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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacagactcactgaaatggtaatatgttagtttggtacgccgttgggtatatcaacttgggcaatttttgtacatgtgtagGTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAG

Basic information

species Glycine max
transcript GLYMA15G40110.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os02g01280.1 (Oryza sativa), 3'ss of exon 9
----------------gtaacagactcactg-aaatggtaatatgttagtttggtacgcc-gttgggtatatcaacttgggcaatttttgtacatg---tgtagGTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAG
                | ||  ||  || || |  || |||| |  || |  | | |    |  |   |||     ||| | |||     ||| ||   ||||||| || ||||| || || |||||||| |||||||||||| |||| ||||||||||| || ||||| || |||
gtgatctcgatgttctgcaattgaaccaatgcacttgttaatgtactactaggctgcatttgcagaagataattg-ttgtgaaatgacgctacttgttatgtagGTAGGAGCACAGACAGAAACTGAGCTTAAGGAAAAGAAACTGAGGGTTGAAGATGCACTGAATGCAACCAAG

upper sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G015989_T01 (Zea mays), 3'ss of exon 9
------------------------------------gtaacagactcactgaaatggtaatatgtta-----gtttggtacgccgttgggtatatcaacttgggcaatttttgtacatgt-gtagGTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAG
                                     | | |  || | |    |  |  | | ||      | || | |           |    ||| ||       ||  |   | | |||||| || ||||| || || |||||||||||||||||||||||||| ||||| ||||| || ||||||||||||
gtaaaccccaatgttaaaccctagttgcctcaatttttcaaaaccttagttgcctcttggtgtatttaggatgcttagcagaataaaaaaaactagaacatgatatgccttgctttgtattgtagGTAGGAGCACAGACAGAAACTGAGCTCAAGGAAAAGAAATTGAGGGTTGAGGATGCCCTGAATGCTACAAAG

upper sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 8
lower sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 9
----gtaacagactcactgaaatggtaatatgttagtttggtacgccgttgggtatatcaacttgggcaatttttgtacatgt-gtagGTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAG
       | | |||   | |  |     | | | | |  | |  |   |  |  |||| || ||  ||   || ||||   ||   ||||||| |||||||||||||| || ||||| || ||||| |||||||||||||||||||||||||| ||||||
gtaaactaaaaactatttaagtttcctttgtctgattaagatgtgtt-tcagagatattaagttaagctcgttatgtattggttaaagGTTGGAGCACAAACTGAGACAGAACTCAAAGAGAAGAAGTTGAGAGTTGAAGATGCTCTTAATGCAACAAAG

upper sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 8
lower sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 9
--gtaacag-actcactgaaatggtaatatgttagtttggtacgccgttgggtatatcaacttgggcaatttttgtacatgt-----gtagGTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAG
    || || | ||||    |   |  |   || || || ||      |  ||  |   |  |    ||  ||| ||||| |       ||||||| || ||||||||||| |||||||| ||||||||  ||||||| ||||||||||||||||||||||||
gtaaaatagtaatcacatggactttcttggatttgtatgatagaagaataagttaagtgatctaattaaagtttttacatcttggttaaagGTTGGAGCTCAAACTGAGACAGAGCTCAAAGAAAAGAAGCTGAGAGTGGAAGATGCTCTTAATGCTACAAAG

upper sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 8
lower sequence: AT5G56500.2 (Arabidopsis thaliana), 3'ss of exon 9
gtaacagactcactgaaatggtaatatgttagtttggtacgccgttgggtatatcaacttgggcaattt-----ttgtacatg-tgtagGTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAG
|| | | ||| |   ||    | | ||| | |       ||  | |     ||  ||   |   ||| |     || || ||  | |||||||| |||||||||||||| ||||| ||||| |||||||| ||||||||||||||||||||||||||||||
gtgagatact-aagaaacaaatcacatgat-gcaaaaagcgtagcttaaggtaataagaagaataatctaaacgttttatattctttagGTTGGAGCACAAACTGAGACAGAGCTTAAGGAGAAGAAATTAAGAGTTGAAGATGCTCTTAATGCTACAAAG

upper sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 9
--------gtaacagactcactgaaatggtaatatgttagtttggtac-gccgttgggta-tatcaacttgggcaatttttgtacatgtgtagGTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAG
         ||       || | |||   | |||  | | ||    |  || | ||  || |||| | ||    | |  ||| || | || ||||||| |||||||||||||| ||||| || ||||||||| ||||||| ||||| ||||| ||||| || |||
gtaaattcttagttagtccagttaaa-atttataaatgatttcatcattgcaggtgcttagtatcta-ttaattattcattgaacttttgaagGTTGGAGCACAAACTGAGACAGAGCTTAAAGAAAAGAAACTGAGAGTAGAAGACGCTCTCAATGCAACGAAG

upper sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ33580 (Selaginella moellendorffii), 3'ss of exon 8
gtaacagactcactgaaatggtaatatgttagtttggtacgccgttgggtatatcaacttgggcaatttttgtacatgtgtagGTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAG
                        || |||  ||| | |     ||  | |   || |||   |  | | |||| || || |||||||||||||||||||||| ||  | || |||||||| || ||||| ||||||||| | ||||| || |||
-----------------------gtaagtttattttgcagtatttttagcagcacatctttaact-tctctgtaaat-tgaagGTTGGTGCACAAACTGAGACAGAATTAAAAGAAAAGAAGTTAAGAGTGGAAGATGCTTTGAATGCGACGAAG

upper sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 8
lower sequence: EFJ36935 (Selaginella moellendorffii), 3'ss of exon 8
gtaacagactcactgaaatggtaatatgttagtttggtacgccgttgggtatatcaacttgggcaatttttgtacatgtgtagGTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAG
                        || |||  ||| | |     ||  | |   || | |   |  ||| |||| || || |||||||||||||||||||||| || || || |||||||| || ||||| ||||||||| | ||||| || |||
-----------------------gtaagtttattttgcagtatttttagcagcacatcgttaact-tttctgtaaat-tgaagGTTGGTGCACAAACTGAGACAGAACTAAAAGAAAAGAAGTTAAGAGTGGAAGATGCTTTGAATGCAACGAAG

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:     AGCTGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAG                         GTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAA
genomic: AGCTGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAGgtaacagact ... acatgtgtagGTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAA
EST: gi|16278868|gb|BI943136.1|BI943136
EST:     AGCTGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAG                         GTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAA
genomic: AGCTGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAGgtaacagact ... acatgtgtagGTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAA
EST: gi|16278211|gb|BI942785.1|BI942785
EST:     AGCTGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAG                         GTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAA
genomic: AGCTGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAGgtaacagact ... acatgtgtagGTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAA
EST: gi|208337500|gb|GE133496.1|GE133496
EST:     AGCTGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAG                         GTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATT
genomic: AGCTGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAGgtaacagact ... acatgtgtagGTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATT
EST: gi|193718581|gb|FK652579.1|FK652579
EST:     TGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAG                         GTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAA
genomic: TGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAGgtaacagact ... acatgtgtagGTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAA
EST: gi|208255225|gb|GE053942.1|GE053942
EST:     GGTGGTGTGGCTGTCATACAG                         GTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAA
genomic: GGTGGTGTGGCTGTCATACAGgtaacagact ... acatgtgtagGTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAA
EST: gi|26046015|gb|CA783382.1|CA783382
EST:     AGCTGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAG                         GTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAA
genomic: AGCTGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAGgtaacagact ... acatgtgtagGTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAA
EST: gi|16279768|gb|BI943606.1|BI943606
EST:     AGCTGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAG                         GTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAA
genomic: AGCTGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAGgtaacagact ... acatgtgtagGTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAA
EST: gi|298192668|gb|HO033102.1|HO033102
EST:     AGCTGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAG                         GTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAA
genomic: AGCTGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAGgtaacagact ... acatgtgtagGTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAA
EST: gi|16276840|gb|BI942072.1|BI942072
EST:     AGCTGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAG                         GTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAA
genomic: AGCTGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAGgtaacagact ... acatgtgtagGTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAA
EST: gi|193661261|gb|FK603559.1|FK603559
EST:     AGCTGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAG                         GTTGGTGCACAAACTGAGA
genomic: AGCTGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAGgtaacagact ... acatgtgtagGTTGGTGCACAAACTGAGA
EST: gi|208166285|gb|GD965477.1|GD965477
EST:     AGCTGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAG                         GTTGGTGCACAAACTGAGACTAGAAGACTCAAGGAAAAGAAATT
genomic: AGCTGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAGgtaacagact ... acatgtgtagGTTGGTGCACAAACTGAGACT-GA-G-CTCAAGGAAAAGAAATT
EST: gi|193658934|gb|FK602087.1|FK602087
EST:     AGCTGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAG                         GTTGGTGCACAAACTGAGA
genomic: AGCTGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAGgtaacagact ... acatgtgtagGTTGGTGCACAAACTGAGA
EST: gi|298170123|gb|HO018747.1|HO018747
EST:     AGCTGAATGAGACAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAG                         GTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAA
genomic: AGCTGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAGgtaacagact ... acatgtgtagGTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAA
EST: gi|193523440|gb|FK478287.1|FK478287
EST:     AGCTGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAG                         GTTGGTGCACAAACTGAGA
genomic: AGCTGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAGgtaacagact ... acatgtgtagGTTGGTGCACAAACTGAGA
EST: gi|15589717|gb|BI674333.1|BI674333
EST:     AGCTGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAG                         GTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAA
genomic: AGCTGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAGgtaacagact ... acatgtgtagGTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAA
EST: gi|207784127|gb|GD758437.1|GD758437
EST:     AGCTGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAG                         GTTGGTGCACAAACTGAGACTGAAGACTCAAGGAAAAGAAATT
genomic: AGCTGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAGgtaacagact ... acatgtgtagGTTGGTGCACAAACTGAGACTGA-G-CTCAAGGAAAAGAAATT
EST: gi|208199569|gb|GD996450.1|GD996450
EST:     GAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAG                         GTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAA
genomic: GAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAGgtaacagact ... acatgtgtagGTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAA
EST: gi|193403060|gb|FK369006.1|FK369006
EST:     TTGCTAAATTATCTGGTGGTGTGGCTGTCATACAG                         GTTGGTGCACAAAACTAGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTG
genomic: TTGCTAAATTATCTGGTGGTGTGGCTGTCATACAGgtaacagact ... acatgtgtagGTTGGTGCAC-AAACT-GAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTG
EST: gi|207847652|gb|GD818243.1|GD818243
EST:     AGCTGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAG                         GTTGGTGCACAAACTGAGACTGAGACTCAAGGAAAAGAAATT
genomic: AGCTGAATGAGAGAATTGCTAAATTATCTGGTGGTGTGGCTGTCATACAGgtaacagact ... acatgtgtagGTTGGTGCACAAACTGAGACTGAG-CTCAAGGAAAAGAAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttagtttggtacgccgttgggtatatcaacttgggcaatttttgtacatgtgtagGTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAG
                                    aatttttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacagactcactgaaatggtaatatgttagtttggtacgccgttgggtatatcaacttgggcaatttttgtacatgtgtagGTTGGTGCACAAACTGAGACTGAGCTCAAGGAAAAGAAATTGAGAGTTGAAGATGCTCTTAATGCTACAAAG

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