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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgacctatgtaattgctataaagctgagatcatacaccatagacatggtcttctccggtttcactttaatttttcattgcatgtgtatgcatccacagATTTGCAGATGATATTGACTTGAACGTGCAAGATCCTGTGGCTCATAAACACATACCGTATGTTGTCATTCTTGTCAAGATGGCTGATGAGTGGGCCCAA

Basic information

species Glycine max
transcript GLYMA12G10540.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G10540.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G05180.1 (Arabidopsis thaliana), 3'ss of exon 5
-------gttgacctatgtaattgctataaag----ctgagatcat---acaccatagac----atggtcttctccggtttcactttaatttttcattgcatgtgtatgcatccacagATTTGCAGATGATATTGACTTGAACGTGCAAGATCCTGTGGCT---CATAAACACATACCGTATGTTGTCATTCTTGTCAAGATGGCTGATGAGTGGGCCCAA
       | |  | |||    |  || ||       |||  ||| |   |||  || |      |||| |  ||  |   | |||   ||| || |||   |    ||| | |  ||| ||||  ||    |||||  |||| ||   ||| || |  |||   ||||| |||||||| || || ||||||||||| ||||||||||| ||||||||    
gtccactgctctcatatcctctcactttatgttgttctggcatcctttaacattatggttgtggatggacgactgagtacttactgatattcttaattattta---atg-aacggcagTTTTGTGGAGACCATTGATCTGAATGTATCAGAGCCGGCCGCTGCACATAAGCACATACCTTACGTCGTCATTCTTGTAAAGATGGCTGAGGAGTGGGCT---

upper sequence: GLYMA12G10540.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv12s0059g00610.t01 (Vitis vinifera), 3'ss of exon 5
------------------------------------------------------------------------------------------gttgacct----atgtaattgctataaagctgagatcatacaccatagacatggtcttctccgg--tttcactttaatttttcattgcatgtgtatgcatccacagATTTGCAGATGATATTGACTTGAACGTGCAAGATCCTGTGGCTCATAAACACATACCGTATGTTGTCATTCTTGTCAAGATGGCTGATGAGTGGGCCCAA
                                                                                           |||| ||    ||||| |||| |  |  ||    |  ||     ||  |  |    |  | ||  ||| |   ||    |||  ||  ||||||| || ||| || ||||||||    || || || || |||  ||||||||| |  ||||| |||| ||| |||||||| ||||||||||||||||||||  ||||| || ||
gtaagattttttctatccatattaatattttttattgactctgtctgtgcatgtcttctttttgtatatttattattattacaggtgtgtattgaacttgacatgtatttgc-acgactctagctttctatcttgtaccccagaaagtacctggagttttatagtagaaattc--tgattgtgtat-caaccatagGTTTGCAGAGACCATCGATTTAAATGTGTCAGATCCTGTTGTCCATAAGCACACACCATATGTTGTTATTCTTGTCAAGATGGCTGAGCAGTGGACCAAA
















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|193558234|gb|FK514885.1|FK514885
EST:     CATTTTTTGGATGATCTCCGGTTAAATAATCCTTGGCCTAAACTCAAGAG                         ATTTGCAGATGTATTATTGACTTGAACGTGCAAGATCCTGTGGCTCATAAA
genomic: CATTTTTTGGATGATCTCCGGTTAAATAATCCTTGGCCTAAACTCAAGAGgtataaagta ... gcatccacagATTTGCAGATG-A-TATTGACTTGAACGTGCAAGATCCTGTGGCTCATAAA
EST: gi|208300249|gb|GE097284.1|GE097284
EST:     CATTTTTTGGATGATCTCCGGTTAAATAATCCTTGGCCTAAACTCAAGAG                         ATTTGCAGATGATATTGACTTGAACGTGCAAGATCCTGTGGCTCATAAACA
genomic: CATTTTTTGGATGATCTCCGGTTAAATAATCCTTGGCCTAAACTCAAGAGgtataaagta ... gcatccacagATTTGCAGATGATATTGACTTGAACGTGCAAGATCCTGTGGCTCATAAACA
EST: gi|208058253|gb|GD860258.1|GD860258
EST:     CATTTTTTGGATGATCTCCGGTTAAATAATCCTTGGCCTAAACTCAAGAG                         ATTTGCAGATGATATTGACTTGAACGTGCAAGATCCTGTGGCTCATAAACN
genomic: CATTTTTTGGATGATCTCCGGTTAAATAATCCTTGGCCTAAACTCAAGAGgtataaagta ... gcatccacagATTTGCAGATGATATTGACTTGAACGTGCAAGATCCTGTGGCTCATAAACA
EST: gi|193694654|gb|FK627754.1|FK627754
EST:     CA-TTTTTGGATGATCTCCGGTTAAATAATCCTTGGCCTAAACTCAAGAG                         ATTTGCAGATGATATTGACTTGAACGTGCAAGATCCTGTGGCTCATAAACA
genomic: CATTTTTTGGATGATCTCCGGTTAAATAATCCTTGGCCTAAACTCAAGAGgtataaagta ... gcatccacagATTTGCAGATGATATTGACTTGAACGTGCAAGATCCTGTGGCTCATAAACA
EST: gi|208268443|gb|GE067254.1|GE067254
EST:     CATTTTTTGGATGATCTCCGGTTAAATAATCCTTGGCCTAAACTCAAGAG                         ATTTGCAGATGATATTGACTTGAACGTGCAAGATCCTGTGGCTCATAAACA
genomic: CATTTTTTGGATGATCTCCGGTTAAATAATCCTTGGCCTAAACTCAAGAGgtataaagta ... gcatccacagATTTGCAGATGATATTGACTTGAACGTGCAAGATCCTGTGGCTCATAAACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catggtcttctccggtttcactttaatttttcattgcatgtgtatgcatccacagATTTGCAGATGATATTGACTTGAACGTGCAAGATCCTGTGGCTCATAAACACATACCGTATGTTGTCATTCTTGTCAAGATGGCTGATGAGTGGGCCCAA
                    ctttaat  putative branch site (score: 4)
               tttcactttaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgacctatgtaattgctataaagctgagatcatacaccatagacatggtcttctccggtttcactttaatttttcattgcatgtgtatgcatccacagATTTGCAGATGATATTGACTTGAACGTGCAAGATCCTGTGGCTCATAAACACATACCGTATGTTGTCATTCTTGTCAAGATGGCTGATGAGTGGGCCCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - -cctatgt
- - - - - - - -tgctata
- - - - - - - - - - - - - - - - catacac
- - - - - - - - - - - - - - - - - - - - - -gacatgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatgt