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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtagtttcatttggcaactcttgaaaatcgggaaaatttaattttcttcgtttactaaatctcacatgtttcaattttgtatttttcatgtctaattggaactcgtttaatggttctttcgcacagtagatcttttcccctctttttgaattaaagtttgcccttcgcagTGTCATCAAGATTGTGCTTCAGTTTTGCAAAGAAAATTCGTTGCATCAGACTTTTCAGATGCTGCAGAACGAATGCCAGGTTTCTCTGAACACCGTTGAC

Basic information

species Glycine max
transcript GLYMA08G13560.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G13560.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os01g21940.1 (Oryza sativa), 3'ss of exon 1
gtaagtagtttcatttggcaactcttgaaaatcgggaaaatttaattttcttcgtttactaaatctcacatgtttcaattttgtatttttcatgtctaattggaactcgtttaatggttctttcgcacagtagat--cttttcccctctttttgaattaaagtttgcccttcgcagTGTCATCAAGATTGTGCTTCAGTTTTGCAAAGAAAATTCGTTGCATCAGACTTTTCAGATGCTGCAGAACGAATGCCAGGTTTCTCTGAACACCGTTGAC
                                                                            ||         |  |||     | ||  |    ||      || || ||||  || | |   |||     | ||| |    | | ||       | |||| ||  | ||||| ||||| ||||| ||||| || || ||| |||| ||||| || |||| |||||||||||| |||||||| || || |||||||| |||
---------------------------------------------------------------------------gaaccccccccctcccattgggtagtgctatagcttaggaaattattacgcaaggttgctaggtttgatagtgtttcttgcgtgatgtccatggat-gcagCGTGGTGAAGATAGTGCTGCAGTTCTGCAAGGAGAACTCGCTGCAGCAGACGTTCCAGACGCTGCAGAACGAGTGCCAGGTCTCGCTCAACACCGTCGAC

upper sequence: GLYMA08G13560.2 (Glycine max), 3'ss of exon 1
lower sequence: AT1G73720.1 (Arabidopsis thaliana), 3'ss of exon 1
gtaagtagtttcatttggcaactcttgaaaatcgggaaaatttaattttcttcgtttactaaatctcacatgtttcaattttgtatttttcatgtctaattggaactcgtttaatggttctttcgcaca----gtagatcttttcccctctttttgaattaaagt-ttgcccttcgcagTGTCATCAAGATTGTGCTTCAGTTTTGCAAAGAAAATTCGTTGCATCAGACTTTTCAGATGCTGCAGAACGAATGCCAGGTTTCTCTGAACACCGTTGAC
                                                                             ||||||  ||  | || |   || |  |    ||| ||| |   |     |     |||||||||   ||||  |       ||  || |||    || |||||| || |||||| |||||||||| |||||||||||||| ||| ||||||| || ||||   | || | ||| || ||||||||  |||| || || |||
-----------------------------------------------------------------------------attttg--ttagtaatattggatggagaacgttttgatgctatatgtcagctttgtgtagatcttcatccctaatagctctctattgtgttgaatgtctcagTGTAATAAAGATTATGCTTCAGTTCTGCAAAGAAAATTCCTTGAATCAGACATTCCAGACATTACAAAGCGAGTGTCAGGTTTCCTTGAATACAGTAGAC

upper sequence: GLYMA08G13560.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv17s0000g08930.t01 (Vitis vinifera), 3'ss of exon 1
gtaagtagtttcatttggcaactcttgaaaatcgggaaaatttaattttcttcgtttactaaatctcacatgtttcaattttgtatttttca-tgtctaattggaactcgtttaatggttctttcgcacagtagatcttttcccctctttttgaattaaagtttgcccttcgcagTGTCATCAAGATTGTGCTTCAGTTTTGCAAAGAAAATTCGTTGCATCAGACTTTTCAGATGCTGCAGAACGAATGCCAGGTTTCTCTGAACACCGTTGAC
                                                                 | | |||| |   |  | ||| ||    ||||||||    |||  | || || || |   |   |||| ||||  |      ||| || |||    | | |   |  ||||||||| ||||| |||||||||||||| ||||||||||| ||||| || || |||||||   | || |  || || ||||| ||| |||| || || |||
-----------------------------------------------------------ggttgtttatatgtattcttcctatatcttcagctgtctaat----actt-tatagtg-ttttgatgtgaagtaaatctaat------tttatgtatt----tcttcatctttcagTGTCATTAAGATCGTGCTTCAGTTTTGTAAAGAAAATTCCTTGCACCAAACGTTTCAGACATTACAAAGTGAGTGTCAGGTATCTTTGAATACGGTCGAC

upper sequence: GLYMA08G13560.2 (Glycine max), 3'ss of exon 1
lower sequence: PP1S31_68V6.1 (Physcomitrella patens), 3'ss of exon 1
gtaagtagtttcatttggcaactcttgaaaatcgggaaaatttaattttcttcgtttactaaatctcacatgtttcaattttgtatttttcatgtctaattggaactcgtttaatggttctttcgcacagtagatcttttcccctctttttgaattaaagtttgcccttcgcagTGTCATCAAGATTGTGCTTCAGTTTTGCAAAGAAAATTCGTTGCATCAGACTTTTCAGATGCTGCAGAACGAATGCCAGGTTTCTCTGAACACCGTTGAC
                                                                 |   | | |  ||    | |||||| |  |  |  | ||| ||| |  ||  ||||    ||| ||   |  | |     | |||         ||  |  ||  |||||||||| ||||| ||||| ||||| || ||||| || || ||||| |||||||| ||||  || || || || || ||||||||||| ||||| || |||
---------------------------------------------------------------cgtagtacgatgaaacagagcatttttgaatttgagctagaattcggtggat--ttctcctccactgtgtgtggtctaaagaccttt---------gtggggactgtgcagTGTCATTAAGATAGTGCTGCAGTTCTGTAAAGAGAACTCATTGCAGCAGACTTTCCAGACACTACAAAATGAGTGTCAGGTTTCTCTCAACACTGTGGAC

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|193421880|gb|FK387967.1|FK387967
EST:     ACTCCAATCGACATAGCAGCAATGTCTACGCTCGAAATTGAAGCTCGAGA                         TGTCATCAAGATTGTGCTTCAGTTTTGCAAAGAAA-TTCGTTGCATCAGAC
genomic: ACTCCAATCGACATAGCAGCAATGTCTACGCTCGAAATTGAAGCTCGAGAgtaagtagtt ... cccttcgcagTGTCATCAAGATTGTGCTTCAGTTTTGCAAAGAAAATTCGTTGCATCAGAC
EST: gi|209710368|gb|BW681267.1|BW681267
EST:     ACTCCAATCGACATAGCAGCAATGTCTACGCTCGAAATTGAAGCTCGAGA                         TGTCATCAAGATTGTGCTTCAGTTTTGCAAAGAAAATTCGTTGCATCAGAC
genomic: ACTCCAATCGACATAGCAGCAATGTCTACGCTCGAAATTGAAGCTCGAGAgtaagtagtt ... cccttcgcagTGTCATCAAGATTGTGCTTCAGTTTTGCAAAGAAAATTCGTTGCATCAGAC
EST: gi|151399243|gb|EV269114.1|EV269114
EST:     ACTCCAATCGACATAGCAGCAATGTCTACGCTCGAAATTGAAGCTCGAGA                         TGTCATCAAGATTGTGCTTCAGTTTTGCAAAGAAAATTCGTTGCATCAGAC
genomic: ACTCCAATCGACATAGCAGCAATGTCTACGCTCGAAATTGAAGCTCGAGAgtaagtagtt ... cccttcgcagTGTCATCAAGATTGTGCTTCAGTTTTGCAAAGAAAATTCGTTGCATCAGAC
EST: gi|209709054|gb|BW658770.1|BW658770
EST:     ACTCCAATCGACATAGCAGCAATGTCTACGCTCGAAATTGAAGCTCGAGA                         TGTCATCAAGATTGTGCTTCAGTTTTGCAAAGAAAATTCGTTGCATCAGAC
genomic: ACTCCAATCGACATAGCAGCAATGTCTACGCTCGAAATTGAAGCTCGAGAgtaagtagtt ... cccttcgcagTGTCATCAAGATTGTGCTTCAGTTTTGCAAAGAAAATTCGTTGCATCAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttcgcacagtagatcttttcccctctttttgaattaaagtttgcccttcgcagTGTCATCAAGATTGTGCTTCAGTTTTGCAAAGAAAATTCGTTGCATCAGACTTTTCAGATGCTGCAGAACGAATGCCAGGTTTCTCTGAACACCGTTGAC
                                         tttgcccttc  CT-rich tract
                           tttttgaattaaagtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtagtttcatttggcaactcttgaaaatcgggaaaatttaattttcttcgtttactaaatctcacatgtttcaattttgtatttttcatgtctaattggaactcgtttaatggttctttcgcacagtagatcttttcccctctttttgaattaaagtttgcccttcgcagTGTCATCAAGATTGTGCTTCAGTTTTGCAAAGAAAATTCGTTGCATCAGACTTTTCAGATGCTGCAGAACGAATGCCAGGTTTCTCTGAACACCGTTGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG