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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaaccacatacaccatgggaaagagaaaattattgtgtgaaagattttgcacataacatttttatatgatatagtttgtgatctttctatccatcgcagGAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAATGGATCAATTATACCATCAGAAC

Basic information

species Glycine max
transcript GLYMA15G19670.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G19670.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv11s0016g00900.t01 (Vitis vinifera), 3'ss of exon 3
--ttaaccacatacaccatgggaaagagaaaattattgtgtgaaagattttgcacataacatttttatatgatatagtttgtgatctttc-tatccatcgcagGAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAATGGATCAATTATACCATCAGAAC
    ||  || |  |  ||     |||  || || | |  |     |  || | |    |||||| | || |     ||| | || |||  | | | | |||||||||| |||||||||||||||||  ||||||| ||||  ||||| | |||||||| || ||||| || ||||
atacaaaaacctcaataatctttcagatgaatttttggccttgtttacctttctcc---cattttcaaataactccattttttattttttatttgctttgcagGAAATTGTTGATATGTGTGATTATGCTGTTGGGTTAAGTCGACAAATAAATGGATCCATCATACCTTCTGAAC
















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|192311334|gb|FK003791.1|FK003791
EST:     TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAG                         GAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
genomic: TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAGgtatcacaat ... tccatcgcagGAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
EST: gi|298176954|gb|HO026961.1|HO026961
EST:     TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAG                         GAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
genomic: TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAGgtatcacaat ... tccatcgcagGAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
EST: gi|208138184|gb|GD936818.1|GD936818
EST:     TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAG                         GAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGC
genomic: TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAGgtatcacaat ... tccatcgcagGAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGC
EST: gi|254315873|gb|GR825682.1|GR825682
EST:     TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAG                         GAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
genomic: TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAGgtatcacaat ... tccatcgcagGAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
EST: gi|193695881|gb|FK635655.1|FK635655
EST:     TGTCTCTTGAGATGGGAAAAATTCNCCCAGAAGGAAT-GGGGAAGTTCAG                         GAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAAT
genomic: TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAGgtatcacaat ... tccatcgcagGAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAAT
EST: gi|192296158|gb|FG989743.1|FG989743
EST:     TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAG                         GAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGGCAATTGAAT
genomic: TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAGgtatcacaat ... tccatcgcagGAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
EST: gi|192311335|gb|FK003792.1|FK003792
EST:     TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAG                         GAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
genomic: TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAGgtatcacaat ... tccatcgcagGAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
EST: gi|151412062|gb|EV281874.1|EV281874
EST:     TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAG                         GAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
genomic: TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAGgtatcacaat ... tccatcgcagGAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
EST: gi|15813460|gb|BI785735.1|BI785735
EST:     TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAG                         GAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
genomic: TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAGgtatcacaat ... tccatcgcagGAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
EST: gi|27446368|gb|CA953491.1|CA953491
EST:     TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAG                         GAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
genomic: TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAGgtatcacaat ... tccatcgcagGAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
EST: gi|254317668|gb|GR826652.1|GR826652
EST:     TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAG                         GAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
genomic: TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAGgtatcacaat ... tccatcgcagGAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
EST: gi|209718196|gb|BW657828.1|BW657828
EST:     TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAG                         GAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT
genomic: TGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAGgtatcacaat ... tccatcgcagGAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgcacataacatttttatatgatatagtttgtgatctttctatccatcgcagGAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAATGGATCAATTATACCATCAGAAC
      acataac  putative branch site (score: 3)
                                     tctttctatccatc  putative PPT
      acataacatttttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaaccacatacaccatgggaaagagaaaattattgtgtgaaagattttgcacataacatttttatatgatatagtttgtgatctttctatccatcgcagGAAATTATTGATATGTGTGATTATTGTGTTGGGCTAAGCAGACAATTGAATGGATCAATTATACCATCAGAAC

- - - -catacac
- - - - - - - - - - -aagagaaa
- - - - - - - - - - - - - - - - - tgtgtga
- - - - - - - - - - - - - - - - - - - - - - - - tgcacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtttgtg