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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatttattttcctttatctttgaggtcaaggttttggtttttcatagatgtgtgtgatttaaatctccactttgtttccctaactagcttcaacttccagGGCATGAGTCAGCTGGAGTTGGAAGATGAAGTCCAAGATGATTTAAAACGTGCAACTGGAGAGTTCATCAAGGATGGGGATGATGCAAATAAGCTAAACC

Basic information

species Vitis vinifera
transcript Vv04s0008g02320.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g02320.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os01g17430.1 (Oryza sativa), 3'ss of exon 1
--tatttattttcct--ttatctttgaggtcaaggttttggtttttcatagatgtgtgtgatttaaatctccactttgtttccctaactagcttcaacttccagGGCATGAGTCAGCTGGAGTTGGAAGATGAAGTCCAAGATGATTTAAAACGTGCAACTGGAGAGTTCATCAAGGATGGGGATGATGCAAATAAGCTAAACC
  | |  || |   |  | | ||||    ||  |  |     ||   |||    ||  | |||||  |||||   ||  |    |       |     | | |||||||||||||||| ||||||||||||||||| |||||||| || ||   ||||||||| | ||| |  |||||||   |||||||||| |  || ||||
ggtgtcaatctggttgataacctttcctttcctgagtgcaagtt---atatgc-tgccttatttatgtctccttgttagtaaaatgtgacattgtttttcctagGGCATGAGTCAGCTTGAGTTGGAAGATGAAGTTCAAGATGACTTGAAGGCTGCAACTGGTGGGTTTACTAAGGATGCATATGATGCAAACAGACTTAACC

upper sequence: Vv04s0008g02320.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os11g07280.1 (Oryza sativa), 3'ss of exon 1
tatttattttcctttatctttgaggtcaaggttttggtttttcatagatgtgtgtgatttaaatctccactttgtttccctaa--ctagc--ttcaa-cttccagGGCATGAGTCAGCTGGAGTTGGAAGATGAAGTCCAAGATGATTTAAAACGTGCAACTGGAGAGTTCATCAAGGATGGGGATGATGCAAATAAGCTAAACC
    |    |    | |   | | || |  |||||    | ||    || ||      |    |       ||  ||| ||||  |  ||  ||||  ||| ||||| ||||| || || ||||||||||||| ||||||||||||||| ||   ||| ||||| || || |  || ||||  ||||| ||||| |  || || |
----tggactgacgtgttact-atgttactgttttttcctgtctagtatttgaaaagatggcctgcggttctttcttcactaaaacatgccattcattcttgcagGGAATGAGCCAACTTGAGTTGGAAGATGCAGTCCAAGATGATTTGAAGGCTGCTACTGGTGAATTTACAAAAGATGCAGATGACGCAAACAGACTGAATC

upper sequence: Vv04s0008g02320.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G378906_T01 (Zea mays), 3'ss of exon 1
tatttattttcctttatctttgaggtcaaggttttggtttttcatagatgtgtgtgatttaaatctccactttgtttccctaactagcttcaacttccagGGCATGAGTCAGCTGGAGTTGGAAGATGAAGTCCAAGATGATTTAAAACGTGCAACTGGAGAGTTCATCAAGGATGGGGATGATGCAAATAAGCTAAACC
    | || |   ||    |||      |  ||     ||||  |       |   || |  | || || ||  |    |   |||  ||    |   |||||||||| ||||| |||||||||||||| || || |||||||| ||   ||||||||| | ||| |  |||||||  ||||||||||| ||||| ||||
ctggtgttgtgtattgggcttggatgataccttgccacttttagtgtggccttcacatctgtaccttcagttattaaagcatgctattttgttatcatagGGCATGAGCCAGCTTGAGTTGGAAGATGAGGTGCACGATGATTTGAAGGCTGCAACTGGTGGGTTTACTAAGGATGCAGATGATGCAAACAAGCTCAACC

upper sequence: Vv04s0008g02320.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G011101_T01 (Zea mays), 3'ss of exon 1
tatttattttcctttatctttgaggtcaaggttttggtttttcatagatgtgtgtgatttaaatctccactttgtttccctaactagcttcaacttc-cagGGCATGAGTCAGCTGGAGTTGGAAGATGAAGTCCAAGATGATTTAAAACGTGCAACTGGAGAGTTCATCAAGGATGGGGATGATGCAAATAAGCTAAACC
  | |  | |  | |   ||||      |  ||     || |  |     | |   ||||     | || ||  |    |   |||  ||     ||  |||||||||| ||||| |||||||||||||| || || |||||||| ||   ||||||||| | ||| | ||||||||  ||||| ||||| ||||| ||||
-gtctggtgttgtcttggtttgcacgacaccttgccacttctagtgtggctttcacatttgctctttcagttattaaagcatgctatttttgttgtcatagGGCATGAGCCAGCTTGAGTTGGAAGATGAGGTGCATGATGATTTGAAGGCTGCAACTGGTGGGTTTACCAAGGATGCAGATGACGCAAACAAGCTCAACC

upper sequence: Vv04s0008g02320.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G094699_T01 (Zea mays), 3'ss of exon 1
tatttattttcctttatctttgaggtcaaggttttggtttttcatagatgtgtgtgatttaaatctccactttgtttccctaa--ctagcttcaacttc-cagGGCATGAGTCAGCTGGAGTTGGAAGATGAAGTCCAAGATGATTTAAAACGTGCAACTGGAGAGTTCATCAAGGATGGGGATGATGCAAATAAGCTAAACC
   ||   |   |  | | |||      || |||  |   |    |      | |  |||   | ||     |      ||||   | ||||     || ||||| ||||||||||| ||| ||||||||| ||| ||||||||||| ||   |||||| ||  | || |  |||||||  |||||| |  | ||||||||||
---ttccctatatccacccttgtatgggagctttcagcactgggcatgctctttttctttgtgtttctttcatacactgctaaatttggcttttttgtcacagGGAATGAGTCAGCTTGAGCTGGAAGATGCAGTTCAAGATGATTTGAAGGCTGCAACCGGCCAATTTACTAAGGATGCAGATGATACTGACAAGCTAAACC

upper sequence: Vv04s0008g02320.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G31480.2 (Arabidopsis thaliana), 3'ss of exon 3
tatttattttcctttatctttgaggtcaaggttttggtttttcatag-atgtgtgtg-atttaaatctccactttgtttccctaactagcttcaacttccagGGCATGAGTCAGCTGGAGTTGGAAGATGAAGTCCAAGATGATTTAAAACGTGCAACTGGAGAGTTCATCAAGGATGGGGATGATGCAAATAAGCTAAACC
  ||| |     | |       || || |   ||     |  |||   |||| | |  ||||   ||   | ||    |  || || |       ||| ||||| |||||||| || |||||||||||  |||| ||||||||  |||| |||||||||||||| |||| |||||| | | | ||||| || || || ||||
--tttttcgcattctcaaagaaagttcgaaagttgatagtggcatgttatgtttatttatttcggtcagtagttgaaattactgacgataagtttctttcagGGAATGAGTCAACTTGAGTTGGAAGACCAAGTACAAGATGACCTAAAGCGTGCAACTGGAGAATTCACCAAGGACGAGAACGATGCTAACAAACTTAACC

upper sequence: Vv04s0008g02320.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G31490.1 (Arabidopsis thaliana), 3'ss of exon 2
tatttattttcctttatctttgaggtcaaggttttggtttttcatag-atgtgtgtga-tttaaatctccactttgtttccctaactagcttcaacttccagGGCATGAGTCAGCTGGAGTTGGAAGATGAAGTCCAAGATGATTTAAAACGTGCAACTGGAGAGTTCATCAAGGATGGGGATGATGCAAATAAGCTAAACC
  ||     |  || |     || | |||   | |    |  |||   |||| | |   |||   |||  |  |    |  || |  |       ||| ||||| |||||||| || |||||||||||  | || ||||||||  |||| |||||||||||||| |||| |||||| | | | ||||| || || || ||||
--ttctccatttttaaagaaagatggcaaaagtatataatggcatgttatgtttatttcttttggtctgtagatgagcttactgatgataaatttctttcagGGAATGAGTCAACTTGAGTTGGAAGACCAGGTACAAGATGACCTAAAGCGTGCAACTGGAGAATTCACCAAGGACGAGAACGATGCTAACAAACTTAACC

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|110706436|gb|EE081959.1|EE081959
EST:     ATGCCCAGCCAGATGACCTCATTGACTTTTACCATTTAAAGAGCAGGAAG                         GGCATGAGTCAGCTGGAGTTGGAAGATGAAGTCCAAGATGATTTAAAACGT
genomic: ATGCCCAGCCAGATGACCTCATTGACTTTTACCATTTAAAGAGCAGGAAGgtaagaaaac ... caacttccagGGCATGAGTCAGCTGGAGTTGGAAGATGAAGTCCAAGATGATTTAAAACGT
EST: gi|110688733|gb|EE067621.1|EE067621
EST:     ATGCCCAGCCAGATGACCTCATTGACTTTTACCATTTAAAGAGCAGGAAG                         GGCATGAGTCAGCTGGAGTTGGAAGATGAAGTCCAAGATGATTTAAAACGT
genomic: ATGCCCAGCCAGATGACCTCATTGACTTTTACCATTTAAAGAGCAGGAAGgtaagaaaac ... caacttccagGGCATGAGTCAGCTGGAGTTGGAAGATGAAGTCCAAGATGATTTAAAACGT
EST: gi|110703886|gb|EE081212.1|EE081212
EST:     ATGCCCAGCCAGATGACCTCATTGACTTTTACCATTTAAAGAGCAGGAAG                         GGCATGAGTCAGCTGGAGTTGGAAGATGAAGTCCAAGATGATTTAAAACGT
genomic: ATGCCCAGCCAGATGACCTCATTGACTTTTACCATTTAAAGAGCAGGAAGgtaagaaaac ... caacttccagGGCATGAGTCAGCTGGAGTTGGAAGATGAAGTCCAAGATGATTTAAAACGT
EST: gi|110356586|gb|EC919522.1|EC919522
EST:     TGCCCAGCCAGATGACCTCATTGACTTTTACCATTTAAAGAGCAGGAAG                         GGCATGAGTCAGCTGGAGTTGGAAGATGAAGTCCAAGATGATTTAAAACGT
genomic: TGCCCAGCCAGATGACCTCATTGACTTTTACCATTTAAAGAGCAGGAAGgtaagaaaac ... caacttccagGGCATGAGTCAGCTGGAGTTGGAAGATGAAGTCCAAGATGATTTAAAACGT
EST: gi|18458012|gb|BM436290.1|BM436290
EST:     ATGCCCAGCCAGATGACCTCATTGACTTTTACCATTTAAAGAGCAGGAAG                         GGCATGAGTCAGCTGGAGTTGGAAGATGATGTCCAAGATGATTTAAAACGT
genomic: ATGCCCAGCCAGATGACCTCATTGACTTTTACCATTTAAAGAGCAGGAAGgtaagaaaac ... caacttccagGGCATGAGTCAGCTGGAGTTGGAAGATGAAGTCCAAGATGATTTAAAACGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatgtgtgtgatttaaatctccactttgtttccctaactagcttcaacttccagGGCATGAGTCAGCTGGAGTTGGAAGATGAAGTCCAAGATGATTTAAAACGTGCAACTGGAGAGTTCATCAAGGATGGGGATGATGCAAATAAGCTAAACC
                                ccctaac  putative branch site (score: 2)
                                                cttcc  putative PPT
         tgatttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tatttattttcctttatctttgaggtcaaggttttggtttttcatagatgtgtgtgatttaaatctccactttgtttccctaactagcttcaacttccagGGCATGAGTCAGCTGGAGTTGGAAGATGAAGTCCAAGATGATTTAAAACGTGCAACTGGAGAGTTCATCAAGGATGGGGATGATGCAAATAAGCTAAACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - -gtgtgtg