Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcatctattgagtgtttttccttttcaatagttgtttttctctatggtttcatgattgctttctaattgaatgctttcacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCTGAAGTAAGGGAGCTTATTCATGATTTCTATTCAAG

Basic information

species Vitis vinifera
transcript Vv15s0048g01980.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0048g01980.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM5G829967_T01 (Zea mays), 3'ss of exon 1
gcat-ctattg-agtgtttttccttttcaatagttgtttttc--tctatggtttcatgattgctttctaattgaatgctttcacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCTGAAGTAAGGGAGCTTATTCATGATTTCTATTCAAG
|  | | |||  |||  ||    |||  |   |    | |||  | |||| |    |  |     | | ||||  |||      ||   |||| ||||| || |||||| |||||||||| |||||  ||||| | || |||||||||||||||||  || |||||||  || ||||
gtttgccattatagtacttaatttttctagcggaacatgttccatttatgctgctgttctcaaaatgtgattgcttgcacatttttcatagAACAAAGTCATCGACAATATCAACTTCCGTAACTTTCTAGAGCTGGTGCCTGAAGTAAGGGAGCTGGTTAATGATTTTAATGCAAG

upper sequence: Vv15s0048g01980.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA03G01880.1 (Glycine max), 3'ss of exon 3
--------------gcatctattgagtgtttttccttttcaatagttgtttttctctatggtttcatgattgctttctaattgaatgctttcacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCTGAAGTAAGGGAGCTTATTCATGATTTCTATTCAAG
                ||   |    || || | |||||||||        ||        | || |  ||  ||  |  ||   |      |  ||||||| ||||||||||||||||  ||||||||| || ||||||||||||||||||||||||||||| || ||  ||||||| || |||||
gcaagctctccattatattgttgtgatggttcttcttttcaatctgaaacattgatggcattgtctttgttttttcttttttctttttcaatatctggcagAGTAAAGTTATAGACAATTCCAACTTCCGCAATTTCTTAGAGTTAGTACCTGAAGTAAGGGAACTGATAAATGATTTTTACTCAAG

upper sequence: Vv15s0048g01980.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA07G08370.1 (Glycine max), 3'ss of exon 3
--------------gcatctattgagtgtttttccttttcaatagttgtttt----tctctatggtttcatgattgctttctaattgaatgctttca---cttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCTGAAGTAAGGGAGCTTATTCATGATTTCTATTCAAG
                ||   |    || || | ||||| |||   || | |      |  |||   |  |  ||| |||||  ||      |||||    ||||||||  |||||||||||||||  ||||||||| || ||||||||||||||||||||||||||||| || ||  ||||||| || |||||
gcaagtactccattatattgttacgatggttcttcttttgaatgactgctctgaaacgttgatgacattgtctttgttttctcttttttccttttcaatatttggcagAGCAAAGTTATAGACAATTCCAACTTCCGCAATTTCTTAGAGTTAGTACCTGAAGTAAGGGAACTGATAAATGATTTTTACTCAAG

upper sequence: Vv15s0048g01980.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT3G61140.1 (Arabidopsis thaliana), 3'ss of exon 3
gcatctattgagtgtttttccttttcaatagttgtttttctctatggtttcatgattgctttctaattgaatgctttcacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCTGAAGTAAGGGAGCTTATTCATGATTTCTATTCAAG
|||| |||    | |||  | |||    ||  | |     | |    |   |   ||| | | ||| | | |    | | || |||| | ||||| || |||||| ||||||||||||| ||||| ||| |||| ||||| || ||||| |||||  | ||||||||||||||
gcatgtatcc--tatttagcatttcttttaactctgccatttttc--tccaacacttggtctataacttagt---ctaattttgcagCAAAAAGTCATTGACAATATCAACTTCCGGAATTTCTTGGAGCTAGTGCCTGATGTGAGGGAACTTATCAACGATTTCTATTCAAG

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|110699322|gb|EE076217.1|EE076217
EST:     CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAG                         AATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
genomic: CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAGgcatctattg ... cacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
EST: gi|351052819|gb|FQ456547.1|FQ456547
EST:     CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAG                         AATAAAGTTATAGACAATTTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
genomic: CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAGgcatctattg ... cacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
EST: gi|351038425|gb|FQ461117.1|FQ461117
EST:     CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAG                         AATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
genomic: CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAGgcatctattg ... cacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
EST: gi|110718443|gb|EE095284.1|EE095284
EST:     CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAG                         AATAAAGTTATAGACAATCTCAACTTCCGGAACTTCATAGAGTTAGTACCT
genomic: CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAGgcatctattg ... cacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
EST: gi|349814204|gb|FQ414823.1|FQ414823
EST:     CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAG                         AATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
genomic: CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAGgcatctattg ... cacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
EST: gi|352786554|gb|FQ479761.1|FQ479761
EST:     CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAG                         AATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
genomic: CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAGgcatctattg ... cacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
EST: gi|351044672|gb|FQ443203.1|FQ443203
EST:     CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAG                         AATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
genomic: CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAGgcatctattg ... cacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
EST: gi|110369076|gb|EC933221.1|EC933221
EST:     CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAG                         AATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
genomic: CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAGgcatctattg ... cacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
EST: gi|351034216|gb|FQ463150.1|FQ463150
EST:     CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAG                         AATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
genomic: CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAGgcatctattg ... cacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
EST: gi|351053350|gb|FQ455686.1|FQ455686
EST:     CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAG                         AATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
genomic: CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAGgcatctattg ... cacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
EST: gi|351033986|gb|FQ463041.1|FQ463041
EST:     CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAG                         AATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
genomic: CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAGgcatctattg ... cacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
EST: gi|351035868|gb|FQ463713.1|FQ463713
EST:     CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAG                         AATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
genomic: CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAGgcatctattg ... cacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
EST: gi|349828231|gb|FQ416184.1|FQ416184
EST:     CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAG                         AATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAAAGTTAGTACCT
genomic: CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAGgcatctattg ... cacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
EST: gi|110418008|gb|EC984114.1|EC984114
EST:     CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAG                         AATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
genomic: CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAGgcatctattg ... cacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
EST: gi|351045624|gb|FQ440809.1|FQ440809
EST:     CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAG                         AATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
genomic: CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAGgcatctattg ... cacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
EST: gi|110378199|gb|EC943318.1|EC943318
EST:     CAGAGCTGAAG                         AATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
genomic: CAGAGCTGAAGgcatctattg ... cacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
EST: gi|352798742|gb|FQ478377.1|FQ478377
EST:     CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAG                         AATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
genomic: CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAGgcatctattg ... cacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
EST: gi|352791446|gb|FQ481025.1|FQ481025
EST:     CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAG                         AATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
genomic: CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAGgcatctattg ... cacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
EST: gi|351038112|gb|FQ465229.1|FQ465229
EST:     CCTATGGTGGTCTTTGTGCACTTGTAAGCTTTGACCGTACAGAGCTGAAG                         AATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
genomic: CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAGgcatctattg ... cacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
EST: gi|351048369|gb|FQ449461.1|FQ449461
EST:     CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAG                         AATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
genomic: CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAGgcatctattg ... cacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
EST: gi|349823325|gb|FQ402524.1|FQ402524
EST:     CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAG                         AATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
genomic: CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAGgcatctattg ... cacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
EST: gi|352794164|gb|FQ479406.1|FQ479406
EST:     CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAG                         AATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
genomic: CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAGgcatctattg ... cacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
EST: gi|351045527|gb|FQ440712.1|FQ440712
EST:     CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAG                         AATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
genomic: CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAGgcatctattg ... cacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
EST: gi|351051967|gb|FQ450658.1|FQ450658
EST:     CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAG                         AATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
genomic: CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAGgcatctattg ... cacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
EST: gi|351054564|gb|FQ462671.1|FQ462671
EST:     CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAG                         AATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
genomic: CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAGgcatctattg ... cacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
EST: gi|351052534|gb|FQ456382.1|FQ456382
EST:     CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAG                         AATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
genomic: CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAGgcatctattg ... cacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
EST: gi|349820411|gb|FQ406967.1|FQ406967
EST:     CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAG                         AATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
genomic: CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAGgcatctattg ... cacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
EST: gi|351056545|gb|FQ442373.1|FQ442373
EST:     CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAG                         AATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
genomic: CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAGgcatctattg ... cacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
EST: gi|349821444|gb|FQ411065.1|FQ411065
EST:     CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAG                         AATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
genomic: CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAGgcatctattg ... cacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
EST: gi|351047650|gb|FQ455047.1|FQ455047
EST:     CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAG                         AATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
genomic: CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAGgcatctattg ... cacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
EST: gi|110367302|gb|EC931231.1|EC931231
EST:     CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAG                         AATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
genomic: CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAGgcatctattg ... cacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
EST: gi|351023589|gb|FQ432972.1|FQ432972
EST:     CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAG                         AATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT
genomic: CCTATGGTGGTCTTTGTGCACTTGCAAGCTTTGACCGTACAGAGCTGAAGgcatctattg ... cacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttttctctatggtttcatgattgctttctaattgaatgctttcacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCTGAAGTAAGGGAGCTTATTCATGATTTCTATTCAAG
                            ttctaat  putative branch site (score: 2)
                                         ctttcactt  putative PPT
                           tttctaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatctattgagtgtttttccttttcaatagttgtttttctctatggtttcatgattgctttctaattgaatgctttcacttggcagAATAAAGTTATAGACAATCTCAACTTCCGGAACTTCTTAGAGTTAGTACCTGAAGTAAGGGAGCTTATTCATGATTTCTATTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT