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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtttcttgtttctcttgattatcgttgtctctgaatttcttaattggggtttggtttcaagtctattgtttttttaatcatgtgttttaatcttgtttcttgctaattgatttgatggttggttgaaataaaattagGGTTTTGAGGCTTCAGGCTGGACACAAGTACTGCTTGCTTGGCCGGCTTTCCTCAGAGGTTGGATGGAACCATTACGATACCATCAGA

Basic information

species Vitis vinifera
transcript Vv07s0005g06490.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g06490.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G090422_T01 (Zea mays), 3'ss of exon 2
gttagtttcttgtttctcttgattatcgttgtctctgaatttcttaattggggtttggtttcaagtctattgtttttttaatcatgtgttttaatcttgtttcttgctaattg-atttgatggt-tggttgaaataaaa-ttagGGTTTTGAGGCTTCAGGCTGGACACAAGTACTGCTTGCTTGGCCGGCTTTCCTCAGAGGTTGGATGGAACCATTACGATACCATCAGA
                                               |  | ||||   | |   | |    ||| | | ||     |     |||||| ||  ||  | | |  | ||||| | |  |||   |     |||||||| ||||||| ||| ||||||||||||||||| | || |||  ||| ||    ||||| || |||||| |  | || |||||||| 
----------------------------------------------gtacgtgtttccatccgtatttgggatttatctgattgcaggca--gatcttgctttgtgacattcgtgtctgatgctattcttgttgtggttcttagGGTTCTGAGGCTACAGCCTGGACACAAGTACTGCCTCCTCGGCGAGCTCTCTAAGGAGGTCGGGTGGAACTACCATGACACCATCAGG

upper sequence: Vv07s0005g06490.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G24830.1 (Arabidopsis thaliana), 3'ss of exon 2
gttagtttcttgtttctcttgattatcgttgtctctgaatttcttaattggggtttggtttcaagtctattgtttttttaatcatgtgttttaatct-tgtttcttgctaattgatttgatggttggttgaaataaaattagGGTTTTGAGGCTTCAGGCTGGACACAAGTACTGCTTGCTTGGCCGGCTTTCCTCAGAGGTTGGATGGAACCATTACGATACCATCAGA
                                    | | |  ||   ||    || |||  |    | ||||  ||||  | ||||   | ||| | | ||   ||  || || |||  | ||| |||    |    ||||||| ||||||||||||||||| ||||||||||||||| | || ||  | || || || ||||| ||||||||||||||||||||||  
------------------------------------gtaatgttt--ctgcaactttgttcta----tcttgtaattttggttatgt---tcaatgtgttttagctgtcaactggttt--tcgtttgttttgttttgtttagGGTGTTGAGGCTTCAGGCTGGTCACAAGTACTGCTTGTTGGGACGTTTGTCTTCTGAAGTTGGCTGGAACCATTACGATACCATCAAG

upper sequence: Vv07s0005g06490.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT5G48760.1 (Arabidopsis thaliana), 3'ss of exon 2
gttagtttcttgtttctcttgattatcgttgtctctgaatttcttaattggggtttggtttcaagtctattgtttttttaatcatgtgttttaatcttgtttcttgctaattgatt-tgatggttggttgaaataaaattagGGTTTTGAGGCTTCAGGCTGGACACAAGTACTGCTTGCTTGGCCGGCTTTCCTCAGAGGTTGGATGGAACCATTACGATACCATCAGA
                                               || |    |  |  ||  | | || || | ||    ||  ||     |  |  |||  ||  ||||||  | ||  |||  ||        | ||||| ||||||||||| ||||| ||||| |||||  |  | ||||| ||||| || || ||||| |||||||||||||| |||||||  
----------------------------------------------gtttgttccttttaccatttttgttcttctcttttggatccgtaactgttctacttcgggc--attgatgattatcattg--tggctcttcttcagGGTGTTGAGGCTTCAAGCTGGTCACAAATACTGTCTATTGGGCCGTCTTTCTTCTGAAGTTGGGTGGAACCATTACGACACCATCAAG

upper sequence: Vv07s0005g06490.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S80_110V6.1 (Physcomitrella patens), 3'ss of exon 3
---------------------------------gttagtttcttgtttctcttgattatcgttgtctctgaatttcttaattggggtttggtttca-agtcta-ttgtttttttaatcatgtgttttaatcttgtttcttgctaattgattt----gatggttggttgaaataaaattagGGTTTTGAGGCTTCAGGCTGGACACAAGTACTGCTTGCTTGGCCGGCTTTCCTCAGAGGTTGGATGGAACCATTACGATACCATCAGA------------
                                 || |  ||   | |    ||     |  ||  || | |   ||  ||||||  | |  |   | ||| || ||   |   ||| ||     |   |  || | | |    |    | ||    | |  |   ||  |   |||  |||||  ||||||| ||  |||||||||||| ||| ||| | |||||  | |||   |||||||||||| |||||||||||||||||| |            
gtgagtctctcataatatttatgatctcacttggtaaagttaaagatggcgttctaagttatttgctttaagcatca-aattggtctgtactcctacagtgtaattccgtaactaagcagcacatgcgactttatatttcaacatagaagttctcaggtactaactttcatacaaaacagGGTACTGAGGCTGCAACCTGGACACAAGTTCTGTTTGTTGGGCCGTTTGTCCGAGGAGGTTGGATGGCACCATTACGATACCATCAAAGAGTTGGAGGAG

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|294965121|gb|GW836952.1|GW836952
EST:     CCTCCACCATATGATAAGATGAAGAGGATGGTCATTCCTGATGCACTCAA                         GGTTTTGAGGCTTCAGGCTGGACACAAGTACTGCTTGCTTGGCCGGCTTTC
genomic: CCTCCACCATATGATAAGATGAAGAGGATGGTCATTCCTGATGCACTCAAgttagtttct ... ataaaattagGGTTTTGAGGCTTCAGGCTGGACACAAGTACTGCTTGCTTGGCCGGCTTTC
EST: gi|37188674|gb|CF608023.1|CF608023
EST:     CCTCCACCATATGATAAGATGAAGAGGATGGTCATTCCTGATGCACTCAA                         GGTTTTGAGGCTTCAGGCTGGACACAAGTACTGCTTGCTTGGCCGGCTTTC
genomic: CCTCCACCATATGATAAGATGAAGAGGATGGTCATTCCTGATGCACTCAAgttagtttct ... ataaaattagGGTTTTGAGGCTTCAGGCTGGACACAAGTACTGCTTGCTTGGCCGGCTTTC
EST: gi|32456523|gb|CD797697.1|CD797697
EST:     CCTCCCCCATATGATAAGATGAAGAGGATGGTCATTCCTGATGCACTCAA                         GGTTTTGAGGCTTCAGGCTGGACACAAGTACTGCTTGCTTGGCCGGCTTTC
genomic: CCTCCACCATATGATAAGATGAAGAGGATGGTCATTCCTGATGCACTCAAgttagtttct ... ataaaattagGGTTTTGAGGCTTCAGGCTGGACACAAGTACTGCTTGCTTGGCCGGCTTTC
EST: gi|37185713|gb|CF605066.1|CF605066
EST:     CCTCCACCATATGATAAGATGAAGAGGATGGTCATTCCTGATGCACTCAA                         GGTTTTGAGGCTTCAGGCTGGACACAAGTACTGCTTGCTTGGCCGGCTTTC
genomic: CCTCCACCATATGATAAGATGAAGAGGATGGTCATTCCTGATGCACTCAAgttagtttct ... ataaaattagGGTTTTGAGGCTTCAGGCTGGACACAAGTACTGCTTGCTTGGCCGGCTTTC
EST: gi|110384420|gb|EC948855.1|EC948855
EST:     CCTCCACCATATGATAAGATGAAGAGGATGGTCATTCCTGATGCACTCAA                         GGTTTTGAGGCTTCAGGCTGGACACAAGTACTGCTTGCTTGGCCGGCTTTC
genomic: CCTCCACCATATGATAAGATGAAGAGGATGGTCATTCCTGATGCACTCAAgttagtttct ... ataaaattagGGTTTTGAGGCTTCAGGCTGGACACAAGTACTGCTTGCTTGGCCGGCTTTC
EST: gi|87584078|gb|DY473371.1|DY473371
EST:     CCTCCACCATATGATAAGATGAAAAGGATGGTCATTCCTGATGCACTCAA                         GGTTTTGAGGCTTCANGCTGGACACAAGTACTGCTTGCTTGNCCGGCTTTC
genomic: CCTCCACCATATGATAAGATGAAGAGGATGGTCATTCCTGATGCACTCAAgttagtttct ... ataaaattagGGTTTTGAGGCTTCAGGCTGGACACAAGTACTGCTTGCTTGGCCGGCTTTC
EST: gi|26262092|gb|CA813155.1|CA813155
EST:     CCTCCACCATATGATAAGATGAAGAGGATGGTCATTCCTGATGCACTCAA                         GGTTTTGAGGCTTCAGGCTGGACACAAGTACTGCTTGCTTGGCCGGCTTTC
genomic: CCTCCACCATATGATAAGATGAAGAGGATGGTCATTCCTGATGCACTCAAgttagtttct ... ataaaattagGGTTTTGAGGCTTCAGGCTGGACACAAGTACTGCTTGCTTGGCCGGCTTTC
EST: gi|37187763|gb|CF607116.1|CF607116
EST:     CCTCCACCATATGATAAGATGAAGAGGATGGTCATTCCTGATGCACTCAA                         GGTTTTGAGGCTTCAGGCTGGACACAAGTACTGCTTGCTTGGCCGGCTTTC
genomic: CCTCCACCATATGATAAGATGAAGAGGATGGTCATTCCTGATGCACTCAAgttagtttct ... ataaaattagGGTTTTGAGGCTTCAGGCTGGACACAAGTACTGCTTGCTTGGCCGGCTTTC
EST: gi|71856679|gb|DT005734.1|DT005734
EST:     CCTCCACCATATGATAAGATGAAGAGGATGGTCATTCCTGATGCACTCAA                         GGTTTTGAGGCTTCAGGCTGGACACAAGTACTGCTTGCTT
genomic: CCTCCACCATATGATAAGATGAAGAGGATGGTCATTCCTGATGCACTCAAgttagtttct ... ataaaattagGGTTTTGAGGCTTCAGGCTGGACACAAGTACTGCTTGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttaatcttgtttcttgctaattgatttgatggttggttgaaataaaattagGGTTTTGAGGCTTCAGGCTGGACACAAGTACTGCTTGCTTGGCCGGCTTTCCTCAGAGGTTGGATGGAACCATTACGATACCATCAGA
                                        ttgaaataaaatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtttcttgtttctcttgattatcgttgtctctgaatttcttaattggggtttggtttcaagtctattgtttttttaatcatgtgttttaatcttgtttcttgctaattgatttgatggttggttgaaataaaattagGGTTTTGAGGCTTCAGGCTGGACACAAGTACTGCTTGCTTGGCCGGCTTTCCTCAGAGGTTGGATGGAACCATTACGATACCATCAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA