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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtaatagcttcctaaagcattggtctttgagcagatgaagccttttaggcatactcttttttctagtacaacgatcatctgcctttttcatgttatttagtgatttgatttattttttctttttcatttttgttgctaaatgctaaaaggggttttaatctgatagtgcctttctgtgacaaaactgcagGCTATGTAATATGGACATCATTTCACATGTACAGCAAGTCATTTGCTTTGCTTTTCATGATAGCAAGCTTCTCATGGAAACATGCCAAGAGGCCAAAAAT

Basic information

species Vitis vinifera
transcript Vv05s0094g01380.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0094g01380.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G022090_T02 (Zea mays), 3'ss of exon 3
gtttgtaatagcttcctaaagcattggtctttgagcagatgaagccttttaggcatactcttttttctagtacaacgatcatctgcctttttcatgttatttagtgatttgatttattttttctttttcatttttgttgctaaatgctaaaaggg-gttttaatctgatagtgcctttctgtgacaaaactgcagGCTATGTAATATGGACATCATTTCACATGTACAGCAAGTCATTTGCTTTGCTTTTCATGATAGCAAGCTTCTCATGGAAACATGCCAAGAGGCCAAAAAT
                                                                                                | |   ||   |   ||||||||||   | |  |||  | |   |     ||| ||       || || |  ||||| |   ||||  |||  || |||| |||| |||||||||||||| ||  | || || || || || ||||| || || ||||| |||||||| || |||||||||||||| |||||||| || 
--------------------------------------------------------------------------------------------ggattgaaagaggagtcacatttatttttatctctgtattaatatgtattgtgactagaataccacctttatatc-tagtggcaa-ctgttgcaat-cttcagGTTATGCAATATGGACATCATCTCCAAGGTCCAACAGGTGATCTGCTTCGCGTTCCATGACAGCAAGCTGCTGATGGAAACATGCCAGGAGGCCAAGAAC

upper sequence: Vv05s0094g01380.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA17G00330.1 (Glycine max), 3'ss of exon 5
gtttgtaatagcttcctaaagcattggtctttgagcagatgaagccttttaggcatactcttttttctagtacaacgatcatctgcctttttcatgttatttagtgatttgatttattttttctttttcatttttgttgctaaatgctaaaaggggttttaatctgatagtgcctttctgtgacaaaactgcagGCTATGTAATATGGACATCATTTCACATGTACAGCAAGTCATTTGCTTTGCTTTTCATGATAGCAAGCTTCTCATGGAAACATGCCAAGAGGCCAAAAAT
                                                                                          | || | ||| | || |||   | | |||||| |     | || ||||  ||   | ||||   | ||      | ||  | |||| |  ||    |  |||||||||||||||||||| |||||||| || || ||||||||||||||||||||||| |||||||| | | | ||||||||||| || ||||| || ||||||
------------------------------------------------------------------------------------------tgcaggctatattgttatt-attattttttttttgagaaagttatgttattactgggtaaa---gattggggagttatttttccttccattgtttcacatgcagGCTATGTAATATGGATATCATTTCGCACGTGCAGCAAGTCATTTGCTTTGCTTTCCATGATAGTAGGTTGCTCATGGAAACTTGTCAAGAAGCAAAAAAT

upper sequence: Vv05s0094g01380.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA07G40350.2 (Glycine max), 3'ss of exon 5
gtttgtaatagcttcctaaagcattggtctttgagcagatgaagccttttaggcatactcttttttctagtacaacgatcatctgcctttttcatgttatttagtgatttgatttattttttctttttcatttttgttgctaaatgctaaaaggggttttaatctgatagtgcctttctgtgacaaaactgcagGCTATGTAATATGGACATCATTTCACATGTACAGCAAGTCATTTGCTTTGCTTTTCATGATAGCAAGCTTCTCATGGAAACATGCCAAGAGGCCAAAAAT
                                                                                          | || | ||| |  | |||  |||| ||| || |     |  | ||||| ||  |   |  |  | ||      | ||  |  ||| |  ||    |  |||||||||||||||||||| |||||||| || || ||||||||||||||||||||||| ||||||||   | | ||||||||||| || ||||| || ||||||
-----------------------------------------------------------------------------------------atgcaggctatattattatt--attt-tttgttttgagaaagctatgttgtta--ttgcagtaaagattgggccattattttttcttccattgtttcacatgcagGCTATGTAATATGGATATCATTTCGCACGTGCAGCAAGTCATTTGCTTTGCTTTCCATGATAGTCGGTTGCTCATGGAAACTTGTCAAGAAGCAAAAAAT

upper sequence: Vv05s0094g01380.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT3G59870.1 (Arabidopsis thaliana), 3'ss of exon 5
gtttgtaatagcttcctaaagcattggtctttgagcagatgaagccttttaggcatactcttttttctagtacaacgatcatctgcctttttcatgttatttagtgatttgatttattttttctttttcatttttgttgctaaatgctaaaaggggttttaatctgatagtgcctttctgtgacaaaactgcagGCTATGTAATATGGACATCATTTCACATGTACAGCAAGTCATTTGCTTTGCTTTTCATGATAGCAAGCTTCTCATGGAAACATGCCAAGAGGCCAAAAAT
                                              |||    |  ||   | |||    |||| || |       |      | | |   |  |||   ||| || |    | || |    |   ||      | || | | |  | |  |  | |  ||    |  ||         |||||||||||||| ||||| ||||| ||||| || || ||| ||||||||||||| ||||||||||| |||||||||||||| ||||| ||||| || | ||||
---------------------------------------------gtttgtcactcaccactctttaccataca-cggtagcaaaaccgagaaaagatggcttatga---gatatagtgaaacattgtagaatcaatt------ttctgagacgtatctccaagtaa--gtaaaatggtg-attggttttgcagGCTATGTAACATGGATATCATATCACAAGTGCAACAAATCATTTGCTTTGCGTTTCATGATAGTAAGCTTCTCATGGAGACATGTCAAGAAGCTAGAAAT

upper sequence: Vv05s0094g01380.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT2G43945.1 (Arabidopsis thaliana), 3'ss of exon 5
gtttgtaatagcttcctaaagcattggtctttgagcagatgaagccttttaggcatactcttttttctagtacaacgatcatctgcctttttcatgttatttagtgatttgatttattttttctttttcatttttgttgctaaatgctaaaaggggttttaatctgatagtgcctttctgtgacaaaactgcagGCTATGTAATATGGACATCATTTCACATGTACAGCAAGTCATTTGCTTTGCTTTTCATGATAGCAAGCTTCTCATGGAAACATGCCAAGAGGCCAAAAAT
                                                                                                                ||| |   |       ||||  | |  ||       | | ||  | | || || || | |    | | |    |   |||||| | ||||||||||||||||| ||||| || || ||||| || ||||| || |||||||| || |||||||| ||||| ||||| ||||| |||||||||
---------------------------------------------------------------------------------------------------------------gtttgtgaataaaaaaccattgatatacctttggtgaagatggaatctgaacctcattg-gttaatatatatttatg-tgcagGTTGTGTAATATGGACATCATATCACAAGTTCAACAAGTGATCTGCTTCGCGTTTCATGACAGTAAGCTTCTTATGGAGACATGTCAAGAAGCCAAAAAT

upper sequence: Vv05s0094g01380.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: PP1S323_60V6.1 (Physcomitrella patens), 3'ss of exon 5
gtttgtaatagcttcctaaagcattggtctttgagcagatgaagccttttaggcatactcttttttctagtacaacgatcatctgcctttttcatgttatttagtgatttgatttattttttctttttcatttttgttgctaaatg-ctaaaaggggttttaatctgatagtgcctttctgtgacaaaactgcagGCTATGTAATATGGACATCATTTCACATGTACAGCAAGTCATTTGCTTTGCTTTTCATGATAGCAAGCTTCTCATGGAAACATGCCAAGAGGCCAAAAAT
                                                                                           |  ||||  ||    ||||  || | | | |    ||     ||  |   ||||  ||  | ||    |  ||||  |    |  | ||  ||      ||||| ||||| || |||||||| || |||||||| || ||||| || |||||||| ||||||||||| ||  | |||||||| || ||    || || ||||| 
------------------------------------------------------------------------------------------gtagtgtttattttctatttt-ttcagtctctggacttttcaattactatgaaataactcgatggaagatgcatctt-tgactctgtgcttcgatttgtatgcagACTATGCAACATGGACATTATATCACATGTGCAACAAGTTATATGCTTTGCCTTTCATGATAGTAATTTACTCATGGAGACTTGTAGTGAAGCTAAAAAC

upper sequence: Vv05s0094g01380.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: EFJ38716 (Selaginella moellendorffii), 3'ss of exon 4
gtttgtaatagcttcctaaagcattggtctttgagcagatgaagccttttaggcatactcttttttctagtacaacgatcatctgcctttttcatgttatttagtgatttgatttattttttctttttcatttttgttgctaaatgctaaaaggggttttaatctgatagtgcctttctgtgacaaaactgcagGCTATGTAATATGGACATCATTTCACATGTACAGCAAGTCATTTGCTTTGCTTTTCATGATAGCAAGCTTCTCATGGAAACATGCCAAGAGGCCAAAAAT
                                                                                                                  | ||||    ||| ||||||  |   |        |  |  |||||  |  | |  || |   | | |       | |||  | || |||||||||||  ||||||| |||||||| |||||||| ||||| || ||||| ||||   | |||||||||||||||   || ||||| | |
-----------------------------------------------------------------------------------------------------------------gtgttttcgtctttccattttcttctttgctcaagcatcgatgttttctttggcttctgaccaccgg-gcttgctttccagATTGTGCAATATGGACATTCTTTCACACGTACAGCAGGTCATTTGTTTTGCCTTCCATGACAGCAGATTACTCATGGAAACATGCAGCGAAGCCAAGAGT

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|18459061|gb|BM437339.1|BM437339
EST:     GTAATAGAGAAGCCTTACAATGATCATCTTCCTTTGATAGAAGCCAGCAG                         GCTATGTAATATGGACATCATTTCACATGTACAGCAAGTCATTTGCTTTGC
genomic: GTAATAGAGAAGCCTTACAATGATCATCTTCCTTTGATAGAAGCCAGCAGgtttgtaata ... aaaactgcagGCTATGTAATATGGACATCATTTCACATGTACAGCAAGTCATTTGCTTTGC
EST: gi|71870474|gb|DT019529.1|DT019529
EST:     GTAATAGAGAAGCCTTACAATGATCATCTTCCTTTGATAGAAGCCAGCAG                         GCTATGTAATATGGACATCATTTCACATGTACAGCAAGTCATTTGCTTTGC
genomic: GTAATAGAGAAGCCTTACAATGATCATCTTCCTTTGATAGAAGCCAGCAGgtttgtaata ... aaaactgcagGCTATGTAATATGGACATCATTTCACATGTACAGCAAGTCATTTGCTTTGC
EST: gi|30320624|gb|CD003886.1|CD003886
EST:     GTAATAGAGAAGCCTTACAATGATCATCTTCCTTTGATAGAAGCCAGCAG                         GCTATGTAATATGGACATCATTTCACATGTACAGCAAGTCATTTGCTTTGC
genomic: GTAATAGAGAAGCCTTACAATGATCATCTTCCTTTGATAGAAGCCAGCAGgtttgtaata ... aaaactgcagGCTATGTAATATGGACATCATTTCACATGTACAGCAAGTCATTTGCTTTGC
EST: gi|110420391|gb|EC986663.1|EC986663
EST:     GTAATAGAGAAGCCTTACAATGATCATCTTCCTTTGATAGAAGCCAGCAG                         GCTATGTAATATGGACATCATTTCACATGTACAGCAAGTCATTTGCTTTGC
genomic: GTAATAGAGAAGCCTTACAATGATCATCTTCCTTTGATAGAAGCCAGCAGgtttgtaata ... aaaactgcagGCTATGTAATATGGACATCATTTCACATGTACAGCAAGTCATTTGCTTTGC
EST: gi|30321162|gb|CD004424.1|CD004424
EST:     GTAATAGAGAAGCCTTACAATGATCATCTTCCTTTGATAGAAGCCAGCAG                         GCTATGTAATATGGACATCATTTCACATGTACAGCAAGTCATTTGCTTTGC
genomic: GTAATAGAGAAGCCTTACAATGATCATCTTCCTTTGATAGAAGCCAGCAGgtttgtaata ... aaaactgcagGCTATGTAATATGGACATCATTTCACATGTACAGCAAGTCATTTGCTTTGC
EST: gi|110374681|gb|EC939602.1|EC939602
EST:     GTAATAGAGAAGCCTTACAATGATCATCTTCCTTTGATAGAAGCCAGCAG                         GCTATGTAATATGGACATCATTTCACATGTACAGCAAGTCATTTGCTTTGC
genomic: GTAATAGAGAAGCCTTACAATGATCATCTTCCTTTGATAGAAGCCAGCAGgtttgtaata ... aaaactgcagGCTATGTAATATGGACATCATTTCACATGTACAGCAAGTCATTTGCTTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaaatgctaaaaggggttttaatctgatagtgcctttctgtgacaaaactgcagGCTATGTAATATGGACATCATTTCACATGTACAGCAAGTCATTTGCTTTGCTTTTCATGATAGCAAGCTTCTCATGGAAACATGCCAAGAGGCCAAAAAT
                 ttttaatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtaatagcttcctaaagcattggtctttgagcagatgaagccttttaggcatactcttttttctagtacaacgatcatctgcctttttcatgttatttagtgatttgatttattttttctttttcatttttgttgctaaatgctaaaaggggttttaatctgatagtgcctttctgtgacaaaactgcagGCTATGTAATATGGACATCATTTCACATGTACAGCAAGTCATTTGCTTTGCTTTTCATGATAGCAAGCTTCTCATGGAAACATGCCAAGAGGCCAAAAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG