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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaaaacaaaattgctcaagttgcacaataactaaaagaaaagcagttggatgcccaggtttgaattgtgttctatgctaagattttgtgtcattgtcagATATATAAGGAGGGGTACACCAGATGCTGGCTTTGCTCTTTTTGAATCTGAGTCTCTGAAGTGGCCAGGTTTTGTAGAGTTTGATGATGTAAATGGGAAG

Basic information

species Glycine max
transcript GLYMA04G40290.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA04G40290.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g60200.1 (Oryza sativa), 3'ss of exon 3
agaaaacaaaattgctcaagttgcacaataactaaaagaaaagcagttggatgcccaggtttgaattgtgttctatgctaagattttgtgtcattgtcagATATATAAGGAGGGGTACACCAGATGCTGGCTTTGCTCTTTTTGAATCTGAGTCTCTGAAGTGGCCAGGTTTTGTAGAGTTTGATGATGTAAATGGGAAG
||| | | | | | || | | |||| || | | | || |||||| | | | || |||||| | |||| | ||||||||||| || ||||||| || | ||||| |||| |||||||||||||| || ||||||||||| || ||||||
---------------gtaagcttgtcttcctgtgattctgctacggtagtgttatattgtttatatgaatctttttatta---ttttgtct---tttaagGTATATACGACGGGGGAAGCCAGATGCTGGTTTCCCTCTTTTCGAGACAGAGTCCTTGAAATGGCCAGGTTTTGTGGAATTTGATGATGTTAACGGGAAG

upper sequence: GLYMA04G40290.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G138840_T01 (Zea mays), 3'ss of exon 3
agaaaacaaaattgctcaagttgcacaataactaaaagaaaagcagttggatgcccaggtttgaattgtgttctatgctaagattttgtgtcattgtc--agATATATAAGGAGGGGTACACCAGATGCTGGCTTTGCTCTTTTTGAATCTGAGTCTCTGAAGTGGCCAGGTTTTGTAGAGTTTGATGATGTAAATGGGAAG
| | | | || | || ||| | || | ||| || |||| | | ||| | || || || || | || ||| |||||||| || |||||||||| || ||||| |||| ||||| || |||||||||||||||||||| ||||| |||
----------------------gtatgctttgtcaatgcaa--ttgtttttcttcttctttggtcatgtcatcctccttaagtccccctctaattattcaagGTACATTCGGCGAGGACAACCGGATGCTGGTTTCCCTCTTTTTGAGTCCGAGTCCTTGAAATGGCCTGGATTTGTAGAGTTTGATGATGTCAATGGAAAG

upper sequence: GLYMA04G40290.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G145662_T01 (Zea mays), 3'ss of exon 3
agaaaacaaaattgctcaagttgcacaataactaaaagaaaagcagttggatgcccaggtttgaattgtgttctatgctaagattttgtgtcattgtcagATATATAAGGAGGGGTACACCAGATGCTGGCTTTGCTCTTTTTGAATCTGAGTCTCTGAAGTGGCCAGGTTTTGTAGAGTTTGATGATGTAAATGGGAAG
|| || ||| ||| | ||| || ||| | ||| || | | || || | || | || ||| |||||||| || |||||||||| || ||||| |||| ||||| || |||||||||||||| ||||| ||||| | |
---------------------------gtatgctttgtcaatgcaattgtttt------tttatcacgtcatctttcttaaatttccccaaccattcaagGTACGTTCGGCGAGGACAACCGGATGCTGGTTTCCCTCTTTTTGAGTCCGAGTCCTTGAAATGGCCTGGATTTGTAGAGTTTGACGATGTCAATGGAAGG

upper sequence: GLYMA04G40290.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0067g00100.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------------------------------------------agaaaacaaaattgctcaagttgcacaat---aactaaaagaaaagcagttggatgcccaggtttgaattgtgttctatgctaagattttgtgtc---attgtc-agATATATAAGGAGGGGTACACCAGATGCTGGCTTTGCTCTTTTTGAATCTGAGTCTCTGAAGTGGCCAGGTTTTGTAGAGTTTGATGATGTAAATGGGAAG
| | || ||| | |||| || | | | || || | | | || || || | || | | | || ||| || ||||| ||||||||||| | ||| ||||||||||||||||| |||||||||||||| || || ||||| |||||||||||||||||||||||||||||||||
gtgcgtgattctttaaatattctctccttccttcccttctcactgctcctctccaccctccaaataaataaacaaatgaagtaacatttttttgctttagttttctacaatttgttttgctatcttatttttattttttaactgaaaaatcctggttgaattatccagATACATAAGGAGGGGCAAACCGGATGCTGGCTTTGCTCTCTTTGAATCTGAGTCACTTAAATGGCCTGGTTTTGTAGAGTTTGATGATGTAAATGGGAAG

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|58018556|gb|CX705298.1|CX705298
EST:     TATGCTTCAGACAGTTACAGTTCTTTGAAATGCAGAAGCACAAGGATCGA                         ATATATAAGGAGGGGTACACCAGATGCTGGCTTTGCTCTTTTTGAATCTGA
genomic: TATGCTTCAGACAGTTACAGTTCTTTGAAATGCAGAAGCACAAGGATCGAgtatgtattg ... tcattgtcagATATATAAGGAGGGGTACACCAGATGCTGGCTTTGCTCTTTTTGAATCTGA
EST: gi|208121367|gb|GD919846.1|GD919846
EST:     TGCTTCAGACAGTTACAGTTCTTTGAAATGCAGAAGCACAAGGATCGA                         ATATATAAGGAGGGGTACACCAGATGCTGGCTTTGCTCTTTTTGAATCTGA
genomic: TGCTTCAGACAGTTACAGTTCTTTGAAATGCAGAAGCACAAGGATCGAgtatgtattg ... tcattgtcagATATATAAGGAGGGGTACACCAGATGCTGGCTTTGCTCTTTTTGAATCTGA
EST: gi|208222388|gb|GE020826.1|GE020826
EST:     TATGCTTCAGACAGTTACAG-TCTTTGAAATGCAGAAGCACAAGGATCGA                         ATATATAAGGAGGGGTACACCAGATGCTGGCTTTGCTCTTTTTGAATCTGA
genomic: TATGCTTCAGACAGTTACAGTTCTTTGAAATGCAGAAGCACAAGGATCGAgtatgtattg ... tcattgtcagATATATAAGGAGGGGTACACCAGATGCTGGCTTTGCTCTTTTTGAATCTGA
EST: gi|208056872|gb|GD851205.1|GD851205
EST:     AAGCACAAGGATCGA                         ATATATAAGGAGGGGTACACCAGATGCTGGCTTTGCTCTTTTTGAATCTGA
genomic: AAGCACAAGGATCGAgtatgtattg ... tcattgtcagATATATAAGGAGGGGTACACCAGATGCTGGCTTTGCTCTTTTTGAATCTGA
EST: gi|17024092|gb|BM095126.1|BM095126
EST:     TATGCTTCAGACAGTTACAGTTCTTTGAAATGCAGAAGCACAAGGATCGA                         ATATATAAGGAGGGGTACACCAGATGCTGGCTTTGCTCTTTTTGAATCTGA
genomic: TATGCTTCAGACAGTTACAGTTCTTTGAAATGCAGAAGCACAAGGATCGAgtatgtattg ... tcattgtcagATATATAAGGAGGGGTACACCAGATGCTGGCTTTGCTCTTTTTGAATCTGA
EST: gi|193463036|gb|FK427801.1|FK427801
EST:     ACAGTTACAGTTCTTTGAAATGCAGAAGCACAAGGATCGA                         ATATATAAGGAGGGGTACACCAGATGCTGGCTTTGCTCTTTTTGAATCTGA
genomic: ACAGTTACAGTTCTTTGAAATGCAGAAGCACAAGGATCGAgtatgtattg ... tcattgtcagATATATAAGGAGGGGTACACCAGATGCTGGCTTTGCTCTTTTTGAATCTGA
EST: gi|120529430|gb|EH257564.1|EH257564
EST:     TATGCTTCAGACAGTTACAGTTCTTTGAAATGCAGAAGCACAAGGATCGA                         ATATATAAGGAGGGGTACACCAGATGCTGGCTTTGCTCTTTTTGAATCTGA
genomic: TATGCTTCAGACAGTTACAGTTCTTTGAAATGCAGAAGCACAAGGATCGAgtatgtattg ... tcattgtcagATATATAAGGAGGGGTACACCAGATGCTGGCTTTGCTCTTTTTGAATCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttggatgcccaggtttgaattgtgttctatgctaagattttgtgtcattgtcagATATATAAGGAGGGGTACACCAGATGCTGGCTTTGCTCTTTTTGAATCTGAGTCTCTGAAGTGGCCAGGTTTTGTAGAGTTTGATGATGTAAATGGGAAG
                                 taagatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaaaacaaaattgctcaagttgcacaataactaaaagaaaagcagttggatgcccaggtttgaattgtgttctatgctaagattttgtgtcattgtcagATATATAAGGAGGGGTACACCAGATGCTGGCTTTGCTCTTTTTGAATCTGAGTCTCTGAAGTGGCCAGGTTTTGTAGAGTTTGATGATGTAAATGGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- -aaacaaa
- - - - - - - - - - -tgcacaa
- - - - - - - - - - - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - ggatgcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttgtg