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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaccagattactgttctaagaattcagccagtaataaaatcttgagtttcttcaacttgggtggtttatgatgttcacatgcatatatttttaatgacagTGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATGTTGGTGAAGTTGTCAAAGTTATGGGGAAGTCAAAGGTCTTAGTTAAG

Basic information

species Vitis vinifera
transcript Vv09s0002g05800.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os06g39870.1 (Oryza sativa), 3'ss of exon 1
gaccagattactgttctaagaattcagccagtaataaaatcttgagtttcttcaacttgggtggtttatgatgttcaca-tgcatatatttttaatg--acagTGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATGTTGGTGAAGTTGTCAAAGTTATGGGGAAGTCAAAGGTCTTAGTTAAG
     ||||   |   |     ||      | | |      ||| | |         |      |||||  | ||  |  | | |    |||| |||   |||| |  | |||  | ||||||||| |  | || || || || || |||||||||||||| |||||||| |||||||| ||||| |||||  |||| |||
-gtaggattctagactttct--ttgtattgggattcgtgctttgcggtataatgtgctaatatttttattttattttccctccttgcgattttgatgttgcagTTATAACGCTGGGGGAAGAGTTGAAGGTGCTCCATGAACCGGGCTCATATGTTGGTGAGGTTGTCAAGGTTATGGGCAAGTCCAAGGTTCTAGTGAAG

upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G137528_T02 (Zea mays), 3'ss of exon 1
gaccagattactgttctaagaattcagccagtaataaaatcttgagtttcttcaactt---gggtggtttatgatgttcacatgcatatatttttaatgacagTGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATGTTGGTGAAGTTGTCAAAGTTATGGGGAAGTCAAAGGTCTTAGTTAAG
    | ||| ||| | |     ||     || |  | |  |||     |||     ||   |  |    ||   |         | |  | |||||||  |||| || ||||| || |||||||||||  | ||||| |||||||| |||||||||||||| || || || || |||||||| ||||||||  | || |||
---taaatttctgctgtctctgtttcatgagcagcacatccttctacatctattgttttctgattaccatactctaagtttggccttgcaattttaatttcagTTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATGTTGGTGAGGTGGTGAAGGTCATGGGGAAATCAAAGGTTCTGGTGAAG

upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G107362_T04 (Zea mays), 3'ss of exon 1
gaccagattactgttctaagaattcagccagtaataaaatcttg-------agtttcttcaacttgggtggtttatgatgttcacatgcatatatttttaatgacagTGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATGTTGGTGAAGTTGTCAAAGTTATGGGGAAGTCAAAGGTCTTAGTTAAG
      ||| ||| | |     ||     ||||  | | |||||       | | | |||   ||       |    || |   | |||| || || ||  |  |||| || ||||| || |||||||||||  | ||||| |||||||| |||||||||||||| || || || || |||||||| ||||||||  | || |||
-----aattcctgctgtctctgtttcaggagtagcacattcttgtacatgtattgttttctgattaccatactctaaatttggccttgca-atgttgtttttt-cagTTAGAATGCTCAGGGAAGAGTTGCAGTTGCTTCAAGAGCCTGGCTCATATGTTGGTGAGGTGGTGAAGGTCATGGGGAAATCAAAGGTTCTGGTGAAG

upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA07G00420.1 (Glycine max), 3'ss of exon 1
gaccagattactgttctaagaattcagccagtaataaaatcttgagtttcttcaacttgggtggtttatgatgttcacatgcatatatttttaatgacagTGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATGTTGGTGAAGTTGTCAAAGTTATGGGGAAGTCAAAGGTCTTAGTTAAG
                       || || |    |||   | | |   ||||    |       |||    |  | || |   |    |||  |||||||||||||||||  | ||||| || || ||||| ||||| || || || ||||| ||||||||||||||||| ||||| |||   || ||| | || |||
-----------------gtaccctccgctaaccctaa--ccctaaccctcttttcttct-----tttcaattccttacttctcttctatttcgatgacagTGAGGATGCTGCGCGAAGAATTACAGCTTCTGCAGGAACCCGGCTCTTATGTCGGTGAAGTTGTCAAAGTAATGGGCAAGAACAAAGTCCTTGTCAAG

upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G24000.1 (Glycine max), 3'ss of exon 1
gaccagattactgttctaagaattcagccagtaataaaatcttgagtttcttcaacttgggtggtttatgatgttcacatgcatatatttttaatgacagTGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATGTTGGTGAAGTTGTCAAAGTTATGGGGAAGTCAAAGGTCTTAGTTAAG
     | |  ||   ||||     |   |  |||    ||  | | | | ||| | |    |    |  |   | | | || || | || |     ||||||||||||||  | ||||| || || ||| | ||||| || || || ||||||||||||||||||||||| ||||| |||   || ||| | || |||
-gtaggctcgctcccctaa---ccctaaccctaaccctattct-attctattctattccattctcatccgtcatactcttgaatttcttct-----acagTGAGGATGCTGCGCGAAGAATTACAGCTTTTGCAGGAACCAGGCTCTTATGTTGGTGAAGTTGTCAAAGTCATGGGCAAGAACAAAGTCCTTGTCAAG

upper sequence: Vv09s0002g05800.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT5G19990.1 (Arabidopsis thaliana), 3'ss of exon 1
gaccagattactgttctaagaattca--gccagtaat-aaaatcttgagtttcttcaacttgggtggtttatgatgttcaca-tgcatatatttttaat--gacagTGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATGTTGGTGAAGTTGTCAAAGTTATGGGGAAGTCAAAGGTCTTAGTTAAG
   |  |||  ||    |||  ||     | |||  | | ||| |  ||||  |||    |   |     |    ||| ||| |  |  ||||| ||||   |||||||| ||||| ||||||||||| || || ||||| || ||||| || ||||| || ||||| || ||||||||||| |||   |||||||| ||||||
--tcctatttatgcatgaaggttttcttactagtctttataatttgtagttagttc----taaatctcaaacctcgttaacactaaaattatttctaattgaacagTGAGAATGCTCAGAGAAGAGTTACAGCTCCTTCAAGAACCTGGGTCCTATGTGGGAGAAGTGGTAAAAGTTATGGGAAAGAACAAGGTCTTGGTTAAG

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|110393121|gb|EC958077.1|EC958077
EST:     TCACAATCTCAACCGCCTTGAAGCCCAACGCAATGATCTCAATTCTCGAG                         TGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATG
genomic: TCACAATCTCAACCGCCTTGAAGCCCAACGCAATGATCTCAATTCTCGAGgtcactactt ... ttaatgacagTGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATG
EST: gi|110698891|gb|EE076909.1|EE076909
EST:     TCACAATCTCAACCGCCTTGAAGCCCAACGCAATGATCTCAATTCTCGAG                         TGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATG
genomic: TCACAATCTCAACCGCCTTGAAGCCCAACGCAATGATCTCAATTCTCGAGgtcactactt ... ttaatgacagTGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATG
EST: gi|156737153|gb|EV241267.1|EV241267
EST:     TCACAATCTCAACCGCCTTGAAGCCCAACGCAATGATCTCAATTCTCGAG                         TGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATG
genomic: TCACAATCTCAACCGCCTTGAAGCCCAACGCAATGATCTCAATTCTCGAGgtcactactt ... ttaatgacagTGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATG
EST: gi|110713901|gb|EE090225.1|EE090225
EST:     TCACAATCTCAACCGCCTTGAAGCCCAACGCAATGATCTCAATTCTCGAG                         TGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATG
genomic: TCACAATCTCAACCGCCTTGAAGCCCAACGCAATGATCTCAATTCTCGAGgtcactactt ... ttaatgacagTGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATG
EST: gi|26256905|gb|CA807968.1|CA807968
EST:     TCACAATCTCAACCGCCTTGAAGCCCAACGCAATGATCTCAATTCTCGAG                         TGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATG
genomic: TCACAATCTCAACCGCCTTGAAGCCCAACGCAATGATCTCAATTCTCGAGgtcactactt ... ttaatgacagTGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATG
EST: gi|110699382|gb|EE076332.1|EE076332
EST:     TCACAATCTCAACCGCCTTGAAGCCCAACGCAATGATCTCAATTCTCGAG                         TGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATG
genomic: TCACAATCTCAACCGCCTTGAAGCCCAACGCAATGATCTCAATTCTCGAGgtcactactt ... ttaatgacagTGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATG
EST: gi|161709582|gb|FC061406.1|FC061406
EST:     TCACAATCTCAACCGCCTTGAAGCCCAACGCAATGATCTCAATTCTCGAG                         TGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATG
genomic: TCACAATCTCAACCGCCTTGAAGCCCAACGCAATGATCTCAATTCTCGAGgtcactactt ... ttaatgacagTGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATG
EST: gi|110707762|gb|EE084531.1|EE084531
EST:     TCACAATCTCAACCGCCTTGAAGCCCAACGCAATGATCTCAATTCTCGAG                         TGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATG
genomic: TCACAATCTCAACCGCCTTGAAGCCCAACGCAATGATCTCAATTCTCGAGgtcactactt ... ttaatgacagTGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATG
EST: gi|71861768|gb|DT010823.1|DT010823
EST:     TCACAATCTCAACCGCCTTGAAGCCCAACGCAATGATCTCAATTCTCGAG                         TGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATG
genomic: TCACAATCTCAACCGCCTTGAAGCCCAACGCAATGATCTCAATTCTCGAGgtcactactt ... ttaatgacagTGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATG
EST: gi|294964426|gb|GW838229.1|GW838229
EST:     TCACAATCTCAACCGCCTTGAAGCCCAACGCAATGATCTCAATTCTCGAG                         TGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATG
genomic: TCACAATCTCAACCGCCTTGAAGCCCAACGCAATGATCTCAATTCTCGAGgtcactactt ... ttaatgacagTGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATG
EST: gi|161713411|gb|FC063391.1|FC063391
EST:     TCACAATCTCAACCGCCTTGAAGCCCAACGCAATGATCTCAATTCTCGAG                         TGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATG
genomic: TCACAATCTCAACCGCCTTGAAGCCCAACGCAATGATCTCAATTCTCGAGgtcactactt ... ttaatgacagTGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATG
EST: gi|161716828|gb|FC068100.1|FC068100
EST:     TCACAATCTCAACCGCCTTGAAGCCCAACGCAATGATCTCAATTCTCGAG                         TGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATG
genomic: TCACAATCTCAACCGCCTTGAAGCCCAACGCAATGATCTCAATTCTCGAGgtcactactt ... ttaatgacagTGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATG
EST: gi|71858853|gb|DT007908.1|DT007908
EST:     TCACAATCTCAACCGCCTTGAAGCCCAACGCAATGATCTCAATTCTCGAG                         TGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATG
genomic: TCACAATCTCAACCGCCTTGAAGCCCAACGCAATGATCTCAATTCTCGAGgtcactactt ... ttaatgacagTGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttcttcaacttgggtggtttatgatgttcacatgcatatatttttaatgacagTGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATGTTGGTGAAGTTGTCAAAGTTATGGGGAAGTCAAAGGTCTTAGTTAAG
                                           ttttaat  putative branch site (score: 3)
                                        tattttt  CT-rich tract
                                 atgcatatatttttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaccagattactgttctaagaattcagccagtaataaaatcttgagtttcttcaacttgggtggtttatgatgttcacatgcatatatttttaatgacagTGAGGATGCTTAGAGAAGAGTTGCAACTTCTTCAGGAGCCTGGATCATATGTTGGTGAAGTTGTCAAAGTTATGGGGAAGTCAAAGGTCTTAGTTAAG

- - - - - - - - - - - -tcagcca
- - - - - - - - - - - - - - - - aataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgggtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacatgc