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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagttcaagttcatggcactgcagctcttcttgaaaggagggaaaagaaagtggtttagttgttgttggctgtatttttgtgttaatgcgacttcaattttttaatgcttatattggtttcagGGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTGGTA

Basic information

species Glycine max
transcript GLYMA03G40860.4
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G40860.4 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os10g28320.3 (Oryza sativa), 3'ss of exon 4
gttagttcaagttcatggcactgcagctcttcttgaaaggagggaaaagaaagtggtttagttgttgttggctgtatttttgtgttaatgcgactt--caattttttaatgcttatattggtttcagGGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTGGTA
                        ||||| | || ||    | | |       |  |||| |  |||||   || |  |     |   | |  | |  || |  ||  | || |   |||  |||||||| ||||| ||||||||||| |||||||| ||  |||| |||||||| ||||  ||||  |  | |||  | |   | ||  |  | || |  ||||||
--------------------tgttagctcctattcaagtttgtgca-------tcatttactccttgttcattgaacctccacatcgcttcaccgtgccactcattcgaagcattacttgtgttcagGGAGCTTGGCATTGGAATTGTTCCATATAGCCCAATTGGCCGTGGCTTCTTTGCTGGCAGGGCTGCTGTACAGAGCATACCATCTGAGAGTTGGCTGGTA

upper sequence: GLYMA03G40860.4 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os10g28320.1 (Oryza sativa), 3'ss of exon 4
gttagttcaagttcatggcactgcagctcttcttgaaaggagggaaaagaaagtggtttagttgttgttggctgtatttttgtgttaatgcgactt--caattttttaatgcttatattggtttcagGGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTGGTA
                        ||||| | || ||    | | |       |  |||| |  |||||   || |  |     |   | |  | |  || |  ||  | || |   |||  |||||||| ||||| ||||||||||| |||||||| ||  |||| |||||||| ||||  ||||  |  | |||  | |   | ||  |  | || |  |||   
--------------------tgttagctcctattcaagtttgtgca-------tcatttactccttgttcattgaacctccacatcgcttcaccgtgccactcattcgaagcattacttgtgttcagGGAGCTTGGCATTGGAATTGTTCCATATAGCCCAATTGGCCGTGGCTTCTTTGCTGGCAGGGCTGCTGTACAGAGCATACCATCTGAGAGTTGGCTG---

upper sequence: GLYMA03G40860.4 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G024315_T01 (Zea mays), 3'ss of exon 4
gttagttcaagttcatggcactgcagctcttcttgaaaggagggaaaagaaagtggtttagttgttgttggctgtatttttgtgttaatgcgacttcaattttttaatgcttatattggtttcagGGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTGGTA
    |  |||| || |   ||   |  | || ||  ||  | | ||   ||    |  ||   | | ||        |  ||| ||||          ||| |||| ||||    | |  ||||| ||| | || ||||||||||||||||| ||||||||||| ||||| |||||||| || | ||||||    ||| | ||| || |  |       |||   
----gaacaaggtcttaatac-atatgtattgttacaaatacgtaaccaaacaaagcctaccggatatta-------tcatgtattaa---------gattcttta-tgct---gtggacttcagAGAATTGGGCATTGGAATTGTACCATACAGTCCTCTTGGCCGTGGGTTTTTTGGTGGAAGAGGAGTGAAAGAACAAGTGTCTGCTGAATCTAATCTG---

upper sequence: GLYMA03G40860.4 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM5G813143_T02 (Zea mays), 3'ss of exon 4
gttagttcaagttcatggcactgcagctcttcttgaaaggagggaaaagaaagtggtttagttgttgttggctgtatttttgtgttaatgcgacttcaattttttaatgcttatattggtttcagGGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTGGTA
                     ||||  |  |  | ||   | |    |     |   |||  | | ||| | || |  |   | | | |||   |     ||| | ||   |   |||  |||||||| |||||||||||||| || |||||||| || ||||| |||||||| ||||  ||||  | || ||| |||  ||| ||  || | ||     ||   
--------------------ttgcaagttctaattaacttatgcttcatt---tttcttatctttggttcgttgaacatcgatatca-tgcatttatctgtttgtcataaatgc-ttgcattcagGGAGCTTGGTATTGGAATAGTTCCATATAGCCCACTTGGCCGTGGCTTCTTTGCTGGCAGGGCAGCTGTAGAACGTGTTCCATCAGAAAGTCTATTG---

upper sequence: GLYMA03G40860.4 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0030g01960.t01 (Vitis vinifera), 3'ss of exon 4
gttagttcaagttcatggcactgcagctcttcttgaaaggagggaaaagaaagtggtttagttgttgttggctgtatttttgtgttaatgcgacttcaattttttaatgcttatattggtttcagGGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTGGTA
        | | | ||     ||   |  |||||| | ||          || |   |   |   | ||   | ||  | ||   |  ||    |||| || |||||     ||||      |||||| ||||| |||||||| || |||||  |||||||||||||||| |||||||| || |  ||||||||||||| | ||||| || |             
-------aaggattatatgcttgatacctttcttgtatggcta------caactctctctctctctcttaattataaatatgacatgctgt--tttcatttatttaa-----atatg-----cagGGAGCTTGGCATTGGAATAGTTCCATACTGTCCTCTTGGTCGTGGATTTTTTGGTGGTAGGGGAGTTGTGGAAAGTTTGCCTGCATACTTG---------

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|254328403|gb|GR835368.1|GR835368
EST:     TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAG                         G-AACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
genomic: TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAGgttagttcaa ... ttggtttcagGGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
EST: gi|213617996|gb|DB963629.1|DB963629
EST:     TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAG                         GGAACTTGGTAT
genomic: TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAGgttagttcaa ... ttggtttcagGGAACTTGGTAT
EST: gi|48575437|gb|CO036403.1|CO036403
EST:     TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAG                         GGAACTTGGTATTGGAATTGTAC
genomic: TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAGgttagttcaa ... ttggtttcagGGAACTTGGTATTGGAATTGTAC
EST: gi|209703783|gb|BW656888.1|BW656888
EST:     TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAG                         GGAACTTGGTATTGGAATTGTACCATATAGTC
genomic: TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAGgttagttcaa ... ttggtttcagGGAACTTGGTATTGGAATTGTACCATATAGTC
EST: gi|11688271|gb|BF595947.1|BF595947
EST:     TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAG                         GGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
genomic: TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAGgttagttcaa ... ttggtttcagGGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
EST: gi|254337008|gb|GR843187.1|GR843187
EST:     TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAG                         GGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
genomic: TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAGgttagttcaa ... ttggtttcagGGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
EST: gi|213592927|gb|DB966032.1|DB966032
EST:     TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAG                         GGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTT
genomic: TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAGgttagttcaa ... ttggtttcagGGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTT
EST: gi|61241644|gb|DN591035.1|DN591035
EST:     TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAG                         GGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGGNNNNN
genomic: TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAGgttagttcaa ... ttggtttcagGGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
EST: gi|151398527|gb|EV268398.1|EV268398
EST:     TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAG                         GGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
genomic: TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAGgttagttcaa ... ttggtttcagGGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
EST: gi|151394300|gb|EV264171.1|EV264171
EST:     TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAG                         GGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTCTTT
genomic: TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAGgttagttcaa ... ttggtttcagGGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
EST: gi|12496330|gb|BG047010.1|BG047010
EST:     TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAG                         GGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
genomic: TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAGgttagttcaa ... ttggtttcagGGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
EST: gi|298186682|gb|HO037315.1|HO037315
EST:     TGGTCTTTGTGGACTCGTAACATTGAAGAAGAGATAGTCCCTCTCTGCAG                         GGGACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
genomic: TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAGgttagttcaa ... ttggtttcagGGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
EST: gi|192305622|gb|FG994332.1|FG994332
EST:     TGGTCTTTGTGGACTCGTGACATCGAAGAAGAGATAGTCCCTCTCTGCAG                         GGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
genomic: TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAGgttagttcaa ... ttggtttcagGGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
EST: gi|254327803|gb|GR834768.1|GR834768
EST:     TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAG                         GGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
genomic: TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAGgttagttcaa ... ttggtttcagGGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
EST: gi|14011842|gb|BG726764.1|BG726764
EST:     TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAG                         GGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
genomic: TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAGgttagttcaa ... ttggtttcagGGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
EST: gi|254320499|gb|GR826948.1|GR826948
EST:     TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAG                         G-AACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
genomic: TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAGgttagttcaa ... ttggtttcagGGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
EST: gi|16995650|gb|BM085022.1|BM085022
EST:     TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAG                         GGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
genomic: TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAGgttagttcaa ... ttggtttcagGGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
EST: gi|254323788|gb|GR836127.1|GR836127
EST:     TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAG                         GGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
genomic: TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAGgttagttcaa ... ttggtttcagGGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
EST: gi|209699381|gb|BW664100.1|BW664100
EST:     TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAG                         GGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTC
genomic: TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAGgttagttcaa ... ttggtttcagGGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTC
EST: gi|192294676|gb|FG986525.1|FG986525
EST:     TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAG                         GGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
genomic: TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAGgttagttcaa ... ttggtttcagGGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
EST: gi|254347025|gb|GR856695.1|GR856695
EST:     TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAG                         GGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
genomic: TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAGgttagttcaa ... ttggtttcagGGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
EST: gi|192309505|gb|FK002869.1|FK002869
EST:     TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCC-TCTCTGCAG                         GGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
genomic: TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAGgttagttcaa ... ttggtttcagGGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
EST: gi|209712723|gb|BW681577.1|BW681577
EST:     TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAG                         GGAACTTGGTATT
genomic: TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAGgttagttcaa ... ttggtttcagGGAACTTGGTATT
EST: gi|120533769|gb|EH261902.1|EH261902
EST:     TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAG                         GGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
genomic: TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAGgttagttcaa ... ttggtttcagGGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
EST: gi|7590075|gb|AW705836.1|AW705836
EST:     TGGTCTGTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAC                         GGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGTTCGTGGCTTTTC
genomic: TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAGgttagttcaa ... ttggtttcagGGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
EST: gi|18040697|gb|BM308991.1|BM308991
EST:     TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAG                         GGAACTTGGTATTGGAATTGTACCATATANGTCCCCTTGGTCGTGGCTTTT
genomic: TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAGgttagttcaa ... ttggtttcagGGAACTTGGTATTGGAATTGTACCATATA-GTCCTCTTGGTCGTGGCTTTT
EST: gi|192306323|gb|FG995103.1|FG995103
EST:     TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAG                         GGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT
genomic: TGGTCTTTGTGGACTCGTGACATTGAAGAAGAGATAGTCCCTCTCTGCAGgttagttcaa ... ttggtttcagGGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgtatttttgtgttaatgcgacttcaattttttaatgcttatattggtttcagGGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTGGTA
                               ttttaat  putative branch site (score: 3)
                        ttcaattttttaatgc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagttcaagttcatggcactgcagctcttcttgaaaggagggaaaagaaagtggtttagttgttgttggctgtatttttgtgttaatgcgacttcaattttttaatgcttatattggtttcagGGAACTTGGTATTGGAATTGTACCATATAGTCCTCTTGGTCGTGGCTTTTTTGGCGGCAAAGGAGTTGTGGAAAATGTGCCTACAAATAGCTCCCTGGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG