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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttcatgctatttgttgtactggtctagacataggttatgcaagaatattcaaaggatttccaagtgattagtagtgaccaatggctttttgtgattcagAGGATTGTTTGACAAAAACAGAATTGCTAAGTGCAAGAAAGGTGTGGTGATTGTTAACAATGCTCGAGGGGCAATTATGGACACCCAAGCAATTGCTGAT

Basic information

species Glycine max
transcript GLYMA19G01200.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G01200.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0066g01320.t01 (Vitis vinifera), 3'ss of exon 3
------tttcatgctatttgttgtactggtctagacataggttatgcaagaatattcaaaggatttccaagtgattagtagtgaccaatggctttttgtgattcagAGGATTGTTTGACAAAAACAGAATTGCTAAGTGCAAGAAAGGTGTGGTGATTGTTAACAATGCTCGAGGGGCAATTATGGACACCCAAGCAATTGCTGAT
      ||||||  ||    |||      ||||| ||| ||  || | | || |||    |  ||    |    | | |  | |  | |    | |||| |||||||||| ||||  ||||| | || ||||| ||||  || || || ||  | |||||||||||||||||||| ||||| ||||| || |||||  |||| |||
gccccctttcata-taccatttgcttgaatctag-cat-ggcaattctacaaaattt---gtgttgttgaaccctaaattatcagaattttgatcttgtaattcagAGGAATGTTCAACAAAGAGAGGATTGCAAAGTTGAAAAAGGGAGTTCTAATTGTTAACAATGCTCGAGGAGCAATCATGGATACACAAGCTGTTGCCGAT
















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|58017267|gb|CX704009.1|CX704009
EST:     CCAAAGTGTGATGTAATTGTTATCAACATGCCTCTTACTGAACAGACAAG                         AGGATTGTTTGACAAAAACAGAATTGCTAAGTGCAAGAAAGGTGTGGTGAT
genomic: CCAAAGTGTGATGTAATTGTTATCAACATGCCTCTTACTGAACAGACAAGgtatactttc ... tgtgattcagAGGATTGTTTGACAAAAACAGAATTGCTAAGTGCAAGAAAGGTGTGGTGAT
EST: gi|33389257|gb|CA852464.1|CA852464
EST:     CCAAAGTGTGATGTAGTTGTTATCAACATGCCTCTTACTGAACAGACAAG                         AGGATTGTTTGACAAAAACAGAATTGCTAAGTGCAAGAAAGGTGTGGTGAT
genomic: CCAAAGTGTGATGTAATTGTTATCAACATGCCTCTTACTGAACAGACAAGgtatactttc ... tgtgattcagAGGATTGTTTGACAAAAACAGAATTGCTAAGTGCAAGAAAGGTGTGGTGAT
EST: gi|19452974|gb|BM954384.1|BM954384
EST:     CCAAAGTGTGATGTAATTGTTATCAACATGCCTCTTACTGAACAGACAAG                         AGGATTGTTTGACAAAAACAGAATTGCTAAGTGCAAGAAAGGTGTG
genomic: CCAAAGTGTGATGTAATTGTTATCAACATGCCTCTTACTGAACAGACAAGgtatactttc ... tgtgattcagAGGATTGTTTGACAAAAACAGAATTGCTAAGTGCAAGAAAGGTGTG
EST: gi|22521954|gb|BU080765.1|BU080765
EST:     CCAAAGTGTGATGTAATTGTTATCAACATGCCTCTTACTGAACAGACAAG                         AGGATTGTTTGACAAAAACAGAATTGCTAAGTGCAAGAAAGGTGTGGTGAT
genomic: CCAAAGTGTGATGTAATTGTTATCAACATGCCTCTTACTGAACAGACAAGgtatactttc ... tgtgattcagAGGATTGTTTGACAAAAACAGAATTGCTAAGTGCAAGAAAGGTGTGGTGAT
EST: gi|19934596|gb|BQ079626.1|BQ079626
EST:     CCAAAGTGTGATGTAATTGTTATCAACATGCCTCTTACTGAACAGACAAG                         AGGATTGTTTGACAAAAACAGAATTGCTAAGTGCAAGAAAGGTGTGGTGAT
genomic: CCAAAGTGTGATGTAATTGTTATCAACATGCCTCTTACTGAACAGACAAGgtatactttc ... tgtgattcagAGGATTGTTTGACAAAAACAGAATTGCTAAGTGCAAGAAAGGTGTGGTGAT
EST: gi|37996280|gb|CF807869.1|CF807869
EST:     AAGTGTGATGTAATTGTTATCAACATGCCTCTTACTGAACAGACAAG                         AGGATTGTTTGACAAAAACAGAATTGCTAAGTGCAAGAAAGGTGTGGTGAT
genomic: AAGTGTGATGTAATTGTTATCAACATGCCTCTTACTGAACAGACAAGgtatactttc ... tgtgattcagAGGATTGTTTGACAAAAACAGAATTGCTAAGTGCAAGAAAGGTGTGGTGAT
EST: gi|192327787|gb|FK022066.1|FK022066
EST:     CCAAAGTGTGATGTAATTGTTATCAACATGCCTCTTACTGAACAGACAAG                         AGGATTGTTTGACAAAAACAGAATTGCTAAGTGCAAGAAAGGTGTGGTGAT
genomic: CCAAAGTGTGATGTAATTGTTATCAACATGCCTCTTACTGAACAGACAAGgtatactttc ... tgtgattcagAGGATTGTTTGACAAAAACAGAATTGCTAAGTGCAAGAAAGGTGTGGTGAT
EST: gi|254315424|gb|GR825233.1|GR825233
EST:     CCAAAGTGTGATGTAATTGTTATCAACATGCCTCTTACTGAACAGACAAG                         AGGATTGTTTGACAAAAACAGAATTGCTAAGTGCAAGAAAGGTGTGGTGAT
genomic: CCAAAGTGTGATGTAATTGTTATCAACATGCCTCTTACTGAACAGACAAGgtatactttc ... tgtgattcagAGGATTGTTTGACAAAAACAGAATTGCTAAGTGCAAGAAAGGTGTGGTGAT
EST: gi|254315423|gb|GR825232.1|GR825232
EST:     CCAAAGTGTGATGTAATTGTTATCAACATGCCTCTTACTGAACAGACAAG                         AGGATTGTTTGACAAAAACAGAATTGCTAAGTGCAAGAAAGGTGTGGTGAT
genomic: CCAAAGTGTGATGTAATTGTTATCAACATGCCTCTTACTGAACAGACAAGgtatactttc ... tgtgattcagAGGATTGTTTGACAAAAACAGAATTGCTAAGTGCAAGAAAGGTGTGGTGAT
EST: gi|6848238|gb|AW350528.1|AW350528
EST:     CCAAAGTGTGATGTAATTGTTATCAACATGNNNCNTANNGAACAGACAAG                         AGGATTGTNNGACAAAAACAGAATTGNNAAGTGCAAGAAAGGTGTGGTGAT
genomic: CCAAAGTGTGATGTAATTGTTATCAACATGCCTCTTACTGAACAGACAAGgtatactttc ... tgtgattcagAGGATTGTTTGACAAAAACAGAATTGCTAAGTGCAAGAAAGGTGTGGTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atattcaaaggatttccaagtgattagtagtgaccaatggctttttgtgattcagAGGATTGTTTGACAAAAACAGAATTGCTAAGTGCAAGAAAGGTGTGGTGATTGTTAACAATGCTCGAGGGGCAATTATGGACACCCAAGCAATTGCTGAT
                                        ctttttgt  CT-rich tract
                      attagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttcatgctatttgttgtactggtctagacataggttatgcaagaatattcaaaggatttccaagtgattagtagtgaccaatggctttttgtgattcagAGGATTGTTTGACAAAAACAGAATTGCTAAGTGCAAGAAAGGTGTGGTGATTGTTAACAATGCTCGAGGGGCAATTATGGACACCCAAGCAATTGCTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- tcatgct
- - - - - - tgttgta
- - - - - - - - - - - - - - - - - - - tgcaaga