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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taattggtaatagcggaatgctaactgaaatgcatgggattgattgattctgttaatattctctccacgtttatggtgataattatggtgctttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAAGCTGGAGCATCTACAGTATCT

Basic information

species Glycine max
transcript GLYMA02G44250.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G44250.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G121820_T01 (Zea mays), 3'ss of exon 1
-taattggtaatagcggaatgctaa--ctgaaatgcatgggattgattgattctgttaatattctctccacgtttatggtgataattatggtgctttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAAGCTGGAGCATCTACAGTATCT
    | |  ||       |||  ||   || | ||  ||   || |    ||    || || | | |    | || |  ||||    ||    |||   |||| ||||||||||| |  ||| ||||||| ||| |||| ||||| |||||||| ||||||||||| ||||||||
tctgtagaaaacctttagatgacaagcttgtattgtgtgcctttcaaattttagagtagtactgtttttctgattgt--tgattgg-atacctcttctaacagAGATCTTGGTAATTTGAACTTATCTGGTCATCTGGTGCCTGAGCTTGGGAAACTGGAGCATCTTCAGTATCT

upper sequence: GLYMA02G44250.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM5G815009_T01 (Zea mays), 3'ss of exon 1
--taattggtaatagcggaatgctaa--ctgaaatgcatgggattgattgattctgttaatattctctccacgtttatggtgataattatggtgctttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAAGCTGGAGCATCTACAGTATCT
     | |  ||     | ||   ||   || | || |||   |  |    ||    || || | | | |   ||  || |  |   |||  |  ||   |||| ||||||||||| |  ||| ||||||| ||| |||| ||||| ||||||||  |||||||||| ||||| ||
gtctgtagaaaacctttggatttcaaacttgtattgtatgtcttccaaattttagagtagtactgttttctgattgttgct--tggatatctt--ttataacagAGATCTTGGTAATTTGAACTTATCTGGTCATCTGGTGCCTGAGCTTGGGAAATTGGAGCATCTGCAGTACCT

upper sequence: GLYMA02G44250.2 (Glycine max), 3'ss of exon 1
lower sequence: AT3G43740.1 (Arabidopsis thaliana), 3'ss of exon 1
-taattggtaatagcggaatgctaactgaaatgcatgggattgattgattctgttaatattctctccacgtttatggtgataattatggtgctttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAAGCTGGAGCATCTACAGTATCT
 |  |||  ||       || || |    | |  |    | |   || || || |  |||  |   |   ||  |         | |  |  | |   ||||||| | || || || ||| ||||||||||| | |||||||||||||||||||| || ||| |||| |||||
attgttgagaaacttcatatacttatctgattcaacattagtctctg-ttttgctcttatatttggcttcttagtttcctagtatgttttcttcttggcagGGATTTGGGGAATTCAAACTTATCTGGACATCTAGTACCTGAACTTGGGAAGCTTGAACATTTACAATATCT

upper sequence: GLYMA02G44250.2 (Glycine max), 3'ss of exon 1
lower sequence: AT3G43740.2 (Arabidopsis thaliana), 3'ss of exon 1
-taattggtaatagcggaatgctaactgaaatgcatgggattgattgattctgttaatattctctccacgtttatggtgataattatggtgctttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAAGCTGGAGCATCTACAGTATCT----------------------------
 |  |||  ||       || || |    | |  |    | |   || || || |  |||  |   |   ||  |         | |  |  | |   ||||||| | || || || ||| ||||||||||| | |||||||||||||||||||| || ||| |||| |||||                            
attgttgagaaacttcatatacttatctgattcaacattagtctctg-ttttgctcttatatttggcttcttagtttcctagtatgttttcttcttggcagGGATTTGGGGAATTCAAACTTATCTGGACATCTAGTACCTGAACTTGGGAAGCTTGAACATTTACAATATCTGTATGGAATCATCACTCTTTTGCCTTTT

upper sequence: GLYMA02G44250.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0009g01210.t01 (Vitis vinifera), 3'ss of exon 1
-taattggtaatagcggaatgctaactgaaatgcatgg--gattgattgattctgt-taatattctctccacgtttatggtgataattatggtgctttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAAGCTGGAGCATCTACAGTATCT
  || | ||  |     | || | || || |||  |    | || |||  | |  | | ||||| |    |   | ||   ||| ||||   |  | | | ||||||  | ||||| || ||||| ||||| ||| ||||||||||||||||||||||  || |||| ||||||||
taaaattgttgtgattca-tgatgacggagatgtgtttttggtttattagtacattgttatattgtaattatcatcatta-gatcattacatt--tctttgcagGGACTTGGGTAATTCAAACCTCTCTGGTCATCTGGTACCTGAACTTGGGAAGCTCAAGTATCTGCAGTATCT

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|4396362|gb|AI495359.1|AI495359
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGTgtatgcatcc ... ctttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|298181464|gb|HO022903.1|HO022903
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGTgtatgcatcc ... ctttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|298172702|gb|HO019742.1|HO019742
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGTgtatgcatcc ... ctttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|6668064|gb|AW279515.1|AW279515
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGNGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGTgtatgcatcc ... ctttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|209710099|gb|BW653554.1|BW653554
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGTgtatgcatcc ... ctttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|9564436|gb|BE473945.1|BE473945
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGTgtatgcatcc ... ctttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|105633553|gb|DW246916.1|DW246916
EST:     ACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGT
genomic: ACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGTgtatgcatcc ... ctttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGT
EST: gi|120530833|gb|EH258966.1|EH258966
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGTgtatgcatcc ... ctttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|10708996|gb|BF008781.1|BF008781
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGTgtatgcatcc ... ctttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|27426228|gb|CA937748.1|CA937748
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGTgtatgcatcc ... ctttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|7925081|gb|AW831107.1|AW831107
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGTgtatgcatcc ... ctttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|26059546|gb|CA802460.1|CA802460
EST:     TGTACTTGGTTCCTTTTCACCTGCAACCAGGACAACCGAGTCACTCGAGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGTgtatgcatcc ... ctttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|120530964|gb|EH259097.1|EH259097
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGTgtatgcatcc ... ctttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|58020483|gb|CX707225.1|CX707225
EST:     TGTACTTGGTTCCACGTCACNTGCAACCAGGACAACCGAGTCACTCGAGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGTgtatgcatcc ... ctttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|298168193|gb|HO013456.1|HO013456
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGTgtatgcatcc ... ctttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|23726214|gb|BU761091.1|BU761091
EST:     GACAACCGAGTTACTCGAGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: GACAACCGAGTCACTCGAGTgtatgcatcc ... ctttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|21889419|gb|BQ742632.1|BQ742632
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGTgtatgcatcc ... ctttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|151394690|gb|EV264561.1|EV264561
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGTgtatgcatcc ... ctttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|16349170|gb|BI974765.1|BI974765
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGNGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGTgtatgcatcc ... ctttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
EST: gi|120530517|gb|EH258650.1|EH258650
EST:     TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGT                         GGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA
genomic: TGTACTTGGTTCCACGTCACCTGCAACCAGGACAACCGAGTCACTCGAGTgtatgcatcc ... ctttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattctgttaatattctctccacgtttatggtgataattatggtgctttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAAGCTGGAGCATCTACAGTATCT
     tgttaat  putative branch site (score: 3)
                                           tgctttct  putative PPT
     tgttaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taattggtaatagcggaatgctaactgaaatgcatgggattgattgattctgttaatattctctccacgtttatggtgataattatggtgctttctacagGGATCTTGGTAACTCTAACCTATCTGGACATTTGGTACCTGAACTTGGGAAGCTGGAGCATCTACAGTATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA