag------------------------------
|| || ||||| || || |||||||| |||||||||||| |||| ||||||||||| || ||||| || |||||  || ||| |||||   ||        | ||||  |||| | ||   |     ||    |   |  | ||| | | |  ||   |                              
GTAGGAGCACAGACAGAAACTGAGCTTAAGGAAAAGAAACTGAGGGTTGAAGATGCACTGAATGCAACCAAGgtgaatacttctctttgttaatataatttaattttgggattgcattcagagagccttctgatgcacatagagtatatgggtttgttgtttgttacttaatagtttgctctgtggcag

upper sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 9
lower sequence: GRMZM2G015989_T01 (Zea mays), 5'ss of exon 10
GTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAGgtatccttttctt--------tcccaaagttt-----ttagatttcttttgaattctgtttctgta---agctaatagtttgttgactttcag------------------------------------------------------
|| || ||||| || || |||||||||||||||||||||||||| ||||| ||||| || |||||||||||||||     | | |        || || ||| |     |  | | || ||   ||   ||     |    |  ||  | | || |||  || |                                                       
GTAGGAGCACAGACAGAAACTGAGCTCAAGGAAAAGAAATTGAGGGTTGAGGATGCCCTGAATGCTACAAAGgtaaatgctacatatggtggttctcacagtatacctgtatgttctcattcacatagcgtcctgatgcacaattagcactgtgatgatcttaaaatcctatttatttgtgatgagtccttgttagttgatagttttctatatttgcag

upper sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 9
lower sequence: AT5G56500.2 (Arabidopsis thaliana), 5'ss of exon 10
GTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAGgtatccttttctttcc-caaagtttttagatttcttttgaattctgtttctgtaagctaatagtttgttgactttcag----
||||| |||||||||||||| ||||| ||||| |||||||| ||||||||||||||||||||||||||||||||| | |  ||| |   |||||    | ||  | |||  |    | |    |  |   | | ||| |    |||| |     
GTTGGAGCACAAACTGAGACAGAGCTTAAGGAGAAGAAATTAAGAGTTGAAGATGCTCTTAATGCTACAAAGgtaacatcatctctaagcaaagagccttgaaatgtttccatccatatggtagagactaagttgttggac--cttttaattag

upper sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 9
lower sequence: AT3G13470.1 (Arabidopsis thaliana), 5'ss of exon 10
GTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAGgtatccttttctttccca-----aagtttttagatttcttttgaattctgtttctgtaagcta-atagttt-gttgactttcag
||||| || ||||||||||| |||||||| ||||||||  ||||||| ||||||||||||||||||||||||||    || | | |||         | || ||| | || |   | |  ||| | | | |  || ||    |  |||| ||||||
GTTGGAGCTCAAACTGAGACAGAGCTCAAAGAAAAGAAGCTGAGAGTGGAAGATGCTCTTAATGCTACAAAGgtgattttctttatccagctgatggggttataggtatcgtgctactcatgtatatcttaattatatgacctcattgagtttcag

upper sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 9
lower sequence: AT1G55490.1 (Arabidopsis thaliana), 5'ss of exon 10
GTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAGgtatccttttctttcccaaagtttttagatttctt--ttgaattctgttt--ctgtaagctaatagtttgttgact-ttcag
||||| |||||||||||||| || ||||| || ||||| |||||||||||||||||||||||||| ||||||||    || | ||||  |   ||   |    | ||  ||| || ||  |   || |||   |  ||  | || | | |||||
GTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAGgtgattttgtatttctgaggcttgagaagcgtgttatttgcatactcgtgaactataactaatcaggattttaattcttcag

upper sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 9
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 5'ss of exon 10
GTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAGgtatccttttctttcccaaagtttt-----tagatttcttttgaattctgtttctgtaagcta--atagtttgttgactttcag----------------------------
||||| |||||||||||||| ||||| || ||||||||| ||||||| ||||| ||||| ||||| || ||||||    ||||||||   || || |     |  ||| ||  |   |  | ||   |   | |   | ||   |   | | | |                             
GTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAGgta---atttctttcatgaaattatggcactgaattgctagttgctaatattcaagagtgatggcacagccagaacagtattaagtagtatggcattttcaatgattttcag

upper sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 9
lower sequence: EFJ36935 (Selaginella moellendorffii), 5'ss of exon 9
GTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAGgtatccttttctttcccaaagtttttagatttcttttgaattctgtttctgtaagctaatagtttgttgactttcag
|||||||||||||||||||| || || || |||||||| || ||||| ||||||||| | ||||| || ||||||               ||    |  ||||    | ||||  |||   ||||||    ||  |||  |        
GTTGGTGCACAAACTGAGACAGAACTAAAAGAAAAGAAGTTAAGAGTGGAAGATGCTTTGAATGCAACGAAGgta---------------aatagatcggatt---ctggaatattgtgg-tgtaagtgtttaaattgcag--------

upper sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 9
lower sequence: EFJ33580 (Selaginella moellendorffii), 5'ss of exon 9
GTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAGgtatccttttctttcccaaagtttttagatttcttttgaattctgtttctgtaagctaatagtttgttgactttcag
|||||||||||||||||||| ||  | || |||||||| || ||||| ||||||||| | ||||| || ||||||               ||    || ||||    | ||||  |||   ||||||    ||  |||  |        
GTTGGTGCACAAACTGAGACAGAATTAAAAGAAAAGAAGTTAAGAGTGGAAGATGCTTTGAATGCGACGAAGgta---------------aatagattggatt---ctggaatattgtgg-tgtaagtgtttaaattgcag--------

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|207833489|gb|GD806734.1|GD806734
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGGGA
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAGgtatcctttt ... tgactttcagGCAGCTGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGA
EST: gi|16278868|gb|BI943136.1|BI943136
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAGGGTATTGTAGTTGGTGGTGTGT-GCACTCTTCTGAG
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAGgtatcctttt ... tgactttcagGCAGCTGTAGAGGAGGGTATTGTAGTTGGTGGTG-GTTGCACTCTTCTGAG
EST: gi|16278211|gb|BI942785.1|BI942785
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGA
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAGgtatcctttt ... tgactttcagGCAGCTGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGA
EST: gi|16995951|gb|BM085323.1|BM085323
EST:     GAGAGTTGAAGATGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGA
genomic: GAGAGTTGAAGATGCTCTTAATGCTACAAAGgtatcctttt ... tgactttcagGCAGCTGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGA
EST: gi|31475719|gb|CD417747.1|CD417747
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAG                         CCAGCTGTAGAGGAGGGTATTGTAGTTGCTGGTGGTTGCACTCTTCTGAGA
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAGgtatcctttt ... tgactttcagGCAGCTGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGA
EST: gi|207828846|gb|GD798493.1|GD798493
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGA
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAGgtatcctttt ... tgactttcagGCAGCTGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGA
EST: gi|193718581|gb|FK652579.1|FK652579
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAGGGCATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGA
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAGgtatcctttt ... tgactttcagGCAGCTGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGA
EST: gi|208255225|gb|GE053942.1|GE053942
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAG                         GCAACTGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGA
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAGgtatcctttt ... tgactttcagGCAGCTGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGA
EST: gi|26046015|gb|CA783382.1|CA783382
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGA
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAGgtatcctttt ... tgactttcagGCAGCTGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGA
EST: gi|16279768|gb|BI943606.1|BI943606
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAGGGTATTGTAGTTGGTGGTGG
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAGgtatcctttt ... tgactttcagGCAGCTGTAGAGGAGGGTATTGTAGTTGGTGGTGG
EST: gi|298192668|gb|HO033102.1|HO033102
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAGGGTATTGTAGTTGGTGGTAGTTGCACT
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAGgtatcctttt ... tgactttcagGCAGCTGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACT
EST: gi|16276840|gb|BI942072.1|BI942072
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAGGGTATTGTAGTTGGTTGTGGGTGCACTCTTCTGAGA
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAGgtatcctttt ... tgactttcagGCAGCTGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGA
EST: gi|298170123|gb|HO018747.1|HO018747
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGA
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAGgtatcctttt ... tgactttcagGCAGCTGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGA
EST: gi|15589717|gb|BI674333.1|BI674333
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGA
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAGgtatcctttt ... tgactttcagGCAGCTGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGA
EST: gi|31309826|gb|CD395029.1|CD395029
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGA
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAGgtatcctttt ... tgactttcagGCAGCTGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGA
EST: gi|208199569|gb|GD996450.1|GD996450
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGA
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAGgtatcctttt ... tgactttcagGCAGCTGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGA
EST: gi|193403060|gb|FK369006.1|FK369006
EST:     AGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAG                         GCAGCTGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGA
genomic: AGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAGgtatcctttt ... tgactttcagGCAGCTGTAGAGGAGGGTATTGTAGTTGGTGGTGGTTGCACTCTTCTGAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAGgtatccttttctttcccaaagtttttagatttcttttgaattctgtttctgtaagctaatagtttgttgactttcag

- - - - - - - - - - - AGCTCA
- - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - -  AAGATG