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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcgtagatggagggagttaagagttattttctttagtaaaatcaaggggaagatgattttgtcttattctctttttttccccttttcatcatggttgcagGTTGCATTGGATATCGATTACCATCATAATATGTTATTATCCCACCAGAAGGTGAATCCAAAGGAAGTCATTGTCGGATG

Basic information

species Vitis vinifera
transcript Vv13s0019g03470.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g03470.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G098153_T01 (Zea mays), 3'ss of exon 1
gcgtagatggagggagttaagagttattttctttagtaaaatcaaggggaagatgattttgtcttattctctttttttccccttttcatcatggttgcagGTTGCATTGGATATCGATTACCATCATAATATGTTATTATCCCACCAGAAGGTGAATCCAAAGGAAGTCATTGTCGGATG
     |  ||   |  | | |            |     |   |         | |||   ||  |||   |   || |   |  |   |   | ||||||| ||  | || ||||| ||||| ||||| ||||     || |||||||||||||| || ||||||||||| ||||||||
-----gtcggttcggatcacgtccccaaccacctcacggatcgattcattccttcattccatcgcattgggtcacttgctgatgctgggcggtgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAGGTGAACCCCAAGGAAGTCATCGTCGGATG

upper sequence: Vv13s0019g03470.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G098153_T02 (Zea mays), 3'ss of exon 1
gcgtagatggagggagttaagagttattttctttagtaaaatcaaggggaagatgattttgtcttattctctttttttccccttttcatcatggttgcagGTTGCATTGGATATCGATTACCATCATAATATGTTATTATCCCACCAGAAGGTGAATCCAAAGGAAGTCATTGTCGGATG--------------------
     |  ||   |  | | |            |     |   |         | |||   ||  |||   |   || |   |  |   |   | ||||||| ||  | || ||||| ||||| ||||| ||||     || |||||||||||||| || ||||||||||| ||||||||                    
-----gtcggttcggatcacgtccccaaccacctcacggatcgattcattccttcattccatcgcattgggtcacttgctgatgctgggcggtgatgcagGTCGCCATCGACATCGACTACCACCATAACATGTACGCCTCGCACCAGAAGGTGAACCCCAAGGAAGTCATCGTCGGATGGTGAGCAACCCACCCCATCG

upper sequence: Vv13s0019g03470.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA18G03340.1 (Glycine max), 3'ss of exon 1
gcgtagatggagggagttaagagttattttctttagtaa-aatcaaggggaagatgattttgtcttattctctttttttcccctttt---catcatggttgcagGTTGCATTGGATATCGATTACCATCATAATATGTTATTATCCCACCAGAAGGTGAATCCAAAGGAAGTCATTGTCGGATG
   ||  ||       ||  |   ||   |||| |  |  ||  ||     |     || |  || |     | |  |     ||||    ||  |   | ||||||||||||||||| || ||||| || ||||||||| |||||||||| || ||||||||||||||| |||| || |||||
---taactgtctctcttttggttgtagggtcttaaacatcaactaaaaattattctgttctcactaaaaagatgtcctaatatttttgcttattttttctccaGGTTGCATTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAAGTGAATCCAAAGGAAATCATAGTAGGATG

upper sequence: Vv13s0019g03470.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G42210.1 (Glycine max), 3'ss of exon 1
----------------------------------------------gcgtagatggaggg---agttaagagttattt--------tctttagtaaaatcaagg---ggaagatgattttgtcttat-tctctttt-----tttcccc--ttttcatcatggtt----gcagGTTGCATTGGATATCGATTACCATCATAATATGTTATTATCCCACCAGAAGGTGAATCCAAAGGAAGTCATTGTCGGATG
                                                ||  ||         | |   || || |||        || | | | |  |  | |    ||||    |||| | |||| | | ||||     ||| |    ||||     || ||    |||||| || |||||||| || || || |||| ||||||||||||||||||||||||||| ||||||||||| || || |||||
gtcctgcacactatttttactacatttgatttttaatcctattttcatgttaattattattttattctggatttgtttctacgatttcatgaatgatgtttacgtatagaagtccgtttttttttatatatgtttttggagtttacttaatttttgatttgttttctcgcagGTCGCTTTGGATATTGAGTATCAACATAGTATGTTATTATCCCACCAGAAGGTGAACCCAAAGGAAGTTATAGTTGGATG

upper sequence: Vv13s0019g03470.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA11G35020.1 (Glycine max), 3'ss of exon 1
gcgtagatggagggagttaagagttattttctttagtaaaatcaaggggaagatgattttgt-cttattctctttttttccccttttcatcatggt-tgcagGTTGCATTGGATATCGATTACCATCATAATATGTTATTATCCCACCAGAAGGTGAATCCAAAGGAAGTCATTGTCGGATG
   |   |  | |    |      |  ||          || ||      | || ||| ||| || | |   |   |      |  | ||  |  | | |||||||| |||||||| || ||||| || ||||||||| |||||||||| || ||||||||||||||| |||| || |||||
--atccttttaagtgtctctcttctgcttgtagggtcttaaacatcaactaaattattctgttctcactaaataaatgatttttgcttatttttttctccagGTTGCGTTGGATATAGAGTACCACCACAATATGTTAATATCCCACCAAAAAGTGAATCCAAAGGAAATCATAGTAGGATG

upper sequence: Vv13s0019g03470.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA14G06690.1 (Glycine max), 3'ss of exon 1
-------------------------------------------------------gcgtagatggagggagttaagagttattttctttag-taaaat---caaggggaagatgattttgtcttattctc---tttttttccccttttcatcatggtt--gcagGTTGCATTGGATATCGATTACCATCATAATATGTTATTATCCCACCAGAAGGTGAATCCAAAGGAAGTCATTGTCGGATG
                                                          |   ||    |  |  |   || | || | | | | |  |   |  |  ||||    || | |||  || |    |||  ||    ||||  |  |  ||   ||||| || |||||||| || || || |||| ||||||||||||||||||||||||||| ||||||||||| || || || ||
gtcctgcacactctttcgcctacattcaatttttacactccttacccttatttttttattcttgatttgtttctacgattttattttatggatgatgtttacgtgcagaagtccgttatttctgtttttggagtttacttaattttttatttgttttttcacagGTCGCTTTGGATATTGAGTATCACCATAGTATGTTATTATCCCACCAGAAGGTGAACCCAAAGGAAGTTATAGTTGGGTG

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|110706072|gb|EE083646.1|EE083646
EST:     TAGATATTCGCAATTCTTACGCTGTTCCTCACAATGAGTCCTCCGATCAG                         GTTGCATTGGATATCGATTACCATCATAATATGTTATTATCCCACCAGAAG
genomic: TAGATATTCGCAATTCTTACGCTGTTCCTCACAATGAGTCCTCCGATCAGgtctgttttt ... atggttgcagGTTGCATTGGATATCGATTACCATCATAATATGTTATTATCCCACCAGAAG
EST: gi|110380965|gb|EC946269.1|EC946269
EST:     TAGATATTCGCAATTCTTACGCTGTTCCTCACAATGAGTCCTCCGATCAG                         GTTGCATTGGATATCGATTACCATCATAATATGTTATTATCCCACCAGAAG
genomic: TAGATATTCGCAATTCTTACGCTGTTCCTCACAATGAGTCCTCCGATCAGgtctgttttt ... atggttgcagGTTGCATTGGATATCGATTACCATCATAATATGTTATTATCCCACCAGAAG
EST: gi|110688899|gb|EE067979.1|EE067979
EST:     TAGATATTCGCAATTCTTACGCTGTTCCTCACAATGAGTCCTCCGATCAG                         GTTGCATTGGATATCGATTACCATCATAATATGTTATTATCCCACCAGAAG
genomic: TAGATATTCGCAATTCTTACGCTGTTCCTCACAATGAGTCCTCCGATCAGgtctgttttt ... atggttgcagGTTGCATTGGATATCGATTACCATCATAATATGTTATTATCCCACCAGAAG
EST: gi|110401608|gb|EC968223.1|EC968223
EST:     TAGATATTCGCAATTCTTACGCTGTTCCTCACAATGAGTCCTCCGATCAG                         GTTGCATTGGATATCGATTACCATCATAATATGTTATTATCCCACCAGAAG
genomic: TAGATATTCGCAATTCTTACGCTGTTCCTCACAATGAGTCCTCCGATCAGgtctgttttt ... atggttgcagGTTGCATTGGATATCGATTACCATCATAATATGTTATTATCCCACCAGAAG
EST: gi|110712101|gb|EE089334.1|EE089334
EST:     TAGATATTCGCAATTCTTACGCTGTTCCTCACAATGAGTCCTCCGATCAG                         GTTGCATTGGATATCGATTACCATCATAATATGTTATTATCCCACCAGAAG
genomic: TAGATATTCGCAATTCTTACGCTGTTCCTCACAATGAGTCCTCCGATCAGgtctgttttt ... atggttgcagGTTGCATTGGATATCGATTACCATCATAATATGTTATTATCCCACCAGAAG
EST: gi|110387531|gb|EC952206.1|EC952206
EST:     TAGATATTCGCAATTCTTACGCTGTTCCTCACAATGAGTCCTCCGATCAG                         GTTGCATTGGATATCGATTACCATCATAATATGTTATTATCCCACCAGAAG
genomic: TAGATATTCGCAATTCTTACGCTGTTCCTCACAATGAGTCCTCCGATCAGgtctgttttt ... atggttgcagGTTGCATTGGATATCGATTACCATCATAATATGTTATTATCCCACCAGAAG
EST: gi|110375382|gb|EC940363.1|EC940363
EST:     TAGATATTCGCAATTCTTACGCTGTTCCTCACAATGAGTCCTCCGATCAG                         GTTGCATTGGATATCGATTACCATCATAATATGTTATTATCCCACCAGAAG
genomic: TAGATATTCGCAATTCTTACGCTGTTCCTCACAATGAGTCCTCCGATCAGgtctgttttt ... atggttgcagGTTGCATTGGATATCGATTACCATCATAATATGTTATTATCCCACCAGAAG
EST: gi|110726721|gb|EE102749.1|EE102749
EST:     TAGATATTCGCAATTCTTACGCTGTTCCTCACAATGAGTCCTCCGATCAG                         GTTGCATTGGATATCGATTACCATCATAATATGTTATTATCCCACCAGAAG
genomic: TAGATATTCGCAATTCTTACGCTGTTCCTCACAATGAGTCCTCCGATCAGgtctgttttt ... atggttgcagGTTGCATTGGATATCGATTACCATCATAATATGTTATTATCCCACCAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggggaagatgattttgtcttattctctttttttccccttttcatcatggttgcagGTTGCATTGGATATCGATTACCATCATAATATGTTATTATCCCACCAGAAGGTGAATCCAAAGGAAGTCATTGTCGGATG
           ttttgtcttattctct  CT-rich tract
                  ttattctcttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcgtagatggagggagttaagagttattttctttagtaaaatcaaggggaagatgattttgtcttattctctttttttccccttttcatcatggttgcagGTTGCATTGGATATCGATTACCATCATAATATGTTATTATCCCACCAGAAGGTGAATCCAAAGGAAGTCATTGTCGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - -tggaggg
- - - - - - - - - - - - - - - - - - - aaatcaa
- - - - - - - - - - - - - - - - - - - - - - -ggggaaga