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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggggggtgggtggggtggatgcacaccccgtctcttatttctcttgccttaggtgaagctatggagaggttgactgatttatgtttttaacattttcagGGATAGACAGCAACGAGACCATAAAGGTTTATAGAAGTGGTGGAGCAGATCCTGATGGAGATCAACCTGGTGATCTTTATGTTACTATCAAG

Basic information

species Glycine max
transcript GLYMA09G00580.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G00580.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os12g07060.1 (Oryza sativa), 3'ss of exon 12
gggggggtgggtggggtggatgcacacccc-gtctcttatttctcttgccttaggtgaagc--tatggagaggttgactgatttatgtttttaaca---ttttcagGGATAGACAGCAACGAGACCATAAAGGTTTATAGAAGTGGTGGAGCAGATCCTGATGGAGATCAACCTGGTGATCTTTATGTTACTATCAAG
       | |      |      | |  |  ||   |  ||| | |||   |  |    ||  ||     |  |||  ||    ||   |  ||||   ||| |||| || ||   ||| || || || ||||||| | | |  ||||| ||||||  |||  |  || ||||||||||||| |||||||||||||||
------tttgtctccttattcaaatattcaagttattcgtttatattggagtgtgcatggcagtacttgcattttgggtgtgacataaatggaacatcttttccagGCATCGATGACAATGACACTATGAAGGTTTTTGGCAAGGGTGGTGCAGATGTTGAGCGCAATAAACCTGGTGATCTCTATGTTACTATCAAG

upper sequence: GLYMA09G00580.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv13s0064g01360.t01 (Vitis vinifera), 3'ss of exon 12
--gggggggtgggtggggtggatgcacacc-ccgtctcttatttctcttgccttaggtgaagctatggagaggttgactgatttatgtttttaacattttcagGGATAGACAGCAACGAGACCATAAAGGTTTATAGAAGTGGTGGAGCAGATCCTGATGGAGATCAACCTGGTGATCTTTATGTTACTATCAAG
  |   |     ||    |  | |  ||   ||||    | ||   ||     ||  ||  | |||| || |    | | || ||||  ||| | || | ||||  | |||  ||| || ||  ||||||| ||||||||||||||||| |||||||| ||| |||||||||||||||||||||||||||||| |
ttgaaagctaatgtcccctcaaaggtcaaggccgtgagatgttgg-ctgaaggtaaatgttgatatgtagtg--ccattaatgtatgcattttatatgtgcagGAGTGGACGACAATGAAACTCTAAAGGTGTATAGAAGTGGTGGAGCTGATCCTGAAGGAAATCAACCTGGTGATCTTTATGTTACTATCAGG
















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|192326652|gb|FK017309.1|FK017309
EST:     TGCAAAGATTGTCAAAGGAATGAAGTCGATCAAGTTGGATATTATGCCTG                         GGATAGACAGCAACGAGACCATAAAG
genomic: TGCAAAGATTGTCAAAGGAATGAAGTCGATCAAGTTGGATATTATGCCTGgtaattgtca ... acattttcagGGATAGACAGCAACGAGACCATAAAG
EST: gi|7924054|gb|AW830062.1|AW830062
EST:     TGCGAAGATTGTCAAAGGAATGAAGTCGATCAAGTTGGATATTATGCCTG                         GGATAGACAGCAACGAGACCATAAAGGTT
genomic: TGCAAAGATTGTCAAAGGAATGAAGTCGATCAAGTTGGATATTATGCCTGgtaattgtca ... acattttcagGGATAGACAGCAACGAGACCATAAAGGTT
EST: gi|208059639|gb|GD858369.1|GD858369
EST:     TGCAAAGATTGTCAAAGGAATGAAGTCGATCAAGTTGGATATTATGCCTG                         GGATAGACAGCAACGAGACCATAAAGGTTTATAGAAGTGGTGGAGCAGATC
genomic: TGCAAAGATTGTCAAAGGAATGAAGTCGATCAAGTTGGATATTATGCCTGgtaattgtca ... acattttcagGGATAGACAGCAACGAGACCATAAAGGTTTATAGAAGTGGTGGAGCAGATC
EST: gi|7796591|gb|AW781988.1|AW781988
EST:     TGCAAAGATTGTCAAAGGAATGAAGTCGATCAAGTTGGATATTATGCCTG                         GGATAGACAGCAACGAGACCATAAAGGTTTATAGAAGTGGTGGAGCAGATC
genomic: TGCAAAGATTGTCAAAGGAATGAAGTCGATCAAGTTGGATATTATGCCTGgtaattgtca ... acattttcagGGATAGACAGCAACGAGACCATAAAGGTTTATAGAAGTGGTGGAGCAGATC
EST: gi|193368090|gb|FK331656.1|FK331656
EST:     TGCAAAGATTGTCAAAGGAATGAAGTCGATCAAGTTGGATATTATGCCTG                         GGATAGACAGCAACGAGACCATAAAGGTTTATAGAAGTGGTGGAGCAGATC
genomic: TGCAAAGATTGTCAAAGGAATGAAGTCGATCAAGTTGGATATTATGCCTGgtaattgtca ... acattttcagGGATAGACAGCAACGAGACCATAAAGGTTTATAGAAGTGGTGGAGCAGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgccttaggtgaagctatggagaggttgactgatttatgtttttaacattttcagGGATAGACAGCAACGAGACCATAAAGGTTTATAGAAGTGGTGGAGCAGATCCTGATGGAGATCAACCTGGTGATCTTTATGTTACTATCAAG
                                        ttttaac  putative branch site (score: 2)
                                              cattttc  CT-rich tract
                              tgatttatgtttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gggggggtgggtggggtggatgcacaccccgtctcttatttctcttgccttaggtgaagctatggagaggttgactgatttatgtttttaacattttcagGGATAGACAGCAACGAGACCATAAAGGTTTATAGAAGTGGTGGAGCAGATCCTGATGGAGATCAACCTGGTGATCTTTATGTTACTATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
ggggggg
- - gggtggg
- - - - - - - - -ggatgca
- - - - - - - - - - - - - ccccgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggagagg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgactg