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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatagtgataactaataagtataacaggaattatttccattttttagtttctttattaatgttttgtcgtcacattgtgaataaacaacttctcaaacagGGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAG

Basic information

species Glycine max
transcript GLYMA03G00920.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G00920.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0056g01150.t01 (Vitis vinifera), 3'ss of exon 2
tatagtgataactaataag-tataacaggaattatttccattttttagtttctt-tattaatgttttgtcgtcacattgtgaataaacaacttctcaaacagGGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAG
   | ||||    |||    ||  |  | |||  |||     |   |    ||  | | | || ||| || |    ||     |    |  ||||||||||||||||| |||| | | ||| ||||  |||||||||||||||| || ||||| |||||||| ||||||||| |||||||||| ||||| |||
ccaaatgattgtaaatgctctaggatggtaatattttgtgcatcacatgaactgatgtcactgctttatccttt--ttaattttggctattttctcaaacagGGGTAAGGATGGTGAGGGTCAAGAAATTATCAAACCATATACCCCAACTACATTGGATTCTGATGTTGGATATTTTGAACTTGTTATAAAG
















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|192301598|gb|FG994782.1|FG994782
EST:     ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAG                         GGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
genomic: ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAGgttcaattgc ... tctcaaacagGGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
EST: gi|213587981|gb|DB971456.1|DB971456
EST:     ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAG                         GGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
genomic: ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAGgttcaattgc ... tctcaaacagGGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
EST: gi|213617616|gb|DB969328.1|DB969328
EST:     ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAG                         GGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
genomic: ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAGgttcaattgc ... tctcaaacagGGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
EST: gi|209728695|gb|BW655402.1|BW655402
EST:     ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAG                         GGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
genomic: ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAGgttcaattgc ... tctcaaacagGGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
EST: gi|151407227|gb|EV277042.1|EV277042
EST:     ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAG                         GGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
genomic: ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAGgttcaattgc ... tctcaaacagGGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
EST: gi|10236160|gb|BE805048.1|BE805048
EST:     ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAG                         GGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
genomic: ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAGgttcaattgc ... tctcaaacagGGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
EST: gi|151394787|gb|EV264658.1|EV264658
EST:     ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAG                         GGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
genomic: ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAGgttcaattgc ... tctcaaacagGGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
EST: gi|4285741|gb|AI440947.1|AI440947
EST:     ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAG                         GGGTAAAGATGCTCAAGGTGAAAGAGGTTATCAAACCATATACTCCTACTA
genomic: ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAGgttcaattgc ... tctcaaacagGGGTAAAGATGCTCAAGGTGAA-GAGGTTATCAAACCATATACTCCTACTA
EST: gi|58021619|gb|CX708360.1|CX708360
EST:     ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAG                         GGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
genomic: ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAGgttcaattgc ... tctcaaacagGGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
EST: gi|298183643|gb|HO028856.1|HO028856
EST:     ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAG                         GGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
genomic: ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAGgttcaattgc ... tctcaaacagGGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
EST: gi|151401464|gb|EV271278.1|EV271278
EST:     ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAG                         GGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
genomic: ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAGgttcaattgc ... tctcaaacagGGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
EST: gi|193418380|gb|FK385180.1|FK385180
EST:     ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAG                         GGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
genomic: ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAGgttcaattgc ... tctcaaacagGGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
EST: gi|298174935|gb|HO014852.1|HO014852
EST:     ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAG                         GGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
genomic: ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAGgttcaattgc ... tctcaaacagGGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
EST: gi|193327580|gb|FK292971.1|FK292971
EST:     ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAG                         GGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAAACCATATACTCCTACTA
genomic: ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAGgttcaattgc ... tctcaaacagGGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAA-CCATATACTCCTACTA
EST: gi|151403993|gb|EV273803.1|EV273803
EST:     ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAG                         GGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
genomic: ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAGgttcaattgc ... tctcaaacagGGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
EST: gi|207766661|gb|GD738289.1|GD738289
EST:     ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAG                         GGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
genomic: ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAGgttcaattgc ... tctcaaacagGGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
EST: gi|298189804|gb|HO038207.1|HO038207
EST:     ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAG                         GGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
genomic: ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAGgttcaattgc ... tctcaaacagGGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
EST: gi|13788917|gb|BG651508.1|BG651508
EST:     ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAG                         GGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
genomic: ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAGgttcaattgc ... tctcaaacagGGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
EST: gi|37995436|gb|CF807025.1|CF807025
EST:     GGCAACACATAAGTTGCAG                         GGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
genomic: GGCAACACATAAGTTGCAGgttcaattgc ... tctcaaacagGGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
EST: gi|18690778|gb|BM519626.1|BM519626
EST:     ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAG                         GGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
genomic: ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAGgttcaattgc ... tctcaaacagGGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
EST: gi|298186113|gb|HO036746.1|HO036746
EST:     ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAG                         GGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
genomic: ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAGgttcaattgc ... tctcaaacagGGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
EST: gi|151399348|gb|EV269219.1|EV269219
EST:     ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAG                         GGGTAAAGATGCTCAGGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
genomic: ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAGgttcaattgc ... tctcaaacagGGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
EST: gi|298178943|gb|HO024678.1|HO024678
EST:     ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAG                         GGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
genomic: ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAGgttcaattgc ... tctcaaacagGGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTAC
EST: gi|4285622|gb|AI440930.1|AI440930
EST:     ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAG                         GGGTAAAGATGCTCAAGG-GAAAGAGGTTATCAAACCATATACTCCTACTA
genomic: ACACCTACATCTGTTTTGGGTCTTCCAATTGGGCAACACATAAGTTGCAGgttcaattgc ... tctcaaacagGGGTAAAGATGCTCAAGGTGAA-GAGGTTATCAAACCATATACTCCTACTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttctttattaatgttttgtcgtcacattgtgaataaacaacttctcaaacagGGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAG
        tattaat  putative branch site (score: 2)
                                           cttctc  putative PPT
      tttattaatgttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatagtgataactaataagtataacaggaattatttccattttttagtttctttattaatgttttgtcgtcacattgtgaataaacaacttctcaaacagGGGTAAAGATGCTCAAGGTGAAGAGGTTATCAAACCATATACTCCTACTACTTTGGATTCCGATGTTGGACATTTTGAACTAGTTATTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaataaac