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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgaaatatgtcattgctaatgctgttggaacacagatggagggccttaaatcaaattctttctcagaaaataactaaggttcatatttgagggtttcagGCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGATTCTGAGGACATCGAAGAGGAGATTGAAGAAGAAGTTGACAAGGTCTTAA

Basic information

species Vitis vinifera
transcript Vv06s0061g00540.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0061g00540.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os03g01810.1 (Oryza sativa), 3'ss of exon 4
gtgaaatatgtcattgctaatgctgttggaacacagatggagggccttaaatcaaattctttctcagaaaataactaaggttcatatttgagggtttcagGCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGATTCTGAGGACATCGAAGAGGAGATTGAAGAAGAAGTTGACAAGGTCTTAA
      ||||  |||   ||   || |   |         | ||  ||   |    |   | | || |  |   || |  | |  |||   | | |  |||| || || || || || || ||||| |||||||| ||  |||| |||||   ||||||||| || |||||||||||||| || |||||||||||| |  
-----gtatgg-attatgaaa--tgatcacatctcttccaaaggtttttcttgtcctgtatgcccatactagttcttacttcctgattgctgtggtgtagGCTGGTGTAATGGAAGAAATGGTGAACGATGCTGTGGATTCAGCGCTGGACAATGAGGACATTGAGGAGGAGATTGAAGAGGAGGTTGACAAGGTCCTCT

upper sequence: Vv06s0061g00540.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os07g29630.1 (Oryza sativa), 3'ss of exon 4
------------------------------------------------------------------------gtgaaatatgtca--ttgctaatgctgttggaacacagatggagggccttaaat--caaattctttctcagaaaata-actaaggttcat----atttgagggtttcagGCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGATTCTGAGGACATCGAAGAGGAGATTGAAGAAGAAGTTGACAAGGTCTTAA
                                                                         | ||| | ||||  |   | |  |||     | |  |||    |   | || |  |||| |  |  |      ||   ||     |||      |||  |   |  |||| || ||||| || ||||| || || ||||| |||||  ||||  |||| ||||||||||| || ||||| |||||||| || |||||||||||  |  
gtaatccgctatttctgttttcttagttcaatatgtaccatatcaaccatctcttccatttcttgtgcatagtttaaagacgtcaggtctgttactctgcactgatattgatctttgtgttaaactggcaaactgatcattgagccatgtgcttgaactcactgacctttttgcactctagGCTGGTGTGATGGAAGAGATGGTCAACGATGCAGTTGATTCAGCTTTGGACTCTGAGGACATGGAGGAGGAAATTGAAGAGGAGGTTGACAAGGTTCTTG

upper sequence: Vv06s0061g00540.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G165195_T01 (Zea mays), 3'ss of exon 4
gtgaaatatgtcattgctaatgctgttggaacacagatggagggccttaaatcaaattctttctcagaaaataactaaggttcatatttgagggtttcagGCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGATTCTGAGGACATCGAAGAGGAGATTGAAGAAGAAGTTGACAAGGTCTTAA
         || ||  |     ||  |        | | || |   || ||| |  |  |       |    ||||||  ||    | |      |  ||||||| ||||| || ||||| ||||| || || |||||  ||||  |||| ||||||||||| || ||||| || ||||| || |||||||||||  |  
---------gtaatcacgtgcacttcttatttcttgttcgaagat-ttgaattatttagtgctgataactgaaactaacattttactgttcttactctagGCAGGTGTGATGGAAGAGATGGTGAACGAGGCAGTTGATTCAGCTTTGGACTCTGAGGACATGGAGGAGGAAATCGAAGAGGAGGTTGACAAGGTTCTTG

upper sequence: Vv06s0061g00540.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA12G08510.1 (Glycine max), 3'ss of exon 4
--------------------gtgaaatatgtcattgctaatgct---gttggaacacagatggagggccttaaatcaaattctttctcagaaaataactaaggttcatatttgagggtttcagGCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGATTCTGAGGACATCGAAGAGGAGATTGAAGAAGAAGTTGACAAGGTCTTAA
                     ||||  ||   | | | | |  |    |     | |   |    |   ||| |  | ||  ||||   |  | | |  | |  |  | | |     ||||||||||| || || |||||||| || ||||||||||||||||||||||| ||||| |||||||| ||||| ||||| ||||||||||| || || ||||| |
gtatgcctgcaatccttttaatgaagcataagaataccactttttcaatcttgtctcccctctctgtggttagagaagatagtttcattggtagttatgaggaatgctgtctc----tttcagGCAGGAGTTATTGAGGAGATAGTAAATGATGCTGTTGACACAGCACTAGATTCCGAGGACATAGAAGATGAGATAGAAGAAGAAGTCGATAAAGTCTTGA

upper sequence: Vv06s0061g00540.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA04G21900.1 (Glycine max), 3'ss of exon 4
-------------------------------------------gtgaaatatgtcattgctaatgc-tgtt---ggaacacagatggagggccttaaatcaaattctttctcagaaaataactaaggttcatatttgagggtttcagGCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGATTCTGAGGACATCGAAGAGGAGATTGAAGAAGAAGTTGACAAGGTCTTAA
                                            |  ||| | |  |  ||  | | ||||   |||| | || || | |   |||    | ||  || |   |    ||  || ||   || |||     ||||||||||| || ||||| ||||| || ||||||||  |||||||||| || |||||||||||||| ||||| ||||| ||||||||||||||||| ||||| |
gtatgcctgcaatccttttaatgcagaagaaaaataccacttttttcaatcttttctctcttctccgtgtttagggaagatagttgcatgtgtttagtcaagatagttacattgg---tagttatggggaatgtttctc--tttcagGCAGGAGTTATCGAAGAGATAGTAAATGATGCCATTGACACAGCGCTAGATTCTGAGGACATAGAAGATGAGATAGAAGAAGAAGTTGACAAAGTCTTGA

upper sequence: Vv06s0061g00540.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G19930.1 (Glycine max), 3'ss of exon 5
----------------------gtgaaatatgt-cattgctaatgctgttggaacacagatggagggccttaaatcaaattctttctcagaaaataactaaggttcatatttgagggtttcagGCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGATTCTGAGGACATCGAAGAGGAGATTGAAGAAGAAGTTGACAAGGTCTTAA---
                      |    ||| |   |   ||  | |  |     | |   |    |   ||| |  | ||  ||||   |  | | |  | |  |  | | |     || |||||||| || ||||||||||| || |||||||| |||||||||||||| |||||||||||||| ||||| |||||   ||||||||| || || ||  | |   
gtatgcccgcaatccttttaatgccgcataagaataccactttttcaatcttgtctcccctctctgtggttagagaagatagtttcattggtagttatgaggaatgttgtctc----ttccagGCAGGAGTTATCGAGGAGATAGTAAATGATGCCGTTGACACAGCACTAGATTCTGAGGACATAGAAGATGAGAT---AGAAGAAGTCGATAAAGTTCTGACCA

upper sequence: Vv06s0061g00540.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA06G23570.2 (Glycine max), 3'ss of exon 5
-----------------------------------------gtgaaatatgt----cattgctaatgctgttggaacacagatggagg---gccttaaatcaaattctttctcagaaaataactaaggttcatatttgagggtttcagGCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGATTCTGAGGACATCGAAGAGGAGATTGAAGAAGAAGTTGACAAGGTCTTAA
                                          |  ||| | |    | || |   || |    ||| | || |  |     |  || | | ||  |  ||         ||  || ||   || ||||     |||||||||| || ||||||||||| || || ||||| || ||| |||| || |||||||||||||| ||||| ||||| |||||||||||||| || ||||| |
gtatgcctgcaatccttttaatgccgaagaaaaataccacttttcaatcttttctcccttccctgtgtttagtgaagatagttacatacatgtgtttagtgaagatagttac--attggtagttatggggaatgtttgtctcgttcagGCAGGAGTTATCGAGGAGATAGTAAACGATGCCGTCGACTCAGCGCTAGATTCTGAGGACATAGAAGATGAGATAGAAGAAGAAGTTGATAAAGTCTTGA

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|30296312|gb|CB973106.1|CB973106
EST:     CTCCTGAAGTGGCTGTCACGATGCAAGAATTCAGCAAAGAAATGACTAAG                         GCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGAT
genomic: CTCCTGAAGTGGCTGTCACGATGCAAGAATTCAGCAAAGAAATGACTAAGgtatttcctt ... agggtttcagGCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGAT
EST: gi|110718482|gb|EE095363.1|EE095363
EST:     CTCCTGAAGTGGCTGTCACGATGCAAGAATTCAGCAAAGAAATGACTAAG                         GCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGAT
genomic: CTCCTGAAGTGGCTGTCACGATGCAAGAATTCAGCAAAGAAATGACTAAGgtatttcctt ... agggtttcagGCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGAT
EST: gi|110718154|gb|EE094659.1|EE094659
EST:     CTCCTGAAGTGGCTGTCACGATGCAAGAATTCAGCAAAGAAATGACTAAG                         GCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGAT
genomic: CTCCTGAAGTGGCTGTCACGATGCAAGAATTCAGCAAAGAAATGACTAAGgtatttcctt ... agggtttcagGCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGAT
EST: gi|26257618|gb|CA808681.1|CA808681
EST:     CTCCTGAAGTGGCTGTCACGATGCAAGAATTCAGCAAAGAAATGACTAAG                         GCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGTACTGGAT
genomic: CTCCTGAAGTGGCTGTCACGATGCAAGAATTCAGCAAAGAAATGACTAAGgtatttcctt ... agggtttcagGCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGAT
EST: gi|110702376|gb|EE081020.1|EE081020
EST:     CTCCTGAAGTGGCTGTCACGATGCAAGAATTCAGCAAAGAAATGACTAAG                         GCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGAT
genomic: CTCCTGAAGTGGCTGTCACGATGCAAGAATTCAGCAAAGAAATGACTAAGgtatttcctt ... agggtttcagGCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGAT
EST: gi|351031409|gb|FQ445434.1|FQ445434
EST:     CTCCTGAAGTGGCTGTCACGATGCAAGAATTCAGCAAAGAAATGACTAAG                         GCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGAT
genomic: CTCCTGAAGTGGCTGTCACGATGCAAGAATTCAGCAAAGAAATGACTAAGgtatttcctt ... agggtttcagGCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGAT
EST: gi|110702630|gb|EE078767.1|EE078767
EST:     CTCCTGAAGTGGCTGTCACGATGCAAGAATTCAGCAAAGAAATGACTAAG                         GCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGAT
genomic: CTCCTGAAGTGGCTGTCACGATGCAAGAATTCAGCAAAGAAATGACTAAGgtatttcctt ... agggtttcagGCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGAT
EST: gi|110722756|gb|EE099290.1|EE099290
EST:     CTCCTGAAGTGGCTGTCACGATGCAAGAATTCAGCAAAGAAATGACTAAG                         GCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGAT
genomic: CTCCTGAAGTGGCTGTCACGATGCAAGAATTCAGCAAAGAAATGACTAAGgtatttcctt ... agggtttcagGCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGAT
EST: gi|110362725|gb|EC926275.1|EC926275
EST:     CTCCTGAAGTGGCTGTCACGATGCAAGAATTCAGCAAAGAAATGACTAAG                         GCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGAT
genomic: CTCCTGAAGTGGCTGTCACGATGCAAGAATTCAGCAAAGAAATGACTAAGgtatttcctt ... agggtttcagGCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGAT
EST: gi|351014990|gb|FQ444279.1|FQ444279
EST:     CTCCTGAAGTGGCTGTCACGATGCAAGAATTCAGCAAAGAAATGACTAAG                         GCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGAT
genomic: CTCCTGAAGTGGCTGTCACGATGCAAGAATTCAGCAAAGAAATGACTAAGgtatttcctt ... agggtttcagGCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGAT
EST: gi|110396776|gb|EC962475.1|EC962475
EST:     CTCCTGAAGTGGCTGTCACGATGCAAGAATTCAGCAAAGAAATGACTAAG                         GCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGAT
genomic: CTCCTGAAGTGGCTGTCACGATGCAAGAATTCAGCAAAGAAATGACTAAGgtatttcctt ... agggtttcagGCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGAT
EST: gi|26257678|gb|CA808741.1|CA808741
EST:     CTCCTGAAGTGGCTGTCACGATGCAAGAATTCAGCAAAGAAATGACTAAG                         GCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGTACTGGAT
genomic: CTCCTGAAGTGGCTGTCACGATGCAAGAATTCAGCAAAGAAATGACTAAGgtatttcctt ... agggtttcagGCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGAT
EST: gi|110714302|gb|EE091055.1|EE091055
EST:     CTCCTGAAGTGGCTGTCACGATGCAAGAATTCAGCAAAGAAATGACTAAG                         GCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGAT
genomic: CTCCTGAAGTGGCTGTCACGATGCAAGAATTCAGCAAAGAAATGACTAAGgtatttcctt ... agggtttcagGCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaaatcaaattctttctcagaaaataactaaggttcatatttgagggtttcagGCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGATTCTGAGGACATCGAAGAGGAGATTGAAGAAGAAGTTGACAAGGTCTTAA
                       aaataac  putative branch site (score: 2)
                      aaaataactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaaatatgtcattgctaatgctgttggaacacagatggagggccttaaatcaaattctttctcagaaaataactaaggttcatatttgagggtttcagGCAGGGGTGATCGAGGAGATTGTGAATGATGCTGTTGACACAGCACTGGATTCTGAGGACATCGAAGAGGAGATTGAAGAAGAAGTTGACAAGGTCTTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
-tgaaata
- - - - - - - - ctaatgc
- - - - - - - - - - - - - - gaacaca
- - - - - - - - - - - - - - - - - - -tggaggg
- - - - - - - - - - - - - - - - - - - - - - - - aaatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa