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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttttcaataataactattctttgctattcataatagatcatgctacattctgattctcattaacaattatattttttttacctattcccatcagACTCTCAGGGCTCGTGTGGCTGCTAAGACAGAAGAAAAGAAATTGGAGCTGCTGTTTCTTCAGTGGAGTGAGCATCGTAAAAGACTAAGCAATTTTATAA

Basic information

species Glycine max
transcript GLYMA08G19640.3
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G19640.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G102475_T03 (Zea mays), 3'ss of exon 7
gtttgttttcaataataactattctttgctattcataatagatcatgctacattctgattctcattaacaattatattttttttacctattcccatcagACTCTCAGGGCTCGTGTGGCTGCTAAGACAGAAGAAAAGAAATTGGAGCTGCTGTTTCTTCAGTGGAGTGAGCATCGTAAAAGACTAAGCAATTTTATAA
       |    | |   ||  | ||      | | ||      ||   |  |  |   | |  ||  |||| |||   | |||     |     | |||| ||| | |||||||| ||||||||| ||||||||||||  ||||||||| |||   ||||||||| |||||||| |||||| ||   ||||||  |||
------gtaagttcacggcttgttttcatctgttacaactacatatttcaattgatatatttactttgcaatcatacaatctttgatgctcttttttagACGCTCCGCGCTCGTGTAGCTGCTAAGGCAGAAGAAAAGAGGTTGGAGCTGTTGTACATTCAGTGGACTGAGCATCATAAAAGGCTGTCCAATTTCTTAA

upper sequence: GLYMA08G19640.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G15200.3 (Arabidopsis thaliana), 3'ss of exon 7
gtttgttttcaataataactattctttgctattcataatagatcatgctacattctgattc--tcattaacaattatattttttttacctattcccatcagACTCTCAGGGCTCGTGTGGCTGCTAAGACAGAAGAAAAGAAATTGGAGCTGCTGTTTCTTCAGTGGAGTGAGCATCGTAAAAGACTAAGCAATTTTATAA
||  ||   ||    ||| | || ||  || | ||||  |   ||     || |||  |    | |  | |   |||| |   |||| ||  ||  ||||||||||  |||||||||| ||||||||  ||||| |||||||||||||  |||| || ||||| ||||||||||| |  || | ||| |||||||||||||
gtaagtggccagct-taagtttttttctctttgcataccattccaaatggcagtcttgtgtagtaaagatctgatatactcaatttaactggtca-atcagACTCTTCGGGCTCGTGTTGCTGCTAAAGCAGAACAAAAGAAATTGGAATTGCTTTTCCTTCAATGGAGTGAGCACCAAAAGAAACTTAGCAATTTTATAA

upper sequence: GLYMA08G19640.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv12s0055g00360.t01 (Vitis vinifera), 3'ss of exon 7
gtttgttttcaataataactattctttgctattc-ataataga---tcatgctacattctgattctc--------attaacaat-----tatatttttttta--------cctattcccatcagACTCTCAGGGCTCGTGTGGCTGCTAAGACAGAAGAAAAGAAATTGGAGCTGCTGTTTCTTCAGTGGAGTGAGCATCGTAAAAGACTAAGCAATTTTATAA
|||||| || | |  ||| |||  | ||| | || ||  |  |   | |   |  || |   || |         ||  |||||       ||  || |||         | | || | ||||||||||||| |||||||| ||||| ||| ||||||||||||| |||||  |||||||||||| |||||||||||| |  ||||| ||  |||||| | |||
gtttgtgtttact--taattatattgtgcaactctatggtgaagctttaaattgaatcccttttttgtgtgaaaaatagacaatggcttcgtaccttgtttcatcactgccttttttctatcagACTCTCAGAGCTCGTGTTGCTGCCAAGGCAGAAGAAAAGAAGTTGGAATTGCTGTTTCTTCGGTGGAGTGAGCACCAAAAAAGGCTTTGCAATTATCTAA

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|208113975|gb|GD909780.1|GD909780
EST:     TTAGGAAAGAAGAGCGTGAACAGATTGCTGAAAAACGAAGGAGAGACTTG                         ACTCTCAGGGCTCGTGTGGCTGCTAAGACAGAAGAAAAGAAAT
genomic: TTAGGAAAGAAGAGCGTGAACAGATTGCTGAAAAACGAAGGAGAGACTTGgtttgttttc ... ttcccatcagACTCTCAGGGCTCGTGTGGCTGCTAAGACAGAAGAAAAGAAAT
EST: gi|208065323|gb|GD863057.1|GD863057
EST:     TTAGGAAAGAAGAGCGTGAACAGATTGCTGAAAAACGAAGGAGAGACTTG                         ACTCTCAGGGCTCGTGTGGCTGCTAAGACAGAAGAAAAGAAATTGGAGCTG
genomic: TTAGGAAAGAAGAGCGTGAACAGATTGCTGAAAAACGAAGGAGAGACTTGgtttgttttc ... ttcccatcagACTCTCAGGGCTCGTGTGGCTGCTAAGACAGAAGAAAAGAAATTGGAGCTG
EST: gi|207807391|gb|GD777502.1|GD777502
EST:     TTAGGAAAGAAGAGCGTGAACAGATTGCTGAAAAACGAAGGAGAGACTTG                         ACTCTCAGGGCTCGTGTGGCTGCTAAGACAGAAGAAAAGAAATTGGAGCTG
genomic: TTAGGAAAGAAGAGCGTGAACAGATTGCTGAAAAACGAAGGAGAGACTTGgtttgttttc ... ttcccatcagACTCTCAGGGCTCGTGTGGCTGCTAAGACAGAAGAAAAGAAATTGGAGCTG
EST: gi|193359714|gb|FK324134.1|FK324134
EST:     TTAGGAAAGAAGAGCGTGAACAGATTGCTGAAAAACGAAGGAGAGACTTG                         ACTCTCAGGGCTCGTGTGGCTGCTAAGACAGAAGAAAAGAAATTGGAGACT
genomic: TTAGGAAAGAAGAGCGTGAACAGATTGCTGAAAAACGAAGGAGAGACTTGgtttgttttc ... ttcccatcagACTCTCAGGGCTCGTGTGGCTGCTAAGACAGAAGAAAAGAAATTGGAG-CT
EST: gi|207782944|gb|GD754529.1|GD754529
EST:     TTAGGAAAGAAGAGCGTGAACAGATTGCTGAAAAACGAAGGAGAGACTTG                         ACTCTCAGGGCTCGTGTGGCTGCTAAGACAGAAGAAAAGAAATTGGAGCTG
genomic: TTAGGAAAGAAGAGCGTGAACAGATTGCTGAAAAACGAAGGAGAGACTTGgtttgttttc ... ttcccatcagACTCTCAGGGCTCGTGTGGCTGCTAAGACAGAAGAAAAGAAATTGGAGCTG
EST: gi|208341176|gb|GE135008.1|GE135008
EST:     GGAGAGACTTG                         ACTCTCAGGGCTCGTGTGGCTNCTAAGACAGAAGAAAAGAAATTGGAGCTG
genomic: GGAGAGACTTGgtttgttttc ... ttcccatcagACTCTCAGGGCTCGTGTGGCTGCTAAGACAGAAGAAAAGAAATTGGAGCTG
EST: gi|193359311|gb|FK327532.1|FK327532
EST:     TTAGGAAAGAAGAGCGTGAACAGATTGCTGAAAAACGAAGGAGAGACTTG                         ACTCTCAGGGCTCGTGTGGCTGCTAAGACAGAAGAAAAGAAATTGGAGC
genomic: TTAGGAAAGAAGAGCGTGAACAGATTGCTGAAAAACGAAGGAGAGACTTGgtttgttttc ... ttcccatcagACTCTCAGGGCTCGTGTGGCTGCTAAGACAGAAGAAAAGAAATTGGAGC
EST: gi|193532237|gb|FK491945.1|FK491945
EST:     TTAGGAAAGAAGAGCGTGAACAGATTGCTGAAAAACGAAGGNGAGACTTG                         ACTCTCAGGGCTCGTGTGG
genomic: TTAGGAAAGAAGAGCGTGAACAGATTGCTGAAAAACGAAGGAGAGACTTGgtttgttttc ... ttcccatcagACTCTCAGGGCTCGTGTGG
EST: gi|208116357|gb|GD920380.1|GD920380
EST:     TTAGGAAAGAAGAGCGTGAACAGATTGCTGAAAAACGAAGGAGAGACTTG                         ACTCTCAGGGCTCGTGTGGCTGCTAAGACAGAAGAAAAGAAATTGGAGCTG
genomic: TTAGGAAAGAAGAGCGTGAACAGATTGCTGAAAAACGAAGGAGAGACTTGgtttgttttc ... ttcccatcagACTCTCAGGGCTCGTGTGGCTGCTAAGACAGAAGAAAAGAAATTGGAGCTG
EST: gi|207805992|gb|GD778287.1|GD778287
EST:     TTAGGAAAGAAGAGCGTGAACAGATTGCTGAAAAACGAAGGAGAGACTTG                         ACTCTCAGGGCTCGTGTGGCTGCTAAGACAGAAGAAAAGAAATTGGAGCTG
genomic: TTAGGAAAGAAGAGCGTGAACAGATTGCTGAAAAACGAAGGAGAGACTTGgtttgttttc ... ttcccatcagACTCTCAGGGCTCGTGTGGCTGCTAAGACAGAAGAAAAGAAATTGGAGCTG
EST: gi|193377032|gb|FK342669.1|FK342669
EST:     TTAGGAAAGAAGAGCGTGAACAGATTGCTGAAAAACGAAGGAGAGACTTG                         ACTCTCAGGGCTCGTGTGGCTGCTAAGACAGAAGAAAAGAAATTGGAGCTG
genomic: TTAGGAAAGAAGAGCGTGAACAGATTGCTGAAAAACGAAGGAGAGACTTGgtttgttttc ... ttcccatcagACTCTCAGGGCTCGTGTGGCTGCTAAGACAGAAGAAAAGAAATTGGAGCTG
EST: gi|208148242|gb|GD947254.1|GD947254
EST:     TTAGGAAAGAAGAGCGTGAACAGATTGCTGAAAAACGAAGGAGAGACTTG                         ACTCTCAGGGCTCGTGTGGCTGCTAAGACAGAAGAAAAGAAATTGGAGCTG
genomic: TTAGGAAAGAAGAGCGTGAACAGATTGCTGAAAAACGAAGGAGAGACTTGgtttgttttc ... ttcccatcagACTCTCAGGGCTCGTGTGGCTGCTAAGACAGAAGAAAAGAAATTGGAGCTG
EST: gi|208039782|gb|GD842486.1|GD842486
EST:     TTAGGAAAGAAGAGCGTGAACAGATTGCTGAAAAACGAAGGAGAGACTTG                         ACTCTCAGGGCTCGTGTGGCTGCTAAGAC
genomic: TTAGGAAAGAAGAGCGTGAACAGATTGCTGAAAAACGAAGGAGAGACTTGgtttgttttc ... ttcccatcagACTCTCAGGGCTCGTGTGGCTGCTAAGAC
EST: gi|193396761|gb|FK362333.1|FK362333
EST:     TTAGGAAAGAAGAGCGTGAACAGATTGCTGAAAAACGAAGGAGAGACTTG                         ACTCTCAGGGCTCGTGTGGCTGCTAAGACAGAAGAAAAGAAATTGGAGCTG
genomic: TTAGGAAAGAAGAGCGTGAACAGATTGCTGAAAAACGAAGGAGAGACTTGgtttgttttc ... ttcccatcagACTCTCAGGGCTCGTGTGGCTGCTAAGACAGAAGAAAAGAAATTGGAGCTG
EST: gi|193492048|gb|FK453464.1|FK453464
EST:     TTAGGAAAGAAGAGCGTGAACAGATTGCTGAAAAACGAAGGAGAGACTTG                         ACTCTCAGGGCTCGTGTGGCTGCTAAGACAGAAGAAAAGAAATTGGAGCTG
genomic: TTAGGAAAGAAGAGCGTGAACAGATTGCTGAAAAACGAAGGAGAGACTTGgtttgttttc ... ttcccatcagACTCTCAGGGCTCGTGTGGCTGCTAAGACAGAAGAAAAGAAATTGGAGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgctacattctgattctcattaacaattatattttttttacctattcccatcagACTCTCAGGGCTCGTGTGGCTGCTAAGACAGAAGAAAAGAAATTGGAGCTGCTGTTTCTTCAGTGGAGTGAGCATCGTAAAAGACTAAGCAATTTTATAA
                  cattaac  putative branch site (score: 2)
                                ttttttttacctattc  putative PPT
       attctgattctcatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttttcaataataactattctttgctattcataatagatcatgctacattctgattctcattaacaattatattttttttacctattcccatcagACTCTCAGGGCTCGTGTGGCTGCTAAGACAGAAGAAAAGAAATTGGAGCTGCTGTTTCTTCAGTGGAGTGAGCATCGTAAAAGACTAAGCAATTTTATAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA