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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatattttctttctttcttctttgatttattttatatgcttggaagtttcttttttattttctttttattttaatattgttatgtttcatgtggatcagATGAGAAAATAGCATTGCTGGGTGCAATACAGTCTCTATTTGAAGGTTCAATGTACACATTTGTGTTCCTTTGGACTCCTGCTTTGAGTCCGAATGAAGA

Basic information

species Vitis vinifera
transcript Vv02s0025g02420.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os10g37520.1 (Oryza sativa), 3'ss of exon 4
atatattttctttctttcttctttgatttattttatatgcttggaagtttcttttttattttctttttatttta--atattgttatgtttcatgtgga---tcagATGAGAAAATAGCATTGCTGGGTGCAATACAGTCTCTATTTGAAGGTTCAATGTACACATTTGTGTTCCTTTGGACTCCTGCTTTGAGTCCGAATGAAGA
          |   ||| |  | |     ||   | | |     | |||| |||     ||| |||||||||||  ||||      ||||| | || |   |||||||| || || |||||||| || || |||||||| || ||||| |||||||||||||| ||||| ||||| ||||||||||||||||| || ||||| ||
---------gtagatttatcatgtccaccatagcaaagggcataatgtttttttaaatatttttttttattttaacatatcaaatggtttcttttgaaatttcagATGAAAAGATTGCATTGCTTGGAGCTATACAGTCACTGTTTGAGGGTTCAATGTACACTTTTGTTTTCCTGTGGACTCCTGCTTTGAGCCCAAATGATGA

upper sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G021514_T01 (Zea mays), 3'ss of exon 3
atatattttctttctttcttctttgatttattttatatgcttggaagtttcttttttattt-tctttttattttaatattgttatgtttcatgtggatcagATGAGAAAATAGCATTGCTGGGTGCAATACAGTCTCTATTTGAAGGTTCAATGTACACATTTGTGTTCCTTTGGACTCCTGCTTTGAGTCCGAATGAAGA
   |||  |    |  |||  |  || |        ||      |  |   | |   |  | | |||   || |||   |||    ||| || |   |||||||| || || ||||| ||||| || ||||||||  | ||||| || || |||||||||||||| ||||| |||||||| || |||||||| ||||||||
--gtatgcttaacccatctcatcagactg----cgcataaccaaatatgcatatgaaacctgtgtttgccttctaacgctgtc-catttgatct---tcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA

upper sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G064563_T03 (Zea mays), 3'ss of exon 4
atatattttctttctttcttctttgatttattttatatgcttggaagtttcttttttattt-tctttttattttaatattgttatgtttcatgtggatcagATGAGAAAATAGCATTGCTGGGTGCAATACAGTCTCTATTTGAAGGTTCAATGTACACATTTGTGTTCCTTTGGACTCCTGCTTTGAGTCCGAATGAAGA
   |||  |    |  |||  |  || |        ||      |  |   | |   |  | | |||   || |||   |||    ||| || |   |||||||| || || ||||| ||||| || ||||||||  | ||||| || || |||||||||||||| ||||| |||||||| || |||||||| ||||||||
--gtatgcttaacccatctcatcagactg----cgcataaccaaatatgcatatgaaacctgtgtttgccttgtaacgctgtc-catttgatct---tcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCCATGTACACATTTGTCTTCCTATGGACTCCAGCATTGAGTCCAAATGAAGA

upper sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G077669_T01 (Zea mays), 3'ss of exon 4
atatattttctttctttcttctttgattta---ttttatatgcttggaagtttcttttttattttctttttattttaatattgttatgtttcatgtggatcagATGAGAAAATAGCATTGCTGGGTGCAATACAGTCTCTATTTGAAGGTTCAATGTACACATTTGTGTTCCTTTGGACTCCTGCTTTGAGTCCGAATGAAGA
 |||  |||    | |         |   |       | ||  ||     | |      |   ||  ||||    ||| || ||     |  || |   |||||||| || || ||||| ||||| || ||||||||  | ||||| || || |||||||||||||| ||||| |||||||| || ||||| || ||||||||
gtatgctttagcccgtctcatcagaacgcagagaaccaaatatttatgcatatgaaacctgcatttgtttt---ctaacatcgtc-cactggatct---tcagATGAAAAGATTGCATTACTGGGAGCCATACAGTCATTGTTTGAGGGCTCGATGTACACATTTGTCTTCCTATGGACTCCAGCGTTGAGCCCAAATGAAGA

upper sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA04G41090.1 (Glycine max), 3'ss of exon 4
atatattttctttctttcttctttgatttattttatatgcttggaagtttcttttttattttctttttattttaata--ttgttatgtttcatgtggatcagATGAGAAAATAGCATTGCTGGGTGCAATACAGTCTCTATTTGAAGGTTCAATGTACACATTTGTGTTCCTTTGGACTCCTGCTTTGAGTCCGAATGAAGA
 | |  ||   |  | | || ||| ||| || |  | | |||| |   || ||  |  | | |||   |  || ||   ||  ||  ||   ||||  |||||||| |||||||| ||||||||||| ||||||||||| |||||||||||||||||||| |||||||| || ||||||||||| ||||| || ||||| ||
-tcttattctgtgatcttttattttattcatctcttgt-cttgtattcttgttcatattgtacttcccaagttcattgtttactacattctttgtgcttcagATGAAAAAATAGCCTTGCTGGGTGCTATACAGTCTCTCTTTGAAGGTTCAATGTACACCTTTGTGTTTCTGTGGACTCCTGCATTGAGCCCAAATGATGA

upper sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA06G13760.2 (Glycine max), 3'ss of exon 4
atatattttctttctttcttctttgatttattttatatgcttggaagtttcttttttattttctttttattttaatat--tgttatgtttcatgtggatcagATGAGAAAATAGCATTGCTGGGTGCAATACAGTCTCTATTTGAAGGTTCAATGTACACATTTGTGTTCCTTTGGACTCCTGCTTTGAGTCCGAATGAAGA
   |||| | ||    | |  ||| ||| || |  | | |||| |   || ||  |  | | |||   |  || || |  |  |   ||   | ||  |||||||| || ||||| ||||||||||| ||||||||||| |||||||||||||||||||| |||||||| || ||||||||||| ||||| || ||||| ||
-cttattctgttatcatttatttttattcatctcttgt-cttgtattcttgttcatattgtacttcccaagttcattttttactgcattctttctgcctcagATGAAAAGATAGCCTTGCTGGGTGCCATACAGTCTCTCTTTGAAGGTTCAATGTACACCTTTGTGTTTCTATGGACTCCTGCATTGAGCCCAAATGATGA

upper sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT4G27720.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------------------------atatattttctttctttcttctttgatttattttatatgcttggaagtttcttttttattttcttttt------at-tttaatattgttatgtttcatgtg-----gatcagATGAGAAAATAGCATTGCTGGGTGCAATACAGTCTCTATTTGAAGGTTCAATGTACACATTTGTGTTCCTTTGGACTCCTGCTTTGAGTCCGAATGAAGA
                                | || || || | || ||||| || | |||| |    | |  |   ||| ||| | ||| || |  |      || | | ||  |   |   ||  |||       |||||||||||| |||||| |  ||||||| || ||||| || |||||||| || ||||| || ||||| ||||| |||||||||||| | |||||||| || ||
gtgagtagaaaatcttgttgccccttttagattttacttcctgttttgcttctctg-tctattgtgatggttctgtgttttgtttctcattgtcctcattgaagaatgtatgatggtaacaaaatttttgtatcttttatcagATGAGAAGATAGCACTATTGGGTGCTATCCAGTCGCTCTTTGAAGGATCTATGTATACTTTTGTATTCCTCTGGACTCCTGCTCTAAGTCCGAACGATGA

upper sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G49310.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------------------------------atatattttctttctttcttctttgatttattttata-tgcttggaagtttcttttttattttctttttattttaatattgt-tatgtttcatgtggatcagATGAGAAAATAGCATTGCTGGGTGCAATACAGTCTCTATTTGAAGGTTCAATGTACACATTTGTGTTCCTTTGGACTCCTGCTTTGAGTCCGAATGAAGA
                                     |    | |   |    |||   |  ||| ||   ||  ||| |  |  |      | | ||| ||  |   | ||| |   | |||| ||  |     |||||||| || || ||||||||||| || || ||||||||||| ||||  || |||||||| ||||| ||||| ||||| || ||| | || || || || ||
gcaggttcaaagttagcgttaaaactgttgattcaaaaggcttctcaatatactctgtctccattcatcccatcctgcatttatttgcaagctatgtttcctcatctctctaacacaatctatgattatttc---tcagATGAAAAGATTGCATTGCTGGGCGCTATTCAGTCTCTATTCGAAGCCTCGATGTACACCTTTGTTTTCCTCTGGACACCAGCTCTTAGCCCAAACGATGA

upper sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S8_271V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------------------------------------------------------------atatattttctttctttcttctttgat-ttattttatatgcttggaagtttcttttttattttctttttattttaatattgttatgtttcatgtggatcagATGAGAAAATAGCATTGCTGGGTGCAATACAGTCTCTATTTGAAGGTTCAATGTACACATTTGTGTTCCTTTGGACTCCTGCTTTGAGTCCGAATGAAGA
                                                                           |  |  ||  |   | ||  |||| |  |    |  | | || ||  |             ||    |  |    | |  || |||  |        |||||||||| |||||  |  ||||||| || |||||| | ||||| || || |||||||||||||||||||| ||||| || || ||||| || || ||  |
gtaagattgatgagttgtagacatatttcaagctctgactgattcatacttacgaccaaacatagttctgaaagtttcaaattaatgtgtgctcgtttggtactgagatggaggatttgagatcagccaaagtaagtcacgatgctgggttgtgattgtgtcactgaattcgcagATGAGAAGATAGCCCTTTTGGGTGCCATCCAGTCTTTGTTTGAGGGCTCCATGTACACATTTGTGTTCCTCTGGACACCAGCCTTGAGCCCCAACGATCA

upper sequence: Vv02s0025g02420.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: PP1S18_8V6.2 (Physcomitrella patens), 3'ss of exon 4
-----------------------------------------------------------------------atatattttctttctttcttct-ttgatttattttatatgctt------gg----aagtttct--tttttattttctttttattttaatatt-gttatgtttcatgtggatcagATGAGAAAATAGCATTGCTGGGTGCAATACAGTCTCTATTTGAAGGTTCAATGTACACATTTGTGTTCCTTTGGACTCCTGCTTTGAGTCCGAATGAAGA
                                                                       | |  | || ||||| || | | || | |||  |  | |||||      ||    |||||  |    | ||     | || ||| |  | |   || ||| |   |     |||||||||| || || ||| ||||||| || ||||| || |||||||| || ||||| || ||||| ||||||||||| || || ||||| || || ||  |
gtgagaacttaagtgcttatggacgagtttcaagacatttgcacttcattctcgcggtcaaatgaggttgcaaaggtcttgtttctatcatttatttacttaagtactgtgcttttgttcggcaccaagttcgtggcatgtaggaattcttaattctggtctccattgtgtctttggattgacagATGAGAAGATTGCTTTGTTGGGTGCCATCCAGTCCCTGTTTGAAGGATCCATGTATACGTTTGTATTCCTTTGGACACCAGCCTTGAGCCCTAACGATCA

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|351042244|gb|FQ442711.1|FQ442711
EST:     CAAGGACTTGCTTACGCAATTTAAGGGTGCTGCTGTAGCTATTGCATCTG                         ATGAGAAAATAGCATTGCTGGGTGCAATACAGTCTCTA
genomic: CAAGGACTTGCTTATGCAATTTAAGGGTGCTGCTGTAGCTATTGCATCTGgtgcatttct ... tgtggatcagATGAGAAAATAGCATTGCTGGGTGCAATACAGTCTCTA
EST: gi|33405724|gb|CF211351.1|CF211351
EST:     CAAGGACTTGCTTACGCAATTTAAGGGTGCTGCTGTAGCTATTGCATCTG                         ATGAGAAAATAGCATTGCTGGGTGCAATACAGTCTCTATTTGAAGGATCAA
genomic: CAAGGACTTGCTTATGCAATTTAAGGGTGCTGCTGTAGCTATTGCATCTGgtgcatttct ... tgtggatcagATGAGAAAATAGCATTGCTGGGTGCAATACAGTCTCTATTTGAAGGTTCAA
EST: gi|110361276|gb|EC924740.1|EC924740
EST:     AAGGACTTGCTTACGCAATTTAAGGGGTGCTGCTGTAGCTATTGCATCTG                         ATGAGAAAATAGCATTGCTGGGTGCAATACAGTCTCTATTTGAAGGTTCAA
genomic: AAGGACTTGCTTATGCAATTTAA-GGGTGCTGCTGTAGCTATTGCATCTGgtgcatttct ... tgtggatcagATGAGAAAATAGCATTGCTGGGTGCAATACAGTCTCTATTTGAAGGTTCAA
EST: gi|351053919|gb|FQ441685.1|FQ441685
EST:     CAAGGACTTGCTTACGCAATTTAAGGGTGCTGCTGTAGCTATTGCATCTG                         ATGAGAAAATAGCATTGCTGGGTGCAATACAGTCTTCTATTT
genomic: CAAGGACTTGCTTATGCAATTTAAGGGTGCTGCTGTAGCTATTGCATCTGgtgcatttct ... tgtggatcagATGAGAAAATAGCATTGCTGGGTGCAATACAGTCT-CTATTT
EST: gi|110708440|gb|EE085985.1|EE085985
EST:     CAAGGACTTGCTTATGCAATTTAAGGGTGCTGCTGTAGCTATTGCATCTG                         ATGAGAAAATAGCATTGCTGGGTGCAATACAGTCTCTATTTGAAGGTTCAA
genomic: CAAGGACTTGCTTATGCAATTTAAGGGTGCTGCTGTAGCTATTGCATCTGgtgcatttct ... tgtggatcagATGAGAAAATAGCATTGCTGGGTGCAATACAGTCTCTATTTGAAGGTTCAA
EST: gi|351038992|gb|FQ457667.1|FQ457667
EST:     CAAGGACTTGCTTACGCAATTTAAGGGTGCTGCTGTAACTATTGCATCTG                         ATAAGAAAATA
genomic: CAAGGACTTGCTTATGCAATTTAAGGGTGCTGCTGTAGCTATTGCATCTGgtgcatttct ... tgtggatcagATGAGAAAATA
EST: gi|161718597|gb|FC068198.1|FC068198
EST:     CAAGGACTTGCTTACGCAATTTAAGGGTGCTGCTGTAGCTATTGCATCTG                         ATGAGAAAATAGCATTGCTGGGTGCAATACAGTCTCTATTTGAAGGTTCAA
genomic: CAAGGACTTGCTTATGCAATTTAAGGGTGCTGCTGTAGCTATTGCATCTGgtgcatttct ... tgtggatcagATGAGAAAATAGCATTGCTGGGTGCAATACAGTCTCTATTTGAAGGTTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtttcttttttattttctttttattttaatattgttatgtttcatgtggatcagATGAGAAAATAGCATTGCTGGGTGCAATACAGTCTCTATTTGAAGGTTCAATGTACACATTTGTGTTCCTTTGGACTCCTGCTTTGAGTCCGAATGAAGA
                        ttttaat  putative branch site (score: 3)
      ttttttattttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatattttctttctttcttctttgatttattttatatgcttggaagtttcttttttattttctttttattttaatattgttatgtttcatgtggatcagATGAGAAAATAGCATTGCTGGGTGCAATACAGTCTCTATTTGAAGGTTCAATGTACACATTTGTGTTCCTTTGGACTCCTGCTTTGAGTCCGAATGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - -tgcttgg