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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtgcaggggacaaggcatcagaattggaaggcatggaagaagggatattttgttttggctttaagtagtgtttttgacacttttgatatacacacacagGTTTCTTTTTAAGTTCACTGGGCAAGATCAAGAAATTAATCTTTTGGGTGATGGTACTGAGAAAGCTGAGTTTGGGGAATGGTCATGGATATCACCTGAA

Basic information

species Glycine max
transcript GLYMA10G33990.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G33990.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G10620.1 (Arabidopsis thaliana), 3'ss of exon 4
agtgcaggggacaaggcatcagaattggaaggcatggaagaagggatattttgttttggctttaagtagtgtttttgacacttttgatatacacacacagGTTTCTTTTTAAGTTCACTGGGCAAGATCAAGAAATTAATCTTTTGGGTGATGGTACTGAGAAAGCTGAGTTTGGGGAATGGTCATGGATATCACCTGAA
                           |   |  |    ||    ||      |  || | ||   |   |   |||   |   | || |     | |||||||||| | || || |||||| ||||| ||||||| |||||| | || ||||||||||||||| |||||||||| |||||||| ||||  || ||||| 
---------------------------gtgagtctttctgagattatcaagaatcatgtcatttcattacgggcttg-ttcaaataatgtgtttcctcagGTTTCTTCTGAAATTTACTGGGAAAGATGAAGAAATCAATCTTCTTGGCGATGGTACTGAGAAACCTGAGTTTGGTGAATGGTCCTGGACTTCTCCTGAT

upper sequence: GLYMA10G33990.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0056g00030.t01 (Vitis vinifera), 3'ss of exon 4
agtgcaggggacaaggcatcagaattggaaggcatggaagaagggatattttgttttggctttaagtagtgtttttgacacttttgatat----acacacacagGTTTCTTTTTAAGTTCACTGGGCAAGATCAAGAAATTAATCTTTTGGGTGATGGTACTGAGAAAGCTGAGTTTGGGGAATGGTCATGGATATCACCTGAA
      ||     |   ||         |  |          | |    | || | || |  | | |  |||   | | | |||    ||    ||  |  |||||||||| |||| ||||||||  | ||  | ||||| ||||| ||||||||||  ||||  |||||||||||||| || ||||||||||| ||||| || 
---tttggttctcacttatggtcgaccaacagtgctttgtgtgcgtctctctgatctg-cactcattcatgtcactaaaattttcttaatgggaacttatgcagGTTTCTTCTTAAATTCACTGGAAAGGAAGAGGAAATCAATCTCTTGGGTGATGAGACTGCAAAAGCTGAGTTTGGCGAGTGGTCATGGATGTCACCGGAT
















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|151401156|gb|EV270970.1|EV270970
EST:     AAATTAAATATTCAGTGGGGATCTGATTGGAAGGGTCAGGCGCAGAAATG                         GTTTCTTTTTAAGTTCACTAGGCAAGATCAAGAAATTAATCTTTTGGGTGA
genomic: AAATTAAATATTCAGTGGGGATCTGATTGGAAGGGTCAGGCGCAGAAATGgtaaccactt ... acacacacagGTTTCTTTTTAAGTTCACTGGGCAAGATCAAGAAATTAATCTTTTGGGTGA
EST: gi|31466943|gb|CD408971.1|CD408971
EST:     AAATTAAATATTCAGTGGGGATCTGATTGGAAGGGTCAGGCGCAGAAATG                         GTTTCTTTTTAAGTTCACTGGGCAAGATCCAGAAATTAATCTTTTGGGTGA
genomic: AAATTAAATATTCAGTGGGGATCTGATTGGAAGGGTCAGGCGCAGAAATGgtaaccactt ... acacacacagGTTTCTTTTTAAGTTCACTGGGCAAGATCAAGAAATTAATCTTTTGGGTGA
EST: gi|192294285|gb|FG986374.1|FG986374
EST:     AAATTAAATATTCAGTGGGGATCTGATTGGAAGGGTCAGGCGCAGAAATG                         GTTTCTTTTTAAGTTCACTGGGCAAGATCAAGAAATTAATCTTTTGGGTGA
genomic: AAATTAAATATTCAGTGGGGATCTGATTGGAAGGGTCAGGCGCAGAAATGgtaaccactt ... acacacacagGTTTCTTTTTAAGTTCACTGGGCAAGATCAAGAAATTAATCTTTTGGGTGA
EST: gi|193548842|gb|FK508341.1|FK508341
EST:     AAATTAAATATTCAGTGGGGATCTGATTGGAAGGGTCAGGCGCCGAAATG                         GTTTCTTTTTAAGTTCACTGGGCAAGATCAAGAAATTAATCTTTTGGGTGA
genomic: AAATTAAATATTCAGTGGGGATCTGATTGGAAGGGTCAGGCGCAGAAATGgtaaccactt ... acacacacagGTTTCTTTTTAAGTTCACTGGGCAAGATCAAGAAATTAATCTTTTGGGTGA
EST: gi|8282558|gb|BE020119.1|BE020119
EST:     AAATTAAATATTCAGTGGGGATCTGATTGGAAGGGTCAGGCGCAGACATG                         GTTTCTTTTTAAGTTCACTGGGCAAGATCAAGACATTAATCTTTTGGGTGA
genomic: AAATTAAATATTCAGTGGGGATCTGATTGGAAGGGTCAGGCGCAGAAATGgtaaccactt ... acacacacagGTTTCTTTTTAAGTTCACTGGGCAAGATCAAGAAATTAATCTTTTGGGTGA
EST: gi|7926045|gb|AW832071.1|AW832071
EST:     AAATTAAATATTCAGTGGGGATCTGATTGGAAAGGTCAGGCACANAAATG                         GTTTCTTTTTAAGTTCACTGGGCAAGATCAAAAAATTAATCTTTTGAGTGA
genomic: AAATTAAATATTCAGTGGGGATCTGATTGGAAGGGTCAGGCGCAGAAATGgtaaccactt ... acacacacagGTTTCTTTTTAAGTTCACTGGGCAAGATCAAGAAATTAATCTTTTGGGTGA
EST: gi|193545073|gb|FK503104.1|FK503104
EST:     AAATTAAATATTCAGTGGGGATCTGATTGGAAGGGTCAGGCGCCGAAATG                         GTTTCTTTTTAAGTTCACTGGGCAAGATCAAGAAATTAATCTTTTGGGTGA
genomic: AAATTAAATATTCAGTGGGGATCTGATTGGAAGGGTCAGGCGCAGAAATGgtaaccactt ... acacacacagGTTTCTTTTTAAGTTCACTGGGCAAGATCAAGAAATTAATCTTTTGGGTGA
EST: gi|31466222|gb|CD408250.1|CD408250
EST:     AAATTAAATATTCAGTGGGGATCTGATTGGAAGGGTCAGGCGCAGAAATG                         GTTTCTTTTTAAGTTCACTGGGCAAGATCAAGAAATTAATCTTTTGGGTGA
genomic: AAATTAAATATTCAGTGGGGATCTGATTGGAAGGGTCAGGCGCAGAAATGgtaaccactt ... acacacacagGTTTCTTTTTAAGTTCACTGGGCAAGATCAAGAAATTAATCTTTTGGGTGA
EST: gi|193563822|gb|FK517945.1|FK517945
EST:     AAATTAAATATTCAGTGGGGATCTGATTGGAAGGGTCAGGCGCCGAAATG                         GTTTCTTTTTAAGTTCACTGGGCAAGATCAAGAAATTAATCTTTTGGGTGA
genomic: AAATTAAATATTCAGTGGGGATCTGATTGGAAGGGTCAGGCGCAGAAATGgtaaccactt ... acacacacagGTTTCTTTTTAAGTTCACTGGGCAAGATCAAGAAATTAATCTTTTGGGTGA
EST: gi|24135720|gb|BU926230.1|BU926230
EST:     AAATTAAATATTCAGTGGGGATCTGATTGGAAGGGTCAGGCGCAGAAATG                         GGTTCTTTTTAAGTTCACTGGGCAAGATCAAGAAATTAATCTTTTGGGTGA
genomic: AAATTAAATATTCAGTGGGGATCTGATTGGAAGGGTCAGGCGCAGAAATGgtaaccactt ... acacacacagGTTTCTTTTTAAGTTCACTGGGCAAGATCAAGAAATTAATCTTTTGGGTGA
EST: gi|151411273|gb|EV281084.1|EV281084
EST:     AAATTAAATATTCAGTGGGGATCTGATTGGAAGGGTCAGGCGCAGAAATG                         GTTTCTTTTTAAGTTCACTGGGCAAGATCAAGAAATTAATCTTTTGGGTGA
genomic: AAATTAAATATTCAGTGGGGATCTGATTGGAAGGGTCAGGCGCAGAAATGgtaaccactt ... acacacacagGTTTCTTTTTAAGTTCACTGGGCAAGATCAAGAAATTAATCTTTTGGGTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattttgttttggctttaagtagtgtttttgacacttttgatatacacacacagGTTTCTTTTTAAGTTCACTGGGCAAGATCAAGAAATTAATCTTTTGGGTGATGGTACTGAGAAAGCTGAGTTTGGGGAATGGTCATGGATATCACCTGAA
                                    ttttgatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtgcaggggacaaggcatcagaattggaaggcatggaagaagggatattttgttttggctttaagtagtgtttttgacacttttgatatacacacacagGTTTCTTTTTAAGTTCACTGGGCAAGATCAAGAAATTAATCTTTTGGGTGATGGTACTGAGAAAGCTGAGTTTGGGGAATGGTCATGGATATCACCTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- -gcagggg
- - - - - -caaggca
- - - - - - - - - - - - - - - -gcatgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgacact