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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttatgcttaattaaaggttattgaatttcaagtaatattttttttcctgtttggaaaatacttgtttatctattcagcctttcctgttctcttgatcatttacttgatctaacagATAGAAGTGGGTGATGTGATATGTGAGATAGAGACAGACAAAGCCACCCTTGAATTTGAAAGTCTTGAAGAGGG

Basic information

species Vitis vinifera
transcript Vv13s0074g00150.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0074g00150.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os06g30460.3 (Oryza sativa), 3'ss of exon 5
gtttgttatg-cttaattaaaggttattgaatttcaa----gtaatattttttttcctgtttggaaaatacttgtttatctattcagcctttcctgttctcttgatcatttacttgat-ctaacagATAGAAGTGGGTGATGTGATATGTGAGATAGAGACAGACAAAGCCACCCTTGAATTTGAAAGTCTTGAAGAGGG
    |||| |  ||   |   || ||||  ||   |     | || || || |||||  ||  ||   |  || ||| | | ||     ||    |||    | |  | |||  || |  |  ||||||||||| ||||||||||| ||||||||||| || |||||||| || ||||| ||||| || |||||||||||
----gttaggattttgctctgggatatttcataatagaattgaaacatcttgtttccaattcagagt-tctttatttcttttttatatatta---gtttcgatcaaaagttatctgttgtttgcagATAGAAGTTGGTGATGTGATCTGTGAGATAGAAACTGACAAAGCTACGCTTGAGTTTGAGAGCCTTGAAGAGGG

upper sequence: Vv13s0074g00150.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G082664_T01 (Zea mays), 3'ss of exon 7
gtt-tgttatgcttaattaaaggttattgaatttcaa-----gtaatattttttttcctgtttggaaaatacttgtttatctattcagcct-ttcctgttct-----cttgatcatttact----tgatctaacagATAGAAGTGGGTGATGTGATATGTGAGATAGAGACAGACAAAGCCACCCTTGAATTTGAAAGTCTTGAAGAGGG
||| || | |   ||  |     || || || |||||       |||||  | ||||| | || |    | |   ||| | | || |   | ||   |||||     |   ||| || |      || | |  |||||||| || ||||||||||||||||||||||| || || |||||||| ||||| |||||||| |||||||||||
gttgtgcttttgctagctgttatttttttaaattcaataagaaaaatatcctatttccagcttagggtttcccattttttttgtttaatgtgttttagttctgagaacactatcgttgaactttatgttgttgcagATAGAGGTTGGTGATGTGATATGTGAGATAGAAACTGATAAAGCCACTCTTGAGTTTGAAAGCCTTGAAGAGGG

upper sequence: Vv13s0074g00150.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA10G34480.1 (Glycine max), 3'ss of exon 6
----gtttgttatgcttaa---ttaaaggttattgaatttcaagtaatattttttttcctgtttggaaaata--cttgtttatctattcagcctttcctgttctcttgatcatttacttgatctaacagATAGAAGTGGGTGATGTGATATGTGAGATAGAGACAGACAAAGCCACCCTTGAATTTGAAAGTCTTGAAGAGGG
    || | |||  || |     |||  |  |||  | ||    || ||| |||||     |||  ||  |   | ||  |   || |  || | |  | ||    ||| |||||| || ||| ||||||| |||||||||||| |  ||||||||||||||||||||||||| || ||||||||||| ||||||||||||||
gttagtgttttaacctaaggttctaatagagattctacttttcata-tatatttttaatattttaaaatgtgagcatgagtcgttaatgggcatatattttttgtctgaacatttaatttatcaaacagATTGAAGTGGGTGATATATTATGTGAGATAGAGACAGACAAAGCTACACTTGAATTTGAGAGTCTTGAAGAGGG

upper sequence: Vv13s0074g00150.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA20G33080.1 (Glycine max), 3'ss of exon 10
----gtttgttatgcttaa---ttaaaggttattgaa--tttcaagtaatatt--ttttttcctgtttggaaaatacttgtttatc----tattcagcctttcctgttctcttgatcatttacttgatctaacagATAGAAGTGGGTGATGTGATATGTGAGATAGAGACAGACAAAGCCACCCTTGAATTTGAAAGTCTTGAAGAGGG
    || | |||  || |     |||  |  |||| |  |||||  || | ||  | ||||    | || | |  | |  || ||     ||||     | ||   |   |   | |||||| || ||||||||||| |||||||| ||| |  |||||||||| |||||||||||||| || ||||||||||||| ||||||||||||
gttagtgttttaacctaaggttctaatagagattgtacttttcatatatttttaatattttaaaatatgaacatgagtcattaatgcccatattttctttatctgatatgcaataacatttaatttatctaacagATTGAAGTGGGCGATATATTATGTGAGATCGAGACAGACAAAGCTACACTTGAATTTGAAACTCTTGAAGAGGG

upper sequence: Vv13s0074g00150.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA10G34480.1 (Glycine max), 3'ss of exon 2
--------gtttgttatgcttaattaaaggttattgaatttcaagtaatattttttttcctgtttggaaaat--acttgtttatctattcagcctttcctgttctcttgatcatttacttgatctaacagATAGAAGTGGGTGATGTGATATGTGAGATAGAGACAGACAAAGCCACCCTTGAATTTGAAAGTCTTGAAGAGGG
        || | |    ||   | | |  |   |  | |||   |  | ||  |  |    ||| | | ||  |||| |||    | | |     || | ||  | ||   | | | || |||||||||||||||||||| |||||  ||||||| || || || |||||||| || || |||||||||||||||||||||||
gtcagttagtatatagctctgtttcatacttctgtttagttctgtttgtgttgatgctttcattttggagattgacttctttg---aattaattaatcattttgacatgggtactga-ttaatctaacagATAGAAGTGGGGGATGTACTATGTGAAATTGAAACTGACAAAGCTACACTAGAATTTGAAAGTCTTGAAGAGGG

upper sequence: Vv13s0074g00150.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA20G33080.1 (Glycine max), 3'ss of exon 6
--------gtttgttatgctta---attaaaggttattga----atttcaagtaatattttttttcctgtttggaaaat--acttgttt-atctattcagcctttcctgttctcttgatcatttacttgatctaacagATAGAAGTGGGTGATGTGATATGTGAGATAGAGACAGACAAAGCCACCCTTGAATTTGAAAGTCTTGAAGAGGG
        || | |  | ||||    || | |||||| ||    | ||    |  |  |  |  |    ||| | | ||  |||| ||| |  || | |  |||| |       ||| | | ||| || |||||||||||||||||||| |||||  ||||||| || || || |||||||| || || |||||||||||||||||||||||
gtcagttagtatatagttcttatattttgatggttatggatcatacttttgtttgtgctgatgctttcattttggagattgacttctttgaattaattaatcttttcgaca---ttggt-actta-ttaatctaacagATAGAAGTGGGGGATGTACTATGTGAAATTGAAACTGACAAAGCTACACTAGAATTTGAAAGTCTTGAAGAGGG

upper sequence: Vv13s0074g00150.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT3G52200.1 (Arabidopsis thaliana), 3'ss of exon 10
gtttgttatgcttaattaaaggttattgaatt--tcaagtaatattttttttcctgtttggaaaatact-tgtttatctattcagcctttcctgttctcttgatcatttacttgatctaacagATAGAAGTGGGTGATGTGATATGTGAGATAGAGACAGACAAAGCCACCCTTGAATTTGAAAGTCTTGAAGAGGG
           ||| ||   ||| |    ||   | || |   ||| |  || |        ||||    |||||||  | |  |||| |  || |   |       | | || ||  ||||||| |||||||||||||| ||| ||||||| ||||| ||||||||||| || ||||||||||| |||||||||||
----------gttagtttctggtgacccgatgagtaaattggcattgtaatttcaccacaagaaatctgatgtttatgcactt-gcctgtgttgattcttc------tcatttcatgaaacagATTGAAGTGGGTGATGTCATAGGTGAGATCGAGACTGACAAAGCCACTCTGGAATTTGAAAGCCTTGAAGAGGG

upper sequence: Vv13s0074g00150.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT3G52200.2 (Arabidopsis thaliana), 3'ss of exon 6
--------------------------------------------gtttgttatgcttaattaaaggttattgaatttcaagtaatat---tttttttcctgtttggaaaatacttgtttatctattcagcctttcctgttctcttgatcatttacttgatc-taacagATAGAAGTGGGTGATGTGATATGTGAGATAGAGACAGACAAAGCCACCCTTGAATTTGAAAGTCTTGAAGAGGG
                                             | || | |  |  | ||| | | |||  |    ||  |  ||   ||  |    |   ||| ||| |     |    | |  |   | ||     |   |    ||||  ||  || | |||| |||| |||||||||||  ||||||||||||||||||||||||||||  | |||||||| ||||  || || ||
gtgggttatttcttatttttggttgacaaaatttcagtcgacttttatgattttgtctactaatgatcattatacaagaaagacgataaattgataatttagctggcaaagaaaatatagaatgtggaaattctcagtaacaggtatgaatttggttcttcctgacagGTAGAGGTGGGTGATGTACTATGTGAGATAGAGACAGACAAAGCCACTGTAGAATTTGAGAGTCAAGAGGAAGG

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|351024682|gb|FQ433097.1|FQ433097
EST:     AACCAGGGTAACATTGCTAAGTGGAGGAAAAAGGAAGGAGATAAG                         ATAGAAGTGGGTGATGTGATATGTGAGATAGAGACAGACAAAGCCACCCTT
genomic: AACCAGGGTAACATTGCTAAGTGGAGGAAAAAGGAAGGAGATAAGgtttgttatg ... gatctaacagATAGAAGTGGGTGATGTGATATGTGAGATAGAGACAGACAAAGCCACCCTT
EST: gi|351040802|gb|FQ438346.1|FQ438346
EST:     AACCAGGGTAACATTGCTAAGTGGAGGAAAAAGGAAGGAGATAAG                         ATAGAAGTGGGTGATGTGATATGTGAGATAGAGACAGACAAAGCCACCCTT
genomic: AACCAGGGTAACATTGCTAAGTGGAGGAAAAAGGAAGGAGATAAGgtttgttatg ... gatctaacagATAGAAGTGGGTGATGTGATATGTGAGATAGAGACAGACAAAGCCACCCTT
EST: gi|349832802|gb|FQ422896.1|FQ422896
EST:     AACCAGGGTAACATTGCTAAGTGGAGGAAAAAGGAAGGAGATAAG                         ATAGAAGTGGGTGATGTGATATGTGAGATAGAGACAGACAAAGCCACCCTT
genomic: AACCAGGGTAACATTGCTAAGTGGAGGAAAAAGGAAGGAGATAAGgtttgttatg ... gatctaacagATAGAAGTGGGTGATGTGATATGTGAGATAGAGACAGACAAAGCCACCCTT
EST: gi|294966249|gb|GW839472.1|GW839472
EST:     GGAGGAAAAAGGAAGGAGATAAG                         ATAGAAGTGGGTGATGTGATATGTGAGATAGAGACAGACAAAGCCACCCTT
genomic: GGAGGAAAAAGGAAGGAGATAAGgtttgttatg ... gatctaacagATAGAAGTGGGTGATGTGATATGTGAGATAGAGACAGACAAAGCCACCCTT
EST: gi|351015706|gb|FQ427191.1|FQ427191
EST:     AACCAGGGTAACATTGCTAAGTGGAGGAAAAAGGAAGGAGATAAG                         ATAGAAGTGGGTGATGTGATATGTGAGATAGAGACAGACAAAGCCACCCTT
genomic: AACCAGGGTAACATTGCTAAGTGGAGGAAAAAGGAAGGAGATAAGgtttgttatg ... gatctaacagATAGAAGTGGGTGATGTGATATGTGAGATAGAGACAGACAAAGCCACCCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgtttatctattcagcctttcctgttctcttgatcatttacttgatctaacagATAGAAGTGGGTGATGTGATATGTGAGATAGAGACAGACAAAGCCACCCTTGAATTTGAAAGTCTTGAAGAGGG
     ttatctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttatgcttaattaaaggttattgaatttcaagtaatattttttttcctgtttggaaaatacttgtttatctattcagcctttcctgttctcttgatcatttacttgatctaacagATAGAAGTGGGTGATGTGATATGTGAGATAGAGACAGACAAAGCCACCCTTGAATTTGAAAGTCTTGAAGAGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG