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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcacaagctgccacatgtttacagtttgtcttcatttattttattgttcttgatcattgctatattgtccgactgctacctttttttgctgcagATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGATGAAGTAGATGCCATAGGGGGTGCGCGTTTTGATGATGGTGTTGGTGGGGACAATGAGGTCC

Basic information

species Vitis vinifera
transcript Vv09s0002g00170.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G181359_T01 (Zea mays), 3'ss of exon 7
gt-cacaagctgccacatgtttacagtttgtcttcatttattttattgttcttgatcattgctatattgtccgactgctacctttttttgctgcagATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGATGAAGTAGATGCCATAGGGGGTGCGCGTTTTGATGATGGTGTTGGTGGGGACAATGAGGTCC
||  | |    ||      | |  |  |  | | |   | ||||  ||| | || |  |    ||||| || ||    |   || || |   | ||||||| ||||| || |||||||| ||||| || || |||||||| ||||| || || ||||| |||||||||||||| || ||||| ||||||||||| |
gtatatatatggctgtgaatctgtaaatattatcccagtcttttcatgtacgtg-tgttcaacatatt-tctga--aatgaattcttctatggtagATGGCCCGCTCAAAGAAAGCGTGCATTGTATTCTTCGATGAAGTTGATGCTATTGGTGGTGCTCGTTTTGATGATGGGGTGGGTGGCGACAATGAGGTGC

upper sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G110185_T03 (Zea mays), 3'ss of exon 7
gtcacaagctgccacatgtttacagtttgtcttcatttattttattgttcttgatcattgctatattgtccgactgctacctttttttgctgcagATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGATGAAGTAGATGCCATAGGGGGTGCGCGTTTTGATGATGGTGTTGGTGGGGACAATGAGGTCC
          ||      |    |    ||  ||||  | ||| ||         |||    ||||| || ||     |   | || |  || ||||||| ||||| || || || || ||||| || ||||||||||| ||||| || || ||||| |||||||||||||| |||||||| ||||||||||| |
---------ggctgtgaatccgtaaaaggt--tcatccagtttttttcctgcacacatgttaatatt-tctga--aacaaaatattctattgtagATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCAATTGGTGGTGCTCGTTTTGATGATGGGGTTGGTGGTGACAATGAGGTGC

upper sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G110185_T01 (Zea mays), 3'ss of exon 7
----gtcacaagctgccacatgtttacagtttgtcttcatttattttattgttcttgatcattgctatattgtccgactgctacctttttttgctgcagATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGATGAAGTAGATGCCATAGGGGGTGCGCGTTTTGATGATGGTGTTGGTGGGGACAATGAGGTCC
     ||    ||||  | ||   || |   |   | || || ||||  ||  |     |||    ||||| || ||     |   | || |  || ||||||| ||||| || || || || ||||| || ||||||||||| ||||| || || ||||| |||||||||||||| |||||||| ||||||||||| |
gtatatctagggctgtga-atccgtaaaaggttcatccagtttttttcctgcaca----catgttaatatt-tctga--aacaaaatattctattgtagATGGCCCGCTCAAAGAAGGCATGCATTGTATTCTTTGATGAAGTTGATGCAATTGGTGGTGCTCGTTTTGATGATGGGGTTGGTGGTGACAATGAGGTGC

upper sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA03G42370.4 (Glycine max), 3'ss of exon 7
gtcacaagctgccacatgtttacagtttgtcttcatttattttattgttcttgatcattgctatattgtccgactgctacctttttttgctgcagATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGATGAAGTAGATGCCATAGGGGGTGCGCGTTTTGATGATGGTGTTGGTGGGGACAATGAGGTCC------------------
|| |   |||   |      | |  ||| | || || | |||  |||||             || |  || ||||   |  |  | |  ||  ||||||| ||||| || || || || |||||||||||||||||||| ||||| || |||||||| || |||||||||||||||||||| || |||||||| |                  
gtgaatggctaagatgcaccttctatttatttt-atatttttcgttgtttcca--tgacatgatttcatctgactaaaatttgatgtc-ctctagatggcccgctctaagaagGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGTGGTGATAATGAGGTTCAGCGCACTATGCTTGAAA

upper sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA03G42370.2 (Glycine max), 3'ss of exon 7
gtcacaagctgccacatgtttacagtttgtcttcatttattttattgttcttgatcattgctatattgtccgactgctacctttttttgctgcagATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGATGAAGTAGATGCCATAGGGGGTGCGCGTTTTGATGATGGTGTTGGTGGGGACAATGAGGTCC
|| |   |||   |      | |  ||| | || || | |||  |||||             || |  || ||||   |  |  | |  ||  ||||||| ||||| || || || || |||||||||||||||||||| ||||| || |||||||| || |||||||||||||||||||| || |||||||| |
gtgaatggctaagatgcaccttctatttatttt-atatttttcgttgtttcca--tgacatgatttcatctgactaaaatttgatgtc-ctctagATGGCCCGCTCTAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGTGGTGATAATGAGGTTC

upper sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA16G01810.1 (Glycine max), 3'ss of exon 7
gtcacaagctgccacatgtttacagtttgtcttcatttattttattgtt-cttgatcattgctatattgtccgactgctacctttttttgctgcagATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGATGAAGTAGATGCCATAGGGGGTGCGCGTTTTGATGATGGTGTTGGTGGGGACAATGAGGTCC
             | ||   ||     || ||||     ||| || |||  ||         |  ||  |  ||||   |  || | |   || ||||||| || || || || || || |||||||||||||||||||| ||||| || || ||||| || |||||||||||||||||||| ||||||||||| |
-----------gtaaatacataagacgtgccttctagcttttgatcgttgtttccatgaaattcaatcatttgactaaaattttatctc-ttgtagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGAGGTGCACGATTTGATGATGGTGTTGGTGGTGACAATGAGGTTC

upper sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA07G05220.1 (Glycine max), 3'ss of exon 7
gtcacaagctgccacatgtttacagtttgtcttcatttattttattgttcttgatcattgctatattgtccgactgctacctttttttgctgcagATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGATGAAGTAGATGCCATAGGGGGTGCGCGTTTTGATGATGGTGTTGGTGGGGACAATGAGGTCC
     ||  |||   |   |     | |  |||  ||| | | ||||||       |    || ||  |  ||||   |  || |  |  |  ||||||| || || || || || || |||||||||||||||||||| ||||| || || ||||| || ||||||||||| |||||||| ||||||||||| |
---gtaaaatgcacaagactcgtcctctagcttttttt-tatcattgtttccatgaa--aataaatcatttgactaaaattttctcatttt-tagATGGCTCGTTCAAAGAAGGCATGCATTGTGTTTTTTGATGAAGTTGATGCAATTGGAGGTGCACGATTTGATGATGGCGTTGGTGGTGACAATGAGGTTC

upper sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA19G45140.1 (Glycine max), 3'ss of exon 7
gtcacaagctgccacatgtttacagtttgtcttcatttattttattgtt-cttgatcattgctatattgtccgactgctacctttttttgctgcagATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGATGAAGTAGATGCCATAGGGGGTGCGCGTTTTGATGATGGTGTTGGTGGGGACAATGAGGTCC
|| | ||  || |  |  |  ||  ||| | |  |||| ||||   |||  ||          || |  ||  |||   |  || | |  ||  ||||||| || || || || || || ||||||||||| |||||||| ||||| || |||||||| || ||||||||||||||||| || || |||||||| |
gtgagaa--tggctaagatgcactttttttttaaattttttttcccgttatttccatgacatgatttcatcgaactaaaattttatgtc-ctctagATGGCCCGTTCAAAGAAGGCATGCATTGTGTTTTTCGATGAAGTTGATGCAATTGGGGGTGCACGGTTTGATGATGGTGTTGGCGGTGATAATGAGGTTC

upper sequence: Vv09s0002g00170.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S49_256V6.1 (Physcomitrella patens), 3'ss of exon 7
--------gtcacaagctgccacatgttta-cagtttgtcttcatttattttattgttcttgatcattgctatattgtccgactgctacctttttttgctgcagATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGATGAAGTAGATGCCATAGGGGGTGCGCGTTTTGATGATGGTGTTGGTGGGGACAATGAGGTCC
        ||          || | | | |  | | ||| ||||  |    || | |   || | || |   |    |  |  |       || |  ||   ||||||| || || || |||||||| ||||||||||||||||| ||||||||||| || ||||| ||||| || |||||  | || || || || ||||| |
ccgccagtgtattgtttactcaaacgctaagtactgtgtattcacgtggcctact-tcgatgcttatcgtggtgcgatttgtttatggaacttgtgagc---agATGGCCCGTTCAAAGAAAGCGTGCATTGTGTTTTTTGATGAGGTAGATGCCATTGGAGGTGCTCGTTTCGACGATGGGTTGGGAGGTGATAACGAGGTTC

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|351055270|gb|FQ441868.1|FQ441868
EST:     TTCAGAAATACGTTGGCGAGGGGGCTAGGATGGTTCGTGAACTATTTCAG                         ATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTG
genomic: TTCAGAAATACGTTGGCGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtcacaagct ... tttgctgcagATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTG
EST: gi|110381635|gb|EC934981.1|EC934981
EST:     TTCAGAAATACGTTGGCGAGGGGGCTAGGATGGTTCGTGAACTATTTCAG                         ATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGATGAAGTAGATGCC
genomic: TTCAGAAATACGTTGGCGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtcacaagct ... tttgctgcagATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGATGAAGTAGATGCC
EST: gi|161712408|gb|FC061713.1|FC061713
EST:     TTCAGAAATACGTTGGCGAGGGGGCTAGGATGGTTCGTGAACTATTTCAG                         ATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGATGAAGTAGATGCC
genomic: TTCAGAAATACGTTGGCGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtcacaagct ... tttgctgcagATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGATGAAGTAGATGCC
EST: gi|110722901|gb|EE099603.1|EE099603
EST:     TTCAGAAATACGTTGGCGAGGGGGCTAGGATGGTTCGTGAACTATTTCAG                         ATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGATGAAGTAGATGCC
genomic: TTCAGAAATACGTTGGCGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtcacaagct ... tttgctgcagATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGATGAAGTAGATGCC
EST: gi|294966728|gb|GW837747.1|GW837747
EST:     TTCAGAAATACGTTGGCGAGGGGGCTAGGATGGTTCGTGAACTATTTCAG                         ATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGATGAAGTAGATGCC
genomic: TTCAGAAATACGTTGGCGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtcacaagct ... tttgctgcagATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGATGAAGTAGATGCC
EST: gi|71877945|gb|DT027000.1|DT027000
EST:     TTCAGAAATACGTTGGCGAGGGGGCTAGGATGGTTCGTGAACTATTTCAG                         ATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGATGAAGTAGATGCC
genomic: TTCAGAAATACGTTGGCGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtcacaagct ... tttgctgcagATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGATGAAGTAGATGCC
EST: gi|351038545|gb|FQ464411.1|FQ464411
EST:     TTCAGAAATACGTTGGCGAGGGGGCTAGGATGGTTCGTGAACTATTCCAG                         ATGGCACGCTCCAAAAA-GCGTGT
genomic: TTCAGAAATACGTTGGCGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtcacaagct ... tttgctgcagATGGCACGCTCCAAAAAAGCGTGT
EST: gi|110424138|gb|EC990494.1|EC990494
EST:     TTCAGAAATACGTTGGCGAGGGGGCTAGGATGGTTCGTGAACTATTTCAG                         ATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGATGAAGTAGATGCC
genomic: TTCAGAAATACGTTGGCGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtcacaagct ... tttgctgcagATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGATGAAGTAGATGCC
EST: gi|71878819|gb|DT027874.1|DT027874
EST:     TTCAGAAATACGTTGGCGAGGGGGCTAGGATGGTTCGTGAACTATTTCAG                         ATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGATGAAGTAGATGCC
genomic: TTCAGAAATACGTTGGCGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtcacaagct ... tttgctgcagATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGATGAAGTAGATGCC
EST: gi|33404439|gb|CF210066.1|CF210066
EST:     TTCAGAAATACGTTGGCGAGGGGGCTAGGATGGTTCGTGAACTATTTCAG                         ATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGACGAAGTAGATGCC
genomic: TTCAGAAATACGTTGGCGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtcacaagct ... tttgctgcagATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGATGAAGTAGATGCC
EST: gi|161710784|gb|FC059861.1|FC059861
EST:     TTCAGAAATACGTTGGCGATGGGGCTAGGATGGTTCGTGAACTATTTCAG                         ATGGCACGCTCCAAAAAA
genomic: TTCAGAAATACGTTGGCGAGGGGGCTAGGATGGTTCGTGAACTATTTCAGgtcacaagct ... tttgctgcagATGGCACGCTCCAAAAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttattgttcttgatcattgctatattgtccgactgctacctttttttgctgcagATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGATGAAGTAGATGCCATAGGGGGTGCGCGTTTTGATGATGGTGTTGGTGGGGACAATGAGGTCC
        tcttgat  putative branch site (score: 4)
                                 ctgctaccttttttt  putative PPT
                                         ttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcacaagctgccacatgtttacagtttgtcttcatttattttattgttcttgatcattgctatattgtccgactgctacctttttttgctgcagATGGCACGCTCCAAAAAAGCGTGTATTGTGTTTTTTGATGAAGTAGATGCCATAGGGGGTGCGCGTTTTGATGATGGTGTTGGTGGGGACAATGAGGTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG