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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttattgcaatgctgacgtggatggtctggatgcaaattaactatgatcaggtaaaattaaatgaaaatattatctgataaatatgtttttggttctacagTTCGTGATCATGTTTTTGGCTGTAATACGAGTACGAGCCACAGCTGCGCCTTTGAACTCAGCTTACACAGCAGACGAGTTCGAGTTTTACTTATCCGACT

Basic information

species Vitis vinifera
transcript Vv16s0050g00390.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g00390.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA11G31310.2 (Glycine max), 3'ss of exon 1
---ttattgcaatgctgacgtggatggtctggatgcaaattaactatgatcaggtaaaattaaatgaaaa---tattatctgataaatatgt--ttttggttcta---cagTTCGTGATCATGTTTTTGGCTGTAATACGAGTACGAGCCACAGCTGCGCCTTTGAACTCAGCTTACACAGCAGACGAGTTCGAGTTTTACTTATCCGACT
     ||  |  | |  ||   |      |  ||  | | |||  || |  | |  |||  |  |   ||   ||| |  | |||| | |||  |||  |||  |   ||||| ||  |||||||  | || || || || |  ||||||||||| ||||| || ||||| ||||||||||| || |||||||||||||||||||||||||
gttcgatcactctcccaacaaagccaacatttatcaataataataataaaaaagacaaacaacgtaggaaagttataacattataactttgtattttctgtttgatttcagTTTGTAGTCATGTTCCTAGCCGTCATTCGGGCTCGAGCCACAGCCGCGCCGTTAAACTCGGCTTACACAGCGGAAGAGTTCGAGTTTTACTTATCCGACT

upper sequence: Vv16s0050g00390.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G25470.2 (Glycine max), 3'ss of exon 1
ttattgcaatgctgacgtggatggtctggatgcaaat--taactatgatcaggtaaaattaaatgaaaatattatctgataaatatgtttttggttc--tacagTTCGTGATCATGTTTTTGGCTGTAATACGAGTACGAGCCACAGCTGCGCCTTTGAACTCAGCTTACACAGCAGACGAGTTCGAGTTTTACTTATCCGACT
     ||   | | |     ||    | ||  || ||  ||| | |    | || | |  | | |  |   | | ||  |   | | ||| || |||  | ||||| ||  || ||||| | || || || ||||| || |||||||| ||||| || ||| | ||||||||||| || ||||| ||||||||||| |||||||
----agctgcggtaataattattacatagaatcatataataaattttcgtacgttagaaaataaggtagagtaaccttttttttttttttctgtttcattgcagTTTGTTGTCTTGTTTCTAGCCGTCATTCGAGTGCGCGCCACAGCCGCGCCGTTAAACGCGGCTTACACAGCCGAAGAGTTTGAGTTTTACTTGTCCGACT
















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|161721608|gb|FC070818.1|FC070818
EST:     GCGTTAAGGCCGGAGACGTCGTCGCTCTCACCTTCCCAAACACCGTTGAG                         TTCGTGATTATGTTTTTGGCTGTAATACGAGTACGAGCCACGGCTGCGCCT
genomic: GCGTTAAGGCTGGAGACGTCGTCGCTCTCACCTTCCCAAACACCGTTGAGgtatctttat ... ggttctacagTTCGTGATCATGTTTTTGGCTGTAATACGAGTACGAGCCACAGCTGCGCCT
EST: gi|219555092|gb|FG984881.1|FG984881
EST:     GCGTTAAGGCCGGAGACGTCGTCGCTCTCACCTTCCCAAACACCGTTGAG                         TTCGTGATTATGTTTTTGGCTGTAATACGAGT
genomic: GCGTTAAGGCTGGAGACGTCGTCGCTCTCACCTTCCCAAACACCGTTGAGgtatctttat ... ggttctacagTTCGTGATCATGTTTTTGGCTGTAATACGAGT
EST: gi|71883492|gb|DT032547.1|DT032547
EST:     GCGTTAAGGCCGGAGACGTCGTCGCTCTCACCTTCCCAAACACCGTTGAG                         TTCGTGATTATGTTTTTGGCTGTAATACGAGTACGAGCCACGGCTGCGCCT
genomic: GCGTTAAGGCTGGAGACGTCGTCGCTCTCACCTTCCCAAACACCGTTGAGgtatctttat ... ggttctacagTTCGTGATCATGTTTTTGGCTGTAATACGAGTACGAGCCACAGCTGCGCCT
EST: gi|219555309|gb|FG984482.1|FG984482
EST:     GCGTTAAGGCCGGAGACGTCGTCGCTCTCACCTTCCCAAACACCGTTGAG                         TTCGTGATTATGTTTTTGGCTGTAATACGAGTA
genomic: GCGTTAAGGCTGGAGACGTCGTCGCTCTCACCTTCCCAAACACCGTTGAGgtatctttat ... ggttctacagTTCGTGATCATGTTTTTGGCTGTAATACGAGTA
EST: gi|37185424|gb|CF604777.1|CF604777
EST:     GCGTTAAGGCCGGAGACGTCGTCGCTCTCACCTTCCCAAACACCGTTGAG                         TTCGTGATTATGTTTTTGGCTGTAATACGAGTACGAGCCACGGCTGCGCCT
genomic: GCGTTAAGGCTGGAGACGTCGTCGCTCTCACCTTCCCAAACACCGTTGAGgtatctttat ... ggttctacagTTCGTGATCATGTTTTTGGCTGTAATACGAGTACGAGCCACAGCTGCGCCT
EST: gi|30131436|gb|CB916775.1|CB916775
EST:     GCGTTAAGGCGGGAGACGTCGTCGCTCTCACCTTCCCAAACACCGTTGAG                         TTCGTGATTATGTTTTTGGCTGTAATACGAGTACGAGCCACGGCTGCGCCT
genomic: GCGTTAAGGCTGGAGACGTCGTCGCTCTCACCTTCCCAAACACCGTTGAGgtatctttat ... ggttctacagTTCGTGATCATGTTTTTGGCTGTAATACGAGTACGAGCCACAGCTGCGCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcaggtaaaattaaatgaaaatattatctgataaatatgtttttggttctacagTTCGTGATCATGTTTTTGGCTGTAATACGAGTACGAGCCACAGCTGCGCCTTTGAACTCAGCTTACACAGCAGACGAGTTCGAGTTTTACTTATCCGACT
                          atctgat  putative branch site (score: 4)
      taaaattaaatgaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttattgcaatgctgacgtggatggtctggatgcaaattaactatgatcaggtaaaattaaatgaaaatattatctgataaatatgtttttggttctacagTTCGTGATCATGTTTTTGGCTGTAATACGAGTACGAGCCACAGCTGCGCCTTTGAACTCAGCTTACACAGCAGACGAGTTCGAGTTTTACTTATCCGACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - caatgct
- - - - - - - - - - - ggtctgg
- - - - - - - - - - - - - - - - -aaattaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ataaata