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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctagtaacttgctataaaagtgcccattctagctcaaatctattttcttttaaacattttatgcttttagagtaacagcaaaaatgctttccttgcagGTATGGACAACTGGAACCATGGGAGAACTCAGCCCA

Basic information

species Vitis vinifera
transcript Vv14s0128g00100.t01
intron # 27
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0128g00100.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GLYMA10G29770.1 (Glycine max), 3'ss of exon 18
atctagtaacttgctataaaagtgcccattctagctcaaatctattttcttttaaacattttatgctttta--gagtaacagcaaaaatgctttccttgcagGTATGGACAACTGGAACCATGGGAGAACTCAGCCCA
 | ||     | ||  | |   | | | ||||  |||  | |  || ||| |     | |||||      |  |||| | | | | || |||  | |||||| |||||||||| ||||| ||||||||||| ||||||
-tataagttttggccttcatttttctctttctgcctcccaccctttctctctcttcaaatttatatcgagatcgagttataactagaaggctg-cgttgcagATATGGACAACAGGAACAATGGGAGAACTAAGCCCA

upper sequence: Vv14s0128g00100.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GLYMA03G40000.1 (Glycine max), 3'ss of exon 17
atctagtaacttgctataaaagtgcccattctagctcaaatctattttcttttaaacattttatgc---ttttagagtaacagcaaaaatgctttccttgcagGTATGGACAACTGGAACCATGGGAGAACTCAGCCCA
 || |    |  | |     | |    ||   ||    | |  || |    ||| | ||||  | |   || |   || | | | | ||  | |  |||| |||||||||| |||||||| ||||||||||| ||||| 
-tccatagtcgggttggtgtaat--ttatggcagtgttagttgatctctccttatatatttggtccaatttatgttgttataactagaagacctgtcttgaagGTATGGACGACTGGAACAATGGGAGAACTAAGCCCC

upper sequence: Vv14s0128g00100.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: GLYMA19G42530.1 (Glycine max), 3'ss of exon 17
atctagtaacttgctataaaagtgcccattctagctcaaatctattttcttttaaacattttatgc---ttttagagtaacagcaaaaatgctttccttgcagGTATGGACAACTGGAACCATGGGAGAACTCAGCCCA
 || |    |  | |     | |    ||   ||    | | ||| |     || | ||||  | |   || |   || | | | | ||  |||  |||| |||||||||| |||||||| ||||||||||| ||||| 
-tccatagtcgggttggtgtaat--ttatggcagtgttagtttatctctccgtatatatttggtccaatttatgttgttataactagaagacttgtcttgaagGTATGGACGACTGGAACAATGGGAGAACTAAGCCCG

upper sequence: Vv14s0128g00100.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: AT3G05190.1 (Arabidopsis thaliana), 3'ss of exon 17
-atctagtaacttgctataaaagtgcccattctagctcaaatctattttcttttaaacattttatgcttttagagt----aacagcaaaaatgct--ttccttgcagGTATGGACAACTGGAACCATGGGAGAACTCAGCCCA
  |||   | ||| | |   |   |    |    | ||||||| | ||   | |     | |  | || |   |||    ||||  || | |  |  ||  ||  ||||||||||||| ||||| ||||||||||| ||||| 
gttctttcagcttacaacttatcagtttttaaggggtcaaatcgaattatctgtgcctctctctttctctacaagtatctaacaataatagttttgtttttttaaagGTATGGACAACAGGAACTATGGGAGAACTAAGCCCG

upper sequence: Vv14s0128g00100.t01 (Vitis vinifera), 3'ss of exon 27
lower sequence: AT5G27410.2 (Arabidopsis thaliana), 3'ss of exon 27
atctagtaacttgctataaaagtgcccattctagctcaaatctattttcttttaaacattttatgcttttagagtaacagcaaaaatgctttccttgcagGTATGGACAACTGGAACCATGGGAGAACTCAGCCCA
                      | | |||  |  |   ||||| |    | | |||   |   |   |      || ||    | ||     | ||  |||||||||| || ||||| ||||||||||||||||| 
-------------------gtttcctcatcttttccttaatct-tagaatctcaaatgatcactaactaagtgttatcaatccatatcaaaactttctagGTATGGACTACAGGAACTATGGGAGAACTCAGCCCG

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|34362676|gb|CF404261.1|CF404261
EST:     CTTTAGTGGAGCGGAGAATCAGCCTATCAGAGTTTCATACTGCAGATGAG                         GTATGGACAACTGGAACCATGGGAGAACTCAGCCCA
genomic: CTTTAGTGGAGCGGAGAATCAGCCTATCAGAGTTTCATACTGCAGATGAGgtctgttttt ... ttccttgcagGTATGGACAACTGGAACCATGGGAGAACTCAGCCCA
EST: gi|110418692|gb|EC984856.1|EC984856
EST:     CTTTAGTGGAGCGGAGAATCAGCCTATCAGAGTTTCATACTGCAGATGAG                         GTATGGACAACTGGAACCATGGGAGAACTCAGCCCA
genomic: CTTTAGTGGAGCGGAGAATCAGCCTATCAGAGTTTCATACTGCAGATGAGgtctgttttt ... ttccttgcagGTATGGACAACTGGAACCATGGGAGAACTCAGCCCA
EST: gi|33409556|gb|CF215183.1|CF215183
EST:     CTTTAGTGGAGCGGAGAATCAGCCTATCAGAGTTTCATACTGCAGATGAG                         GTATGGACAACTGGAACCATGGGAGAACTCAGCCCA
genomic: CTTTAGTGGAGCGGAGAATCAGCCTATCAGAGTTTCATACTGCAGATGAGgtctgttttt ... ttccttgcagGTATGGACAACTGGAACCATGGGAGAACTCAGCCCA
EST: gi|33402079|gb|CF207706.1|CF207706
EST:     CTTTAGTGGAGCGGAGAATCAGCCTATCAGAGTTTCATACTGCAGATGAG                         GTATGGACAACTGGAACCATGGGAGAACTCAGCCCA
genomic: CTTTAGTGGAGCGGAGAATCAGCCTATCAGAGTTTCATACTGCAGATGAGgtctgttttt ... ttccttgcagGTATGGACAACTGGAACCATGGGAGAACTCAGCCCA
EST: gi|110424723|gb|EC991093.1|EC991093
EST:     CTTTAGTGGAGCGGAGAATCAGCCTATCAGAGTTTCATACTGCAGATGAG                         GTATGGACAACTGGAACCATGGGAGAACTCAGCCCA
genomic: CTTTAGTGGAGCGGAGAATCAGCCTATCAGAGTTTCATACTGCAGATGAGgtctgttttt ... ttccttgcagGTATGGACAACTGGAACCATGGGAGAACTCAGCCCA
EST: gi|22014530|gb|BQ799564.1|BQ799564
EST:     CTTTAGTGGAGCGGAGAATCAGCCTATCAGAGTTTCATACTGCAGATGAG                         GTATGGACAACTGGAACCATGGGAGAACTCAGCCCA
genomic: CTTTAGTGGAGCGGAGAATCAGCCTATCAGAGTTTCATACTGCAGATGAGgtctgttttt ... ttccttgcagGTATGGACAACTGGAACCATGGGAGAACTCAGCCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcttttaaacattttatgcttttagagtaacagcaaaaatgctttccttgcagGTATGGACAACTGGAACCATGGGAGAACTCAGCCCA
                          gagtaac  putative branch site (score: 2)
                                         tgctttcctt  putative PPT
     tttaaacattttatgc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctagtaacttgctataaaagtgcccattctagctcaaatctattttcttttaaacattttatgcttttagagtaacagcaaaaatgctttccttgcagGTATGGACAACTGGAACCATGGGAGAACTCAGCCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - -ataaaag
- - - - - - - - - - - - cccattc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agtaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaaaaa