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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaataaatcatgaacaaacccacaagcaaatcctgtatgatattatctgatctttactgaggacttttcagttgatactcaatttctttccatacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCAGTCTGTTGCGGTCTTGCACGATCGAACCTGAGTGCATTGTTGGGCAACA

Basic information

species Vitis vinifera
transcript Vv17s0000g01240.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g01240.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os02g30460.1 (Oryza sativa), 3'ss of exon 1
aaataaatcatgaacaaacccacaagcaaatcctgtatgatat-tatctgatctttactgaggac---ttttcagttgatactcaatttctttccatacat------cagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCAGTCTGTTGCGGTCTTGCACGATCGAACCTGAGTGCATTGTTGGGCAACA
         |    |      |       | ||||||  || | |    | |  || |  | | |    |||||||| || |||| |        ||  ||      ||||| |||||||  ||||  |  | ||  ||||||||||||| ||||||| | |||||||||| || ||||| || ||||||||||||||  | || || ||
---------acatgcccttttatgtatgtaacctgtaatatttgtgctaggtacttccataagccaaggtttcagttaat-ctcattcctaagttatgtattatgtgcagGACTACCAGCTGACACCCTTGTTGACCGGTATGTGACAGTGGGTGCATACTGTCTGTTGCGCTCATGCACTATTGAACCTGAGTGCATCATCGGTCAGCA

upper sequence: Vv17s0000g01240.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G123966_T01 (Zea mays), 3'ss of exon 1
aaataaatcatgaacaaacc-cacaagcaaatcctgtatgatattatctgatctttactgaggactt--ttcagttgatactcaatttctttccatacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCAGTCTGTTGCGGTCTTGCACGATCGAACCTGAGTGCATTGTTGGGCAACA
    |  |  |      ||   |  |  ||   |  || | | |    |     |||   | | ||   ||   |     |  || ||  | |  |    ||||  | |||||  | ||| || | ||  |||| |||||||| || || | | |||||||||| |||||||| ||||| |||||||||||  |||| || ||
--ccaccttgtacttgtactgtaataataatgtccatacgctgtatggtacctgttaggcaaggctggatttgatctcagcgtaaatttgtgctgtttg-cagGGCTTCCAGCTGAGACACTCGTGGACCGGTACGTGACAGTGGGCGCCTACTGTCTGTTGCGCTCTTGCACCATCGAGCCTGAGTGCATCATTGGCCAGCA

upper sequence: Vv17s0000g01240.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G48680.1 (Arabidopsis thaliana), 3'ss of exon 1
-aaataaatcat-gaacaaacccacaagcaaatcctgtatgatattatctgatctttactgaggacttttcagttgatactcaatttctttccatacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCAGTCTGTTGCGGTCTTGCACGATCGAACCTGAGTGCATTGTTGGGCAACA
    | ||  || || || ||      ||   |  || ||  | | || ||||   ||   |     | | ||  ||||||   |   ||    |   ||||||||||||||||| ||||| ||||| ||||| |||||||||||||||| |||||| ||  | || ||||| |||||||| || |||||  | ||||||||
atcttgaaggatagagcatactgtggtgctgcttttgaat--tttgatatgatagataaaaatctgatcttagaagatactttctactttgatttttttcagGATTACCAGCACAAACATTGATCGATAGGTACGTGACAGTTGGTGCATACAGTCTTTTAAGATCATGCACTATCGAACCAGAATGCATCATCGGGCAACA

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|77577619|gb|DV217551.1|DV217551
EST:     TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAG                         GATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATACA
genomic: TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAGgtcaggattt ... catacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
EST: gi|30136801|gb|CB922139.1|CB922139
EST:     TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAG                         GATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
genomic: TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAGgtcaggattt ... catacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
EST: gi|110699891|gb|EE077311.1|EE077311
EST:     TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAG                         GATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
genomic: TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAGgtcaggattt ... catacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
EST: gi|351037239|gb|FQ457072.1|FQ457072
EST:     TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAG                         GATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATACA
genomic: TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAGgtcaggattt ... catacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
EST: gi|110719796|gb|EE095235.1|EE095235
EST:     TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAG                         GATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
genomic: TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAGgtcaggattt ... catacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
EST: gi|71862128|gb|DT011183.1|DT011183
EST:     TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAG                         GATTACCAGCACACA
genomic: TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAGgtcaggattt ... catacatcagGATTACCAGCACACA
EST: gi|38516611|gb|CF983786.1|CF983786
EST:     TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAG                         GATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATACA
genomic: TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAGgtcaggattt ... catacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
EST: gi|161714708|gb|FC062676.1|FC062676
EST:     TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAG                         GATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATACA
genomic: TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAGgtcaggattt ... catacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
EST: gi|77585371|gb|DV221777.1|DV221777
EST:     TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAG                         GATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATACA
genomic: TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAGgtcaggattt ... catacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
EST: gi|110729870|gb|EE106298.1|EE106298
EST:     TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAG                         GATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
genomic: TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAGgtcaggattt ... catacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
EST: gi|161721500|gb|FC069728.1|FC069728
EST:     TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAG                         GATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATACA
genomic: TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAGgtcaggattt ... catacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
EST: gi|87585129|gb|DY473978.1|DY473978
EST:     TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTCGGAATTCTCCTACAG                         GATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATACA
genomic: TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAGgtcaggattt ... catacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
EST: gi|33402261|gb|CF207888.1|CF207888
EST:     TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAG                         GATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATACA
genomic: TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAGgtcaggattt ... catacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
EST: gi|32245056|gb|CD710875.1|CD710875
EST:     TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAG                         GATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATACA
genomic: TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAGgtcaggattt ... catacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
EST: gi|110732422|gb|EE107696.1|EE107696
EST:     TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAG                         GATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
genomic: TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAGgtcaggattt ... catacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
EST: gi|110390793|gb|EC955721.1|EC955721
EST:     TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAG                         GATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATACA
genomic: TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAGgtcaggattt ... catacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
EST: gi|110720863|gb|EE097155.1|EE097155
EST:     TAATATTCAGGAGAAGTGTGTTATCCCCGCTGCTTGGAATTCTCCTACAG                         GATTACCAGCACACACATTCGTCGAGAGGTATGTGACAGTTGGTGCATCCA
genomic: TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAGgtcaggattt ... catacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
EST: gi|38516610|gb|CF983785.1|CF983785
EST:     AATATTCAGGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAG                         GATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATACA
genomic: AATATTCAGG-AGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAGgtcaggattt ... catacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
EST: gi|77580729|gb|DV219269.1|DV219269
EST:     TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAG                         GATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATACA
genomic: TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAGgtcaggattt ... catacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
EST: gi|30128516|gb|CB913855.1|CB913855
EST:     TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAG                         GATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATATA
genomic: TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAGgtcaggattt ... catacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
EST: gi|110702999|gb|EE079471.1|EE079471
EST:     TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAG                         GATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
genomic: TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAGgtcaggattt ... catacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
EST: gi|110715533|gb|EE093694.1|EE093694
EST:     TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAG                         GATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
genomic: TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAGgtcaggattt ... catacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
EST: gi|349832653|gb|FQ422011.1|FQ422011
EST:     TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAG                         GATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
genomic: TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAGgtcaggattt ... catacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
EST: gi|77582132|gb|DV220023.1|DV220023
EST:     TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAG                         GATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATACA
genomic: TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAGgtcaggattt ... catacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
EST: gi|110700839|gb|EE077846.1|EE077846
EST:     TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAG                         GATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
genomic: TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAGgtcaggattt ... catacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
EST: gi|110708204|gb|EE085477.1|EE085477
EST:     TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAG                         GATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
genomic: TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAGgtcaggattt ... catacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
EST: gi|110701705|gb|EE079581.1|EE079581
EST:     TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAG                         GATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
genomic: TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAGgtcaggattt ... catacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
EST: gi|71857415|gb|DT006470.1|DT006470
EST:     TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAG                         GATTACCAGCACACACATTCATCGAGAGGTATGTGACAG
genomic: TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAGgtcaggattt ... catacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAG
EST: gi|77578701|gb|DV218140.1|DV218140
EST:     TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAG                         GATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATACA
genomic: TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAGgtcaggattt ... catacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
EST: gi|18459532|gb|BM437810.1|BM437810
EST:     TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAG                         GATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATACA
genomic: TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAGgtcaggattt ... catacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
EST: gi|349810417|gb|FQ401863.1|FQ401863
EST:     TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAG                         GATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGCGCATCCA
genomic: TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAGgtcaggattt ... catacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
EST: gi|349828258|gb|FQ416211.1|FQ416211
EST:     TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAG                         GATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA
genomic: TAATATTCAGGAGAGGTGTGTTATCCACGCTGCTTGGAATTCTCCTACAGgtcaggattt ... catacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgatctttactgaggacttttcagttgatactcaatttctttccatacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCAGTCTGTTGCGGTCTTGCACGATCGAACCTGAGTGCATTGTTGGGCAACA
                                ctcaatttctttcc  CT-rich tract
                                   aatttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaataaatcatgaacaaacccacaagcaaatcctgtatgatattatctgatctttactgaggacttttcagttgatactcaatttctttccatacatcagGATTACCAGCACACACATTCATCGAGAGGTATGTGACAGTTGGTGCATCCAGTCTGTTGCGGTCTTGCACGATCGAACCTGAGTGCATTGTTGGGCAACA

aaataaa
- - - - catgaac
- - - - - - - -aaaccca
- - - - - - - - - - - -aagcaaa
- - - - - - - - - - - - - - - - ctgtatg