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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctttttcaaaagtactgcgacgattaatgcctgaaaattaaacgaagaggaaatgctggtataatactgattgattcttctttgtatggtttgtacagAAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATG

Basic information

species Glycine max
transcript GLYMA08G09180.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G09180.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G152757_T01 (Zea mays), 3'ss of exon 1
ttctttttcaaaagtactgcgacgattaatgc--ctgaaaattaaacga---agaggaaatgctggtataatactgattgat-tcttctttgtatggtttgt---acagAAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATG
         ||||| |   |    | | |||     |   |||  |      |||    || | | |  | |   |||| || |||| | ||| | ||||      |||| ||| ||  ||| | || |||| || |  || ||  | ||| |||||||||||||||||||||||||||||||||
--------aaaaagaatcacatatagtgatggggtggcgtatttgattgtttagaccggataccg-tgcagtttggatttatctcttttctgttttgtttcctccccagACAGTTCAACAGGATATTATGCATTCTGGCGTTCAGGCTAAGGCAGACAAAAGTCCTGTCACAGTGGCTGATTATG

upper sequence: GLYMA08G09180.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv04s0044g01480.t01 (Vitis vinifera), 3'ss of exon 1
-----ttctttttcaaaagtactgcgacgattaatgcc-tgaaaattaaacgaagaggaaatgctggtata-atactgattgattcttctttgtatggtttgtacagAAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATG
     ||   |||   | ||  ||||     | ||  | || |   |  |    |   | |||  | ||||  || | ||  ||   |  ||      |||   |||||||| || ||||| ||  ||||||| ||||| || || || ||||| ||||| ||||||||||||||||| ||||
tgaaatttgattttgtatgtg-tgcgtgtcctgatttcatgtatggtttagtgtgtatatatgtggatatatgtatttatgtatgtattatt------ttttctcagAAAGTGCAAAAGGCGCTGTTGCAATCAGATGTCCAATCTAAATCAGATAAAAGCCCTGTCACAGTGGCTGACTATG
















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|192323419|gb|FK015305.1|FK015305
EST:     AATTCGCCGCTGCNNNNNNNGCAGCCACTCTCGCTGCTCGTCTCTGCAAG                         AAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAA
genomic: AATTCGCCGCTGCAAAAAAAGCAGCCACTCTCGCTGCTCGTCTCTGCAAGgcaccacccc ... gtttgtacagAAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAA
EST: gi|21677711|gb|BQ630062.1|BQ630062
EST:     AATTCGCCGCTGCNNNNNNNGCAGCCACTCTCGCTGCTCGTCTCTGCAAG                         AAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAA
genomic: AATTCGCCGCTGCAAAAAAAGCAGCCACTCTCGCTGCTCGTCTCTGCAAGgcaccacccc ... gtttgtacagAAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAA
EST: gi|192311655|gb|FK004874.1|FK004874
EST:     AATTCGCCGCTGCNNNNNNNGCAGCCACTCTCGCTGCTCGTCTCTGCAAG                         AAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAA
genomic: AATTCGCCGCTGCAAAAAAAGCAGCCACTCTCGCTGCTCGTCTCTGCAAGgcaccacccc ... gtttgtacagAAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAA
EST: gi|298190692|gb|HO032813.1|HO032813
EST:     AATTCGCCGCTGCNNNNNNNGCAGCCACTCTCGCTGCTCGTCTCTGCAAG                         AAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAA
genomic: AATTCGCCGCTGCAAAAAAAGCAGCCACTCTCGCTGCTCGTCTCTGCAAGgcaccacccc ... gtttgtacagAAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAA
EST: gi|209712035|gb|BW674180.1|BW674180
EST:     AATTCGCCGCTGCNNNNNNNGCAGCCACTCTCGCTGCTCGTCTCTGCAAG                         AAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAA
genomic: AATTCGCCGCTGCAAAAAAAGCAGCCACTCTCGCTGCTCGTCTCTGCAAGgcaccacccc ... gtttgtacagAAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAA
EST: gi|192311684|gb|FK004875.1|FK004875
EST:     AATTCGCCGCTGCNNNNNNNGCAGCCACTCTCGCTGCTCGTCTCTGCAAG                         AAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAA
genomic: AATTCGCCGCTGCAAAAAAAGCAGCCACTCTCGCTGCTCGTCTCTGCAAGgcaccacccc ... gtttgtacagAAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAA
EST: gi|24205274|gb|BU964527.1|BU964527
EST:     AATTCGCCGCTGCNNNNNNNGCAGCCACTCTCGCTGCTCGTCTCTGCAAG                         AAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAA
genomic: AATTCGCCGCTGCAAAAAAAGCAGCCACTCTCGCTGCTCGTCTCTGCAAGgcaccacccc ... gtttgtacagAAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAA
EST: gi|7587871|gb|AW703678.1|AW703678
EST:     AATTCGCCGCTGCNNNNNNNGCAGCCACTCTCGCTGCTCGTCTCTGCAAG                         AAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAA
genomic: AATTCGCCGCTGCAAAAAAAGCAGCCACTCTCGCTGCTCGTCTCTGCAAGgcaccacccc ... gtttgtacagAAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAA
EST: gi|37996739|gb|CF808328.1|CF808328
EST:     AATTCGCCGCTGCNNNNNNNGCAGCCACTCTCGCTGCTCGTCTCTGCAAG                         AAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAA
genomic: AATTCGCCGCTGCAAAAAAAGCAGCCACTCTCGCTGCTCGTCTCTGCAAGgcaccacccc ... gtttgtacagAAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAA
EST: gi|298163506|gb|HO012239.1|HO012239
EST:     AATTCGCCGCTGCNNNNNNNGCAGCCACTCTCGCTGCTCGTCTCTGCAAG                         AAAGTACAGAAGGCTCTTCTGCAATCTGATGTGCACTCAAAGTCAGACAAA
genomic: AATTCGCCGCTGCAAAAAAAGCAGCCACTCTCGCTGCTCGTCTCTGCAAGgcaccacccc ... gtttgtacagAAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAA
EST: gi|16996758|gb|BM086130.1|BM086130
EST:     AATTCGCCGCTGCNNNNNNNGCAGCCACTCTCGCTGCTCGTCTCTGCAAG                         AAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAA
genomic: AATTCGCCGCTGCAAAAAAAGCAGCCACTCTCGCTGCTCGTCTCTGCAAGgcaccacccc ... gtttgtacagAAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAA
EST: gi|8285675|gb|BE023234.1|BE023234
EST:     AATTCGCCGCTGCNNNNNNNGCAGCCACTCTCGCTGCTCGTCTCTGCAAG                         AAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAA
genomic: AATTCGCCGCTGCAAAAAAAGCAGCCACTCTCGCTGCTCGTCTCTGCAAGgcaccacccc ... gtttgtacagAAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAA
EST: gi|6566797|gb|AW234429.1|AW234429
EST:     AATTCGCCGCTGCNNNNNNNGCAGCCACTCTCGCTGCTCGTCTCTGCAAG                         AAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAA
genomic: AATTCGCCGCTGCAAAAAAAGCAGCCACTCTCGCTGCTCGTCTCTGCAAGgcaccacccc ... gtttgtacagAAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagaggaaatgctggtataatactgattgattcttctttgtatggtttgtacagAAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATG
                tataatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctttttcaaaagtactgcgacgattaatgcctgaaaattaaacgaagaggaaatgctggtataatactgattgattcttctttgtatggtttgtacagAAAGTACAGAAGGCTCTTCTGCAATCCGATGTGCACTCAAAGTCAGACAAAAGTCCTGTCACAGTGGCTGATTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - ctgcgac
- - - - - - - - - - - - - -aatgcct
- - - - - - - - - - - - - - - - - - aaattaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctggt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgattg