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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacacttcaaaattttaatagcattaggcagtaaatatggtactgaagatctccaattgaagtgctggtcaagtactttattatctgttcaaatcttactgttctgatctttcaggtctcacaggctctttttgtcactcagGTTTACCGAGTCTCAGATATGGAACTTGTTAGAGTGCTTCCCAGTGCTGAAGATGAGGTCAATGTAGCTTGCTTTCATCCTTTACCTGGAGGAGGTCTTG

Basic information

species Vitis vinifera
transcript Vv07s0005g04630.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os02g18820.2 (Oryza sativa), 3'ss of exon 13
gtaacacttcaaaattttaatagcattaggcagtaaatatggtactgaagatctccaattgaagtgctggtcaagtactttattatctgttcaaatcttactgttctgatctttcaggtctcacaggctctttttgtcac-tcagGTTTACCGAGTCTCAGATATGGAACTTGTTAGAGTGCTTCCCAGTGCTGAAGATGAGGTCAATGTAGCTTGCTTTCATCCTTTACCTGGAGGAGGTCTTG
                                    || || || |      ||||  ||   ||||   | |    ||   || |          ||||    |     |||     |||||      || ||  |||| | |||| ||  |||| || || ||||| || || ||||| ||||| |||||||||||||| || || || || |||||||||||||  |||||||| |||||||
----------------------------------tcatgtgttaattgcttgctccggtttctgtgccacttacaagctcagttctta--------cttatgaatgaagcctt---aatctcattattcctattcatcacgttagGTCTATAGAGTATCGGACATGGAGCTGGTAAGAGTTCTTCCTAGTGCTGAAGATGAAGTAAACGTTGCATGCTTTCATCCTTCCCCTGGAGGTGGTCTTG

upper sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os09g12550.1 (Oryza sativa), 3'ss of exon 12
gtaacacttcaaaattttaatagcattaggcagtaaatatggtactgaagatctccaattgaagtgctggtcaagtactttattatctgttcaaatcttactgttctgatctttcaggtctcacaggctctttttgtcactc----agGTTTACCGAGTCTCAGATATGGAACTTGTTAGAGTGCTTCCCAGTGCTGAAGATGAGGTCAATGTAGCTTGCTTTCATCCTTTACCTGGAGGAGGTCTTG
                                           ||||  |   | | ||| | |||| |    | |   | || | ||  |  | | | |   |      || |  | |   ||    ||||| |  ||||     |||| ||  |||| ||||| ||||| ||||| |||||  | || |||||||||||||| |||||||| || || ||||||||||  ||||| | ||||||||
-------------------------------------------actgtggggttacgatttatgtgcagt---aatgactaatgacctcat--actttcaggatataaggctatgggctaatactatttctttattgcacttccatagGTGTATAGAGTTTCAGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAAGATGAAGTCAATGTCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTG

upper sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G353548_T01 (Zea mays), 3'ss of exon 12
gtaacacttcaaaattttaatagcattaggcagtaaatatggtactgaagatctccaattgaa-gtgctggtcaagtactttattatctgttcaaatcttactgttctgatctttcaggtctcacaggctctttttgtcactcagGTTTACCGAGTCTCAGATATGGAACTTGTTAGAGTGCTTCCCAGTGCTGAAGATGAGGTCAATGTAGCTTGCTTTCATCCTTTACCTGGAGGAGGTCTTG
                               | | | | || |  | |   ||  ||| |     |  || |||  |||||| |   |  |  ||  |  ||| |    ||||||    | |   |   | ||  |     | |||| ||  |||| ||||||||||| ||||| ||||||||||| ||||| |||||||| |||||||| || ||||||||||||||||| ||||| || ||||
-------------------------------aatgatt-tgcttattatcctccacaactactcatattgctca--tactttgtgtacaatgtaagccaaactatc--aatcttt----ttttttaatttattact-----ttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGTGCCGAAGATGAAGTCAATGTTGCATGCTTTCATCCTTTACCAGGAGGTGGCCTTG

upper sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G007229_T01 (Zea mays), 3'ss of exon 12
gtaacacttcaaaattttaatagcattaggcagtaaatatggtactgaagatctccaattgaagtgctggtcaagtactttattatctgttcaaatcttac-tgttctgatctttcaggtctcacaggctctttttgtcactc--agGTTTACCGAGTCTCAGATATGGAACTTGTTAGAGTGCTTCCCAGTGCTGAAGATGAGGTCAATGTAGCTTGCTTTCATCCTTTACCTGGAGGAGGTCTTG
                                               ||    |  | ||    | ||  |||| ||||  | ||| || ||| |  ||   |    ||    |  |  | |||    ||   ||| | |||   |||| ||  |||| ||||||||||| ||||| ||||||||||| || ||||||||||| || ||||| || ||||||||||||| ||| ||||| || ||||
--------------------------------------------tcaaaataatttacttattatcctcctcaactact--aatat-tgctcatactttgtgtacaatgtaagtcaaattatcattttcttcatttattacttttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGCGCTGAAGATGAAGTTAATGTTGCATGCTTTCATCCTTCACCAGGAGGTGGCCTTG

upper sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA19G35370.3 (Glycine max), 3'ss of exon 11
gtaacacttcaaaattttaatagcattaggcagtaaatatggtactgaagatctccaattgaagtgctggtcaagtactttattatctgttcaaatcttactgttctgatctttcaggtctcacaggctctttttgtcactcagGTTTACCGAGTCTCAGATATGGAACTTGTTAGAGTGCTTCCCAGTGCTGAAGATGAGGTCAATGTAGCTTGCTTTCATCCTTTACCTGGAGGAGGTCTTG
                                        || ||  |   |   || |   |    |  || |   | || || |  |||| |||  |  |  |||||  ||| | ||||       |   ||||||  | |||| ||| |||| |||||||||||||||||||| |||||||| ||||| ||||||||||||||||| || ||||||||||||||  | |||||||| || |
-------------------------------------gccggcacaaattgttgtcattcata----tcatctatgccctttttgta-gttctaatggttttagtctgaa-tttaatgtctt-tgaatttgctttgtcttttagGTATACAGAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAAGATGAGGTCAATGTGGCATGCTTTCATCCTTTTGCCGGAGGAGGACTAG

upper sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA03G32620.4 (Glycine max), 3'ss of exon 11
gtaacacttcaaaattttaatagcattaggcagtaaatatggtactgaagatctccaattgaagtgctggtcaagtactttattatctgttcaaatcttactgttctgatctttcaggtctcacaggctctttttgtcactcagGTTTACCGAGTCTCAGATATGGAACTTGTTAGAGTGCTTCCCAGTGCTGAAGATGAGGTCAATGTAGCTTGCTTTCATCCTTTACCTGGAGGAGGTCTTG
                                       ||| ||  |   |  ||| |   |    |  || |   | || || |  ||||||||  |  |  |||||  ||| | |||| |     |   ||||||  | |||| |||  ||| |||||||||||||||||||| |||||||| ||||| ||||| ||||||||||| || ||||||||||||||  |||| ||||| || |
-------------------------------------gctggcacaaattgttgccattcata----tcatctatgccctttttgta-gttcaaatggttttaatctgaa-tttaatgtct-atgaatttgctttgtcttttagGTATACAAAGTGTCAGATATGGAACTTGTTAGGGTGCTTCCTAGTGCAGAAGACGAGGTCAATGTGGCATGCTTTCATCCTTTTGCTGGGGGAGGACTAG

upper sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT1G04140.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaacacttcaaaattttaatagcattaggcagtaaatatggtactgaagatctccaattgaagtgctggtcaagtactttattatctgttcaaatcttactgttctgatctttcaggtctcacaggctctttttgt-cactcagGTTTACCGAGTCTCAGATATGGAACTTGTTAGAGTGCTTCCCAGTGCTGAAGATGAGGTCAATGTAGCTTGCTTTCATCCTTTACCTGGAGGAGGTCTTG
|||||   |  |   |  | |||   |        |     | |   |  || |  |   || |   |  | |  |  || | ||| |   |      ||   | |     |||    | |      | |||| | | |  |||| ||||| |||| |||||||||||||| || ||||| ||||| ||  | || ||||| || ||||| ||||||||||||||||  ||||| ||||||||||
gtaacgtct--atgctccagtagttatgaatttctagaccagcag-aacaatgtttagcagatgccatt-ttatatcattaactatatacacttggaatatcatacaagagtttagactgtgtttttccctttctattccttcagATTTACAGAGTTTCAGATATGGAACTGGTGAGAGTACTTCCAAGCTCAGAGGATGAAGTTAATGTTGCTTGCTTTCATCCTTCTCCTGGGGGAGGTCTTG

upper sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT5G43930.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaacacttcaaaattttaatagcattaggcagtaaatatggtactgaagatctccaattgaagtgctggtcaagtactttattatctgttcaaatcttactgttctgatctttcaggtctcacaggctctttttgtcactcagGTTTACCGAGTCTCAGATATGGAACTTGTTAGAGTGCTTCCCAGTGCTGAAGATGAGGTCAATGTAGCTTGCTTTCATCCTTTACCTGGAGGAGGTCTTG
                                                           | |||   |   | | || |  ||    |||||| | |||   | | | |     |||  ||       | | |  | |  |||| | ||| |||| ||||||||||| ||||| ||||| || || ||| | || ||||| || || || || || ||||||||||  ||||||||||||||||
----------------------------------------------------------gtaaagccttatgctactagtacatc-catgttcagaacttggagatataaca---cagaacttgt---ttgtgtgggccggtcagATATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTGCCAAGTTCAGAGGATGAAGTGAACGTTGCGTGTTTTCATCCTTCTCCTGGAGGAGGTCTTG

upper sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: PP1S150_95V6.1 (Physcomitrella patens), 3'ss of exon 11
----------------gtaacacttcaaaattttaatagcattaggcagtaaatatggtactgaagatctccaattg-aagtgctggtcaagtacttta---ttatctgttcaaatcttactgttctgatctttcaggtctcacaggctctttttgtcactcagGTTTACCGAGTCTCAGATATGGAACTTGTTAGAGTGCTTCCCAGTGCTGAAGATGAGGTCAATGTAGCTTGCTTTCATCCTTTACCTGGAGGAGGTCTTG
                 |   ||   | | | ||| | |||     |      | |     | || |  |   |  |  |  |   ||    || |      | ||    | || |  |  |  |  |  |   ||   ||  |   ||||| |  |    ||||||||| |||| ||||||||||| ||||| || ||  | || ||||||||||||||||| ||||| || |||||||||||   |  ||| || |||||||
gtttgggattcttttcattcaacccaatagtcttagtggcaagtaactacttgtgtaacttttaaaaaatttgacagtgaacgtcagttctatattcctgcttgattcagttaagtaattttacttgggccaacca---ctgtctctctcttgtgttttaacagGTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAAGATGAGGTGAATGTGGCGTGCTTTCATCCCCAAGTTGGTGGTGGTCTTG

upper sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: PP1S58_234V6.1 (Physcomitrella patens), 3'ss of exon 12
---------------------------gtaacacttcaaaattttaatagcattaggcagtaaatatggtactgaagatctccaattgaagtgctggtcaagtactttattatctgttcaaatcttactgttc-tgatct---ttcaggtctcacaggctctttttgt-cactcagGTTTACCGAGTCTCAGATATGGAACTTGTTAGAGTGCTTCCCAGTGCTGAAGATGAGGTCAATGTAGCTTGCTTTCATCCTTTACCTGGAGGAGGTCTTG
                            |  ||  ||   || |   |  | || |    |  |  || |  |   ||   |||     | ||    |     | |      |  ||| | | || | | ||| ||  ||     ||||| |      || ||| ||| || |||||| ||| |||| ||||||||||| ||||| ||||| |||||||||||||| ||||| || ||||| || || ||||||||   |  ||| || |||||||
gtttgaatatcttctctcagtcacgctcttgcaagtcgctatctgtgtccccttggttccttgacgtgtttttcctgagtcccacagtgaatggcaattctacattcctacttgcgttgataactcaatcttcctggactaagcacaggttttct---ctttttctgttcaatcagGTATACAGAGTTTCAGATATGGAGCTTGTGAGAGTACTTCCCAGTGCTGAGGATGAAGTGAATGTGGCGTGTTTTCATCCCCAAGTTGGTGGCGGTCTTG

upper sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: EFJ26270 (Selaginella moellendorffii), 3'ss of exon 12
gtaacacttcaaaattttaatagcattaggcagtaaatatggtactgaagatctccaattgaagtgctggtcaagtactttattatctgttcaaatcttactgttctgatctttcaggtctcacagg----ctctttttgtcactcagGTTTACCGAGTCTCAGATATGGAACTTGTTAGAGTGCTTCCCAGTGCTGAAGATGAGGTCAATGTAGCTTGCTTTCATCCTTTACCTGGAGGAGGTCTTG
                                                                                                 || |  |     | |||  |    ||  |      || ||||||  ||||| ||||  || | |||||| || |||| ||  |||| || || |||||||||||||| || |||||||| ||||||||||||  |  ||| ||||| ||||
-----------------------------------------------------------------------------------------------gtttgcgctctctgttttttggactccattgaaattttccttttgtttctcagATTTATAGAATATCAGATTTGAAACTAGTGCGAGTTCTCCCAAGTGCTGAAGATGAAGTTAATGTAGCGTGCTTTCATCCTCGAGTTGGCGGAGGGCTTG

upper sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: EFJ14567 (Selaginella moellendorffii), 3'ss of exon 11
gtaacacttcaaaattttaatagcattaggcagtaaatatggtactgaagatctccaattgaagtgctggtcaagtactttattatctgttcaaatcttactgttctgatctttcaggtctcacagg----ctctttttgtcactcagGTTTACCGAGTCTCAGATATGGAACTTGTTAGAGTGCTTCCCAGTGCTGAAGATGAGGTCAATGTAGCTTGCTTTCATCCTTTACCTGGAGGAGGTCTTG
                                                                                                 || |  |    || |||  |    ||  |      || ||||||  ||||| ||||  || | |||||| || |||| ||  |||| || || |||||||||||||| || |||||||| ||||||||||||  |  ||| ||||| ||||
-----------------------------------------------------------------------------------------------gtttgcgctctctattttttggactccattgaaattttccttttgtttctcagATTTATAGAATATCAGATTTGAAACTAGTGCGAGTTCTCCCAAGTGCTGAAGATGAAGTTAATGTAGCGTGCTTTCATCCTCGAGTTGGCGGAGGGCTTG

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|110365229|gb|EC927880.1|EC927880
EST:     GCCTTGTTATCGATGGGGAAACGACATTACCTATTTACACAATTTTGGAG                         GTTTACCGAGTCTCAGATATGGAACTTGTTAGAGTGCTTCCCAGTGCTGAA
genomic: GCCTTGTTATCGATGGGGAAACGACATTACCTATTTACACAATTTTGGAGgtaacacttc ... tgtcactcagGTTTACCGAGTCTCAGATATGGAACTTGTTAGAGTGCTTCCCAGTGCTGAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcaaatcttactgttctgatctttcaggtctcacaggctctttttgtcactcagGTTTACCGAGTCTCAGATATGGAACTTGTTAGAGTGCTTCCCAGTGCTGAAGATGAGGTCAATGTAGCTTGCTTTCATCCTTTACCTGGAGGAGGTCTTG
                            gtctcac  putative branch site (score: 3)
                                      ctctttttgtcactc  putative PPT
                                       tcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacacttcaaaattttaatagcattaggcagtaaatatggtactgaagatctccaattgaagtgctggtcaagtactttattatctgttcaaatcttactgttctgatctttcaggtctcacaggctctttttgtcactcagGTTTACCGAGTCTCAGATATGGAACTTGTTAGAGTGCTTCCCAGTGCTGAAGATGAGGTCAATGTAGCTTGCTTTCATCCTTTACCTGGAGGAGGTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG