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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattaattttattttatttttgagtgagcttgagtggggctttttttatgcgtgtgcttatgtctcagttaatcaaactattttattatgtatattcttgtttgtcatatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATTCCCATGCTGGTTTGTGGCGATTTTAATTCAGTTCCTGGAAG

Basic information

species Vitis vinifera
transcript Vv08s0007g07020.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g07020.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os10g27230.2 (Oryza sativa), 3'ss of exon 7
gtaattaattttattttatttttgagtgagcttgagtggggctttttttatgcgtgtgcttatgtctcagttaatcaaactattttattatgtatattcttgtttgtcatatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATTCCCATGCTGGTTTGTGGCGATTTTAATTCAGTTCCTGGAAG
                       |  || ||     |     ||| |||||||  ||  || |||  ||  | |  |    |  ||   |  | |||   | ||||      |||||||| |||||| ||||||| ||||||||||||||||  ||||| |||||||| ||| |||| ||||| ||||| |||||||| ||||| ||
-----------------------gtctgtgcc---atcacattttctttatgctagt-tttgtgtaacatcttagaatttcagattgacac-tgtatggct-tttg------cagGTTCAAACTCTCCTAAAAGGGTTGGAAAAAATAGCTGTTAGTGCGGACATTCCAATGTTGGTCTGTGGGGATTTCAATTCAGTCCCTGGGAG

upper sequence: Vv08s0007g07020.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os03g07080.3 (Oryza sativa), 3'ss of exon 8
gtaattaattttattttatttttgagtgagcttgagtggggctttttttatgcgtgtgcttatgtctcagttaatcaaactattttattatgtatattcttgtttg---tcatatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATTCCCATGCTGGTTTGTGGCGATTTTAATTCAGTTCCTGGAAG
                             |   ||      || | |||  ||      |||         ||||     |   ||   |  | || |||| | ||   |  | ||||||| | || ||| |||||||||| ||||||||||||| |||||| |||||||| |||||||| ||||| ||||| ||| ||   ||||||||
-----------------------------gtcagatcataactctgttt--gcagaattttacagtatttctaattttcatgaattgacaattgtaatcttctatgaaattctttcagGTTAACACCCTCCTAAAAGGTTTAGAAAAAATAGCTGTCAGTGCGGACATTCCAATGCTGGTCTGTGGAGATTTCAATGCAACCCCTGGAAG

upper sequence: Vv08s0007g07020.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G124051_T01 (Zea mays), 3'ss of exon 8
gtaattaattttattttatttttgagtgagcttgagtggggctttttttatgcgtgtgcttatgtctcagttaatcaaactattttatt-atgtatattcttgtttgtca----tatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATTCCCATGCTGGTTTGTGGCGATTTTAATTCAGTTCCTGGAAG
                             | |  | |    |    |   |  || |  ||   |  || || || ||  | ||| | | ||| || |  | | |||  |    |  ||| ||||||| ||| ||||||| ||||||||||||||||  |||||||||||||| ||| |||| ||||| ||||||||||||  |||||||||
-----------------------------gttcaaatacttccccctccctctgtataatttcataacattttat-aatttctttaactgatgaatctcatggcttgcaaactcttgcagATTCATACCCTCCTAAAAGGGTTGGAAAAAATAGCTGTTAGTGCAGACATTCCAATGTTGGTCTGTGGAGATTTTAATTCAACTCCTGGAAG

upper sequence: Vv08s0007g07020.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G118467_T04 (Zea mays), 3'ss of exon 7
gtaattaattttattttatttttgagtgagcttgagtggggctttttttatgcgtgtgcttatg-tctcagttaatcaaactattttattatgtatattcttgtttgtcatatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATTCCCATGCTGGTTTGTGGCGATTTTAATTCAGTTCCTGGAAG
                                       | |  | |   | | |  |||  || |||| ||||    |  | ||  |  ||    ||   | | | |  |  ||||||||||| ||| ||||||| ||||| || ||||||| ||||||||||||||| ||| |||| ||||| ||||| || |||   ||||| ||
---------------------------------------gtccgtatgactacattcgctagtggtctctgttatctcattttttccaggataacaataactatgttttttcacagGTTCATACCCTCCTAAAAGGATTGGAGAAGATAGCTGTCAGTGCAGACATTCCTATGTTGGTCTGTGGAGATTTCAACTCAACCCCTGGGAG

upper sequence: Vv08s0007g07020.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G043509_T02 (Zea mays), 3'ss of exon 8
gtaattaattttattttatttttgagtgagcttgagtggggctttttttatgcgtgtgcttatg-tctcagttaatcaaactattttattatgtatattcttgtttgtcatatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATTCCCATGCTGGTTTGTGGCGATTTTAATTCAGTTCCTGGAAG
                                       | |  | |     | |  |||  || | || ||||    || | ||  |  ||  ||| |    |  ||  |  ||||||||||| ||||||||||| ||||| || ||||||| ||| ||||||||||| ||| |||| ||||| ||||| || ||    ||||| ||
---------------------------------------gtccgtatgaccacattcgctagtggtttctgttatctcaatt-ttccaggata-ataataccttcagtttttacagGTTCATACCCTCTTAAAAGGATTGGAGAAGATAGCTGTCAGCGCAGACATTCCTATGTTGGTCTGTGGAGATTTCAACTCGCCCCCTGGGAG

upper sequence: Vv08s0007g07020.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA09G15980.2 (Glycine max), 3'ss of exon 7
gtaattaattttattttatttttgagtgagcttgagtggggctttttttatgcgtgtgcttatgtctcag-ttaatcaaactattttattatgtatattcttgtttgtcatatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATTCCCATGCTGGTTTGTGGCGATTTTAATTCAGTTCCTGGAAG
                                 |        ||| |||| |  ||| | ||||  |||  ||  ||  |  |||  | | | ||  ||  |  |    || | |||||||||||||||||||||||||||||||||||||||| |||||||||||||| ||| |||||||||| ||||||||||||||||| |||||
---------------------------------gtaaattattttcttta-gtttgttcgtatgcatcaaattgttctgaacattacagtttctaattttctcct----attttagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCAAGTGCAGACATTCCGATGTTGGTTTGTGGAGATTTTAATTCAGTTCCGGGAAG

upper sequence: Vv08s0007g07020.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA02G26620.1 (Glycine max), 3'ss of exon 7
gtaattaattttattttatttttgagtgagcttgagtggggctttttttatgcgtgtgcttatgtctcag-ttaatcaaactattttattatgtatattcttgtttgtcatatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATTCCCATGCTGGTTTGTGGCGATTTTAATTCAGTTCCTGGAAG
                                                   |  ||| | ||||  |||| ||  |   |  |||  | | | || ||| |    | | |||   ||||||||||||||||||||| ||||||||||||||||| || ||||||||||| ||| |||||||||| ||||||||||||||||| |||||
---------------------------------------------------gtttgttcatatgcatcagattgttttgaacattacaatttcta-attttctcctattata---gGTTCATACTCTCTTAAAAGGGTTGGAAAAAATAGCTGCAAGCGCAGACATTCCGATGTTGGTTTGTGGAGATTTTAATTCAGTTCCAGGAAG

upper sequence: Vv08s0007g07020.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA19G39210.1 (Glycine max), 3'ss of exon 7
gtaattaattttattttatttttgagtgagcttgagtggggctttttttatgcgtgtgcttatgtctcagttaatcaaact--attttattatgtatattcttgtttgtcatatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATTCCCATGCTGGTTTGTGGCGATTTTAATTCAGTTCCTGGAAG
                                   ||  | | ||   | ||  ||| | |||    ||||      |  |  |   |   |  ||||   ||     || | | |||| || |||||||| ||||| ||||| ||||| |||||||||||||||||||| ||| |||||||||| || ||||||||| |||| |||||
-----------------------------------gtaagtcgttcgctttgtttgttcatattgaacagtgtgcttattttgaacatgacagttataaatttccccttctttttagGTGCACACTCTCTTGAAAGGATTGGAGAAAATTGCTGCCAGTGCAGACATTCCAATGTTGGTTTGTGGGGACTTTAATTCAATTCCAGGAAG

upper sequence: Vv08s0007g07020.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT3G58560.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaattaattttattttatttttgagtgagcttgagtggggctttttttatgcgtgtgcttatgtctcagttaatcaaactattttattatgtatattcttgtttgtcatatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATTCCCATGCTGGTTTGTGGCGATTTTAATTCAGTTCCTGGAAG
                          ||  ||| | |    ||  || ||   |    || |  | || | |  | | |  | | | | ||  ||| |  |  ||| |  |  ||||||| ||  | || || ||  |||| |||||||||||||||||||| ||||| ||||| || ||||| ||||| ||  |||| ||||  ||
------------------------gttggtctttattt---ctcattgtaaaagaactctcagatttcggattcttacatcactat-tgatccataatgattcttgcccaaatagGTTCACACATTATTGAAGGGACTGGAGAAAATAGCTGCCAGTGCAGATATTCCAATGCTTGTGTGTGGAGATTTCAACACAGTACCTGCGAG

upper sequence: Vv08s0007g07020.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: PP1S335_77V6.3 (Physcomitrella patens), 3'ss of exon 8
-----------------------------------------------------------------gtaattaattttattttat--ttttgagtgagcttgagtggggctttttttatgcgtgtgcttatgtctcagttaatca-----aactattttattatgtatatt--cttgtttgtcatatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATTCCCATGCTGGTTTGTGGCGATTTTAATTCAGTTCCTGGAAG
                                                                   ||   | |  || || |  |||| | |  ||||      |  |  |||    ||  |||| |  ||||   || ||      |||| ||  |||  | || |   |||| || |  | |||||| ||||||||| | |||||| | || || ||||| ||||| ||||||||||||||||||||   |||||||||||| || |||||||| ||
gtatgcagatcattctatcttcttggttcagatcgcagctccaattatgtgttgaagtataacgttcaaaccactggatgttgtgatttttactatgctttgtctagattaatttc---cgactgctgaattctctaatactcttgtataactgttcgattgaggatttgggcttgatttttgt-tcagGTACATACTCTCCTCAAAGGTCTTGAGAAGATAGCAGCCAGCGCAGACATTCCCATGCTGGTGGCTGGCGATTTTAACTCTGTTCCTGGCAG

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|349808434|gb|FQ405578.1|FQ405578
EST:     ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAG                         GTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATT
genomic: ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAGgtaattaatt ... gtcatatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATT
EST: gi|351051864|gb|FQ455278.1|FQ455278
EST:     ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAG                         GTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATT
genomic: ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAGgtaattaatt ... gtcatatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATT
EST: gi|351052763|gb|FQ456490.1|FQ456490
EST:     ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAG                         GTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATT
genomic: ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAGgtaattaatt ... gtcatatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATT
EST: gi|71875321|gb|DT024376.1|DT024376
EST:     AAGAATTGAAAGATGTCAAGTTGTGGCAG                         GTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATT
genomic: AAGAATTGAAAGATGTCAAGTTGTGGCAGgtaattaatt ... gtcatatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATT
EST: gi|351044388|gb|FQ452940.1|FQ452940
EST:     ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAG                         GTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCACACATT
genomic: ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAGgtaattaatt ... gtcatatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATT
EST: gi|77581062|gb|DV219456.1|DV219456
EST:     ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAG                         GTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATT
genomic: ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAGgtaattaatt ... gtcatatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATT
EST: gi|351048297|gb|FQ449389.1|FQ449389
EST:     ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAG                         GTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATT
genomic: ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAGgtaattaatt ... gtcatatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATT
EST: gi|349810776|gb|FQ403019.1|FQ403019
EST:     ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAG                         GTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATC
genomic: ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAGgtaattaatt ... gtcatatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATT
EST: gi|351037882|gb|FQ465120.1|FQ465120
EST:     ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAG                         GTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATT
genomic: ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAGgtaattaatt ... gtcatatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATT
EST: gi|351054602|gb|FQ456799.1|FQ456799
EST:     ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAG                         GTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATT
genomic: ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAGgtaattaatt ... gtcatatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATT
EST: gi|349813262|gb|FQ411502.1|FQ411502
EST:     ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAG                         GTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATT
genomic: ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAGgtaattaatt ... gtcatatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATT
EST: gi|351016092|gb|FQ432047.1|FQ432047
EST:     ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAG                         GTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATT
genomic: ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAGgtaattaatt ... gtcatatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATT
EST: gi|351039176|gb|FQ457851.1|FQ457851
EST:     ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAG                         GTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATT
genomic: ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAGgtaattaatt ... gtcatatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATT
EST: gi|351048422|gb|FQ448696.1|FQ448696
EST:     ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAG                         GTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATT
genomic: ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAGgtaattaatt ... gtcatatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATT
EST: gi|77585060|gb|DV221616.1|DV221616
EST:     ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAG                         GTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATT
genomic: ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAGgtaattaatt ... gtcatatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATT
EST: gi|351047379|gb|FQ451891.1|FQ451891
EST:     ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAG                         GTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCTGACATT
genomic: ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAGgtaattaatt ... gtcatatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATT
EST: gi|77583147|gb|DV220609.1|DV220609
EST:     ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAG                         GTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATT
genomic: ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAGgtaattaatt ... gtcatatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATT
EST: gi|349815100|gb|FQ410323.1|FQ410323
EST:     ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAG                         GTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATT
genomic: ATACACACATAAATGTTCATCAAGAATTGAAAGATGTCAAGTTGTGGCAGgtaattaatt ... gtcatatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtctcagttaatcaaactattttattatgtatattcttgtttgtcatatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATTCCCATGCTGGTTTGTGGCGATTTTAATTCAGTTCCTGGAAG
        agttaat  putative branch site (score: 4)
          ttaatcaaactatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattaattttattttatttttgagtgagcttgagtggggctttttttatgcgtgtgcttatgtctcagttaatcaaactattttattatgtatattcttgtttgtcatatcagGTTCATACTCTCTTAAAAGGTTTGGAAAAAATAGCTGCCAGTGCAGACATTCCCATGCTGGTTTGTGGCGATTTTAATTCAGTTCCTGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG