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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttttttgttgggatttttttgtgtgttttttttaaggatttaatttgggttttttgtcattgtgttttgttccagGATGATGAGTGATTATAAGGTGGAGATGGTGAATGATGGCATGCAAGAGTTCTATGTCGATTTCCATGGACCCGGTGACA

Basic information

species Vitis vinifera
transcript Vv02s0025g00070.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g00070.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os10g31000.1 (Oryza sativa), 3'ss of exon 1
--------------------------------------------------------------------------------------------gtaagtttttttgt------tgggatttttttgtgtgttttttttaag--gatttaatttgggttttttgtcattgtgttttgttccagGATGATGAGTGATTATAAGGTGGAGATGGTGAATGATGGCATGCAAGAGTTCTATGTCGATTTCCATGGACCCGGTGACA
                                                                                            ||    |   | ||      ||   | || |||| |||| ||||   |  |     ||| ||| ||||  |  ||   | ||||| |||||||||||| || || ||||||||||||||||| ||||| ||||| |||||||  || || ||||  || ||   ||| |
gtgaggatcttgtcctttatttatttattttttttggggggggggggggtggaattgtgtttttgcccggtttgattcttttctttctattggtggtctccatcgtctaatctgatgtgttgttgtttgttgttttgggggtggggggattggggattttcttggtttcttgttgttgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTCGTGGAATTCCGGGGGCCTACTGAAA

upper sequence: Vv02s0025g00070.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AC149818.2_FGT006 (Zea mays), 3'ss of exon 1
---------gtaagtttttttgttgggatttttttgtgtgttttttttaaggatt---taatttgggttttttgtcattgtgttttgttccagGATGATGAGTGATTATAAGGTGGAGATGGTGAATGATGGCATGCAAGAGTTCTATGTCGATTTCCATGGACCCGGTGACA
          |  |   | ||   | ||||||| | || | |||   |  |||||   | || || |||| |  |   |||   |   | |||||||||||| || || ||||||||||||||||| ||||| ||||| ||||||| ||| || || | ||| ||    || |
gtgaggattttgtggcgtgtttcggtgatttttctatgggatttcgatggggattccttgatctgcgtttctactggctgttgatgcctgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAGTTCTTTGTTGAATTTCGTGGGCCTAACGAAA

upper sequence: Vv02s0025g00070.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G053764_T01 (Zea mays), 3'ss of exon 1
-----------------------gtaagtttttttgttgggat------ttttttgtgtgttttttttaaggatttaatttgggttttttgtcattgtgtttt------gttccagGATGATGAGTGATTATAAGGTGGAGATGGTGAATGATGGCATGCAAGAGTTCTATGTCGATTTCCATGGACCCGGTGACA
                       ||  |||||    ||  |        | || ||  || |||||||   ||| |        ||    |   |  || |||      ||  |||||||||||| || || ||||||||||||||||| ||||| ||||| || ||||  ||||| ||| | || || |  || |
gtgaggatgctggacctctcttggtctgttttccaattctgcctgaccgtgttctgcttgcttttttttttgatctggccattcttgccggctttcttggtttatcggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA

upper sequence: Vv02s0025g00070.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G150867_T01 (Zea mays), 3'ss of exon 1
gtaagtttttttgttgggatttttttgtgtgttttttttaaggatt---taatttgggttttttgtcattgtgttttgttccagGATGATGAGTGATTATAAGGTGGAGATGGTGAATGATGGCATGCAAGAGTTCTATGTCGATTTCCATGGACCCGGTGACA
||    |  || | ||   ||||| | |  | |||   |  |||||   | || || |||| |  |   |||   |   | |||||||||||| || || |||||||| |||||||| ||||| ||||| ||||||| ||| || || | ||| ||    || |
gtggcgtgattcggtgat-tttttctataggatttcgatgcggattccttgatctgcgtttctactgcatgttgatgcctgcagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTTCTTTGTTGAATTTCGTGGGCCTAACGAAA

upper sequence: Vv02s0025g00070.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G150867_T02 (Zea mays), 3'ss of exon 1
gtaagtttttttgttgggatttttttgtgtgttttttttaaggattt-aatttgggttttttg----------tcattgtgttttg----ttccagGATGATGAGTGATTATAAGGTGGAGATGGTGAATGATGGCATGCAAGAGTTCTATGTCGATTTCCATGGACCCGGTGACA
|| ||  || | || ||  |  ||  |||  ||||| |  |||||||  ||  || ||  |||            | ||  | |||     | |||||||||||| || || |||||||| |||||||| ||||| ||||| ||||||| ||| || || | ||| ||    || |
gtgaggattctggt-ggcgtgattcggtgattttttctataggatttcgatgcggattccttgatctgcgtttctactgcatgttgatgcctgcagGATGATGAGCGACTACAAGGTGGATATGGTGAACGATGGGATGCAGGAGTTCTTTGTTGAATTTCGTGGGCCTAACGAAA

upper sequence: Vv02s0025g00070.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G053764_T03 (Zea mays), 3'ss of exon 1
gtaagtttttttgttgggattt------ttttgtgtgttttttttaaggatttaatttgggttttttgtcattgtgtttt------gttccagGATGATGAGTGATTATAAGGTGGAGATGGTGAATGATGGCATGCAAGAGTTCTATGTCGATTTCCATGGACCCGGTGACA
||  |||||    ||  |  |       || ||  || |||||||   ||| |        ||    |   |  || |||      ||  |||||||||||| || || ||||||||||||||||| ||||| ||||| || ||||  ||||| ||| | || || |  || |
gtctgttttccaattctgcctgaccgtgttctgcttgcttttttttttgatctggccattcttgccggctttcttggtttatcggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAA

upper sequence: Vv02s0025g00070.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G053764_T06 (Zea mays), 3'ss of exon 1
-----------------------gtaagtttttttgttgggattt------ttttgtgtgttttttttaaggatttaatttgggttttttgtcattgtgtttt------gttccagGATGATGAGTGATTATAAGGTGGAGATGGTGAATGATGGCATGCAAGAGTTCTATGTCGATTTCCATGGACCCGGTGACA--------------------
                       ||  |||||    ||  |  |       || ||  || |||||||   ||| |        ||    |   |  || |||      ||  |||||||||||| || || ||||||||||||||||| ||||| ||||| || ||||  ||||| ||| | || || |  || |                    
gtgaggatgctggacctctcttggtctgttttccaattctgcctgaccgtgttctgcttgcttttttttttgatctggccattcttgccggctttcttggtttatcggcgtcgcagGATGATGAGCGACTACAAGGTGGAGATGGTGAACGATGGGATGCAGGAATTCTTCGTCGAATTCAAGGGGCCGGCCGAAAGTAATAGCCCTCGCGCTGAA

upper sequence: Vv02s0025g00070.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S37_166V6.1 (Physcomitrella patens), 3'ss of exon 1
-------------gtaagtttttttgttgggatttttttg---tgtgttttttttaaggatttaatttg---ggttttttgtcattgtgttttgttccagGATGATGAGTGATTATAAGGTGGAGATGGTGAATGATGGCATGCAAGAGTTCTATGTCGATTTCCATGGACCCGGTGACA
              | | |||| ||||| | |||  |  |   || |   |    |||   ||  | |    |    ||    | |||||  |     |||||||||||||| || ||||| ||||||||||||||||| |||   || |||||||| || || ||||||||  |||| |
ggattgtgttgtgattacttttcttgttcgaattggtgcggtttggggaatcggcaagttgttgttgtatctgacgattcaagaatgtgtgattgggtagGATGATGAGTGACTACAAGGTCGAGATGGTGAATGATGGAATGAGCGAATTCTATGTGGAGTTTCATGGACCGCGTGAGA

upper sequence: Vv02s0025g00070.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ23672 (Selaginella moellendorffii), 3'ss of exon 1
----------------------------------------------------gtaagtttttttgttgggatttttttgtgtgttttttttaaggatttaatttgggttttttgtcattgtgttttgttccagGATGATGAGTGATTATAAGGTGGAGATGGTGAATGATGGCATGCAAGAGTTCTATGTCGATTTCCATGGACCCGGTGACA
                                                     | |      |   |    |   ||| |   | | |  |||    ||  ||    |||||  |     |   |  |||||||||||||||||| || |||||||||||||| || ||||| ||| | |||||  |||| || |||||||||||  | || |
gtgagtctcgcctcctctcgaatttcaattccttcttcgctctccagtggctatgaaaaacctctctttcttcgctttcttcctctctgctaattcattgcttcttctttttgcttcccattcctctttccagGATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATA

upper sequence: Vv02s0025g00070.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ34378 (Selaginella moellendorffii), 3'ss of exon 1
----------------------------------gtaagtttttttgttgggatttttttgtgtgttttttt---------taaggatttaatttgggttttttgtcattgtgttttgttccagGATGATGAGTGATTATAAGGTGGAGATGGTGAATGATGGCATGCAAGAGTTCTATGTCGATTTCCATGGACCCGGTGACA
                                   |  | | |   || |   | | ||| |  | ||| ||         |||    ||  ||    |||||  |     |   |  |||||||||||||||||| || |||||||||||||| || ||||| ||| | |||||  |||| || |||||||||||  | || |
gtgagtctcgcctcctctcgaatttcaattccttcttcgctctccagtggacctctctttcttcgctttcttcctctctgctaattcattgcttcttctttttgcttcccattcctctttccagGATGATGAGTGACTACAAGGTGGAGATGGTAAACGATGGGATGAACGAGTTTAATGTGGAGTTCCATGGACCTCGGGATA

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|77588071|gb|DV223245.1|DV223245
EST:     AGAATCATGTCATCCCCAAGCAAACGCAGAGAGATGGATTTGATGAAACT                         GATGATGAGTGATTATAAGGTGGAGATGGTGAATGATGGCATGCAAGAGTT
genomic: AGAATCATGTCATCCCCAAGCAAACGCAGAGAGATGGATTTGATGAAACTgtaagttttt ... tttgttccagGATGATGAGTGATTATAAGGTGGAGATGGTGAATGATGGCATGCAAGAGTT
EST: gi|349826284|gb|FQ416089.1|FQ416089
EST:     AGAATCATGTCATCCCCAAGCAAACGCAGAGAGATGGATTTGATGAAACT                         GATGATGAGTGATTATAAGGTGGAGATGGTGAATGATGGCATGCAAGAGTT
genomic: AGAATCATGTCATCCCCAAGCAAACGCAGAGAGATGGATTTGATGAAACTgtaagttttt ... tttgttccagGATGATGAGTGATTATAAGGTGGAGATGGTGAATGATGGCATGCAAGAGTT
EST: gi|71875288|gb|DT024343.1|DT024343
EST:     AGAATCATGTCATCCCCAAGCAAACGCAGAGAGATGGATTTGATGAAACT                         GATGATGAGTGATTATAAGGTGGAGATGGTGAATGATGGCATGCAAGAGTT
genomic: AGAATCATGTCATCCCCAAGCAAACGCAGAGAGATGGATTTGATGAAACTgtaagttttt ... tttgttccagGATGATGAGTGATTATAAGGTGGAGATGGTGAATGATGGCATGCAAGAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtgttttttttaaggatttaatttgggttttttgtcattgtgttttgttccagGATGATGAGTGATTATAAGGTGGAGATGGTGAATGATGGCATGCAAGAGTTCTATGTCGATTTCCATGGACCCGGTGACA
                 atttaat  putative branch site (score: 4)
                                            ttttgttcc  putative PPT
     ttttttttaaggattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttttttgttgggatttttttgtgtgttttttttaaggatttaatttgggttttttgtcattgtgttttgttccagGATGATGAGTGATTATAAGGTGGAGATGGTGAATGATGGCATGCAAGAGTTCTATGTCGATTTCCATGGACCCGGTGACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA