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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCCTGCTAGACTTCCTGGGTTCCATGTCTGTGTTGGAAGTGGAGGAGAAAGGTTGCTTCCTGAGTGGTACACAGAGAAAGgtgactttggctttcacccacattgttttagttcagcattattactggatattgttaggatcaatagttgattatattattatatcaagtgaaaggaaaagtaaatggaaaactggatcttaacaacaattttctaatacgaagttactgatgattgcag

Basic information

species Glycine max
transcript GLYMA10G07820.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G07820.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv08s0007g03610.t01 (Vitis vinifera), 5'ss of exon 4
CCCCTGCTAGACTTCCTGGGTTCCATGTCTGTGTTGGAAGTGGAGGAGAAAGGTTGCTTCCTGAGTGGTACACAGAGAAAGgtgactttggctttcac---ccacattgttttagttcagcattattactggatattgttaggatcaat-agttgattatattattatatcaa---gtgaaaggaaaagtaaatggaaaactggat---cttaacaacaattttctaatacgaagttactgatg-attgcag
   |||| ||||||||||| || ||||| ||||||||||| |||||||| ||  | |||||||||||||| | |||||||||| |   |   || ||       |    || || ||      |||   |||||  | | | |   ||| | |   || || || ||||| ||   ||      |||| | |    |  || | ||   ||||| | ||  |||  | ||   |  ||    || |||||||
GAGCTGCAAGACTTCCTGGATTTCATGTTTGTGTTGGAAGCGGAGGAGAGAGACTTCTTCCTGAGTGGTATAAAGAGAAAGgtaatacttttttgcatattttgctgaattctatttattagatatatttggattgtttgaagcaaaatcaatctcttttagtaatatatgaatgtgtttgcacaaaaatcaccaaattacagaattgccttaatagcacgttttcactaaccacctatctttggattgcag
















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|209718426|gb|BW666238.1|BW666238
EST:     TGTTGGAAGTGGAGGAGAAAGGTAGCTTCCTGAGTGGTACACAGAGAAAG                         GGATAGAGTTAATTCTTAGCACAGAAATAGTAAAGGTAGACCTTGCTGCAA
genomic: TGTTGGAAGTGGAGGAGAAAGGTTGCTTCCTGAGTGGTACACAGAGAAAGgtgactttgg ... atgattgcagGGATAGAGTTAATTCTTAGCACAGAAATAGTAAAGGTAGACCTTGCTGCAA
EST: gi|192330173|gb|FK019798.1|FK019798
EST:     TGTTGGAAGTGGAGGAGAAAGGTTGTTTCCTGAGTGGTACACAGAGAAAG                         GGATGGAGTTAATTCTTAGCACAGAAATAGTAAAGGTAGACCTTGCTGCAA
genomic: TGTTGGAAGTGGAGGAGAAAGGTTGCTTCCTGAGTGGTACACAGAGAAAGgtgactttgg ... atgattgcagGGATAGAGTTAATTCTTAGCACAGAAATAGTAAAGGTAGACCTTGCTGCAA
EST: gi|209707196|gb|BW656814.1|BW656814
EST:     TGTTGGAAGTGGAGGAGAAAGGTTGCTTCCTGAGTGGTACACAGAGAAAG                         GGATAGAGTTAATTCTTAGCACATAAATAGTAAAGGTAGACCTTGCTGCAA
genomic: TGTTGGAAGTGGAGGAGAAAGGTTGCTTCCTGAGTGGTACACAGAGAAAGgtgactttgg ... atgattgcagGGATAGAGTTAATTCTTAGCACAGAAATAGTAAAGGTAGACCTTGCTGCAA
EST: gi|213595751|gb|DB955927.1|DB955927
EST:     TGTTGGAAGTGGAGGAGAAAGGTTGCTTCCTGAGTGGTACACAGAGAAAG                         GGATAGAGTTAATTCTTAGCACAGAAATAGTAAAGGTAGACCTTGCTGCAA
genomic: TGTTGGAAGTGGAGGAGAAAGGTTGCTTCCTGAGTGGTACACAGAGAAAGgtgactttgg ... atgattgcagGGATAGAGTTAATTCTTAGCACAGAAATAGTAAAGGTAGACCTTGCTGCAA
EST: gi|151411030|gb|EV280841.1|EV280841
EST:     TGTTGGAAGTGGAGGAGAAAGGTTGTTTCCTGAGTGGTACACAGAGAAAG                         GGATGGAGTTAATTCTTAGCACAGAAATAGTAAAGGTAGACCTTGCTGCAA
genomic: TGTTGGAAGTGGAGGAGAAAGGTTGCTTCCTGAGTGGTACACAGAGAAAGgtgactttgg ... atgattgcagGGATAGAGTTAATTCTTAGCACAGAAATAGTAAAGGTAGACCTTGCTGCAA
EST: gi|209697959|gb|BW673018.1|BW673018
EST:     TGTTGGAAGTGGAGGAGAAAGGTTGCTTCCTGAGTGGTACACAGAGAAAG                         GGATAGAGTTAATTCTTAGCACAGAAATAGTAAAGGTAGACCTTGCTGCAA
genomic: TGTTGGAAGTGGAGGAGAAAGGTTGCTTCCTGAGTGGTACACAGAGAAAGgtgactttgg ... atgattgcagGGATAGAGTTAATTCTTAGCACAGAAATAGTAAAGGTAGACCTTGCTGCAA
EST: gi|213615151|gb|DB963363.1|DB963363
EST:     TGTTGGAAGTGGAGGAGAAAGGTTGCTTCCTGAGTGGTACACAGAGAAAG                         GGATAGAGTTAATTCTTAGCACAGAAATAGTAAAGGTAGACCTTGCTGCAA
genomic: TGTTGGAAGTGGAGGAGAAAGGTTGCTTCCTGAGTGGTACACAGAGAAAGgtgactttgg ... atgattgcagGGATAGAGTTAATTCTTAGCACAGAAATAGTAAAGGTAGACCTTGCTGCAA
EST: gi|192327629|gb|FK021306.1|FK021306
EST:     TGTTGGAAGTGGAGGAGAAAGGTTGCTTCCTGAGTGGTACACAGAGAAAG                         GGATAGAGTTAATTCTTAGCACAGAAATAGTAAAGGTAGACCTTGTTGCAA
genomic: TGTTGGAAGTGGAGGAGAAAGGTTGCTTCCTGAGTGGTACACAGAGAAAGgtgactttgg ... atgattgcagGGATAGAGTTAATTCTTAGCACAGAAATAGTAAAGGTAGACCTTGCTGCAA
EST: gi|192328367|gb|FK020078.1|FK020078
EST:     TGTTGGAAGTGGAGGAGAAAGGTTGTTTCCTGAGTGGTACACAGAGAAAG                         GGATGGAGTTAATTCTTAGCACAGAAATAGTAAAGGTAGACCTTGCTGCAA
genomic: TGTTGGAAGTGGAGGAGAAAGGTTGCTTCCTGAGTGGTACACAGAGAAAGgtgactttgg ... atgattgcagGGATAGAGTTAATTCTTAGCACAGAAATAGTAAAGGTAGACCTTGCTGCAA
EST: gi|209697684|gb|BW655585.1|BW655585
EST:     TGTTGGAAGTGGAGGAGAAAGGTTGCTTCCTGAGTGGTACACAGAGAAAG                         GGATAGAGTTAATTCTTAGCACAGAAATAGTAAAGGTAGACCTTGCTGCAA
genomic: TGTTGGAAGTGGAGGAGAAAGGTTGCTTCCTGAGTGGTACACAGAGAAAGgtgactttgg ... atgattgcagGGATAGAGTTAATTCTTAGCACAGAAATAGTAAAGGTAGACCTTGCTGCAA
EST: gi|254340648|gb|GR854376.1|GR854376
EST:     TGTTGGAAGTGGAGGAGAAAGGTTGCTTCCTGAGTGGTACACAGAGAAAG                         GGATAGAGTTAATTCTTAGCACAGAAATAGTAAAGGTAGACCTTGCTGCAA
genomic: TGTTGGAAGTGGAGGAGAAAGGTTGCTTCCTGAGTGGTACACAGAGAAAGgtgactttgg ... atgattgcagGGATAGAGTTAATTCTTAGCACAGAAATAGTAAAGGTAGACCTTGCTGCAA
EST: gi|209701293|gb|BW653036.1|BW653036
EST:     TGTTGGAAGTGGAGGAGAAAGGTTGCTTCCTGAGTGGTACACAGAGAAAG                         GGATAGAGTTAATTCTTAGCACAGAAATAGTAAAGGTAGACCTTGCTGCAA
genomic: TGTTGGAAGTGGAGGAGAAAGGTTGCTTCCTGAGTGGTACACAGAGAAAGgtgactttgg ... atgattgcagGGATAGAGTTAATTCTTAGCACAGAAATAGTAAAGGTAGACCTTGCTGCAA
EST: gi|192300239|gb|FG989361.1|FG989361
EST:     TGTTGGAAGTGGTGGAGAAAGGTTGCTTCCTGAGTGGTACACAGAGAAGG                         GGATAGAGTTAATTCTTAGCACAGAAATAGTAAAGGTAGACCTTGCTGCAA
genomic: TGTTGGAAGTGGAGGAGAAAGGTTGCTTCCTGAGTGGTACACAGAGAAAGgtgactttgg ... atgattgcagGGATAGAGTTAATTCTTAGCACAGAAATAGTAAAGGTAGACCTTGCTGCAA
EST: gi|21676903|gb|BQ629254.1|BQ629254
EST:     TGTTGGAAGTGGAGGAGAAAGGTTGCTTCCTGAGTGGTACACAGAGAAAG                         GGATAGAGTTAATTCTTAGCACAGAAATAGTAAAGGTAGACCTTGCTGCAA
genomic: TGTTGGAAGTGGAGGAGAAAGGTTGCTTCCTGAGTGGTACACAGAGAAAGgtgactttgg ... atgattgcagGGATAGAGTTAATTCTTAGCACAGAAATAGTAAAGGTAGACCTTGCTGCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCCTGCTAGACTTCCTGGGTTCCATGTCTGTGTTGGAAGTGGAGGAGAAAGGTTGCTTCCTGAGTGGTACACAGAGAAAGgtgactttggctttcacccacattgttttagttcagcattattactggatattgttaggatcaatagttgattatattattatatcaagtgaaaggaaaagtaaatggaaaactggatcttaacaacaattttctaatacgaagttactgatgattgcag

- - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - GGAGAA