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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttacttggatgcaacatagaagagaaattttcagattattatgcgccatattgaattgatcattccatcaatgaattaatgtctctggtttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCTCCACAAGATGTTGCTACCTATGGTGGTCTTTGTGCACTTGCAAGCTTTG

Basic information

species Vitis vinifera
transcript Vv15s0048g01980.t01
intron # 2
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 2
lower sequence: LOC_Os03g02540.1 (Oryza sativa), 3'ss of exon 2
gttacttggatg-caaca-tagaagagaaattttcagattattatgcgccatattgaattgatcattc-catc-aatgaattaatgtctctggtttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCTCCACAAGATGTTGCTACCTATGGTGGTCTTTGTGCACTTGCAAGCTTTG
   | | ||||| ||||| | |   || | |    |  |  |||  |   || |    ||  |  ||  |||  |||    |  ||  | |   |   | | ||||  | || |||||   |||||| || ||||| ||  | ||||| || ||||||||||||||||||  ||||||||  ||||||||||||||    || |
---aatgggatgtcaacaattgtgaagtactccgtatgtatttactcat-atgtcatgttctttgttagcatagaatttgctgctgaatttttctcccttaaagTTTGTTGAGACAGGACATGAACTAGGAAACAATTATTCTGAAGTCATAGCTCCACAAGATGTTGCTGTCTATGGTGCCCTTTGTGCACTTGCTTCTTTCG

upper sequence: Vv15s0048g01980.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA03G01880.1 (Glycine max), 3'ss of exon 2
--gttacttggat-gcaacatagaagagaaattttcagattattatgcgccatattgaattgatcattccatcaatgaattaatgtctctggtttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCTCCACAAGATGTTGCTACCTATGGTGGTCTTTGTGCACTTGCAAGCTTTG
     | |||  | | ||  |    || | ||  |  |  |||   |   ||  |    | | | ||  | |     |  |  | |   |  |||| |  |||||  | ||||||||  |||||||||| |   |||| |  || || ||||| || ||||||||||| || ||||| || ||||||||||||||||  ||||
tcacgatttgattcgaaagctttccgatacatgatttg--tatcccgattcaactgccgtggctaataactttggcaaccttgttttctttatttaat-gcagTTTCTAGAAACAGGACCTGAACTGGGAAGTCACTATAATGACGTAATTGCACCTCAAGATGTTGCAACATATGGAGGACTTTGTGCACTTGCAACATTTG

upper sequence: Vv15s0048g01980.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G61140.1 (Arabidopsis thaliana), 3'ss of exon 2
gttacttggatgcaacatagaagagaaattttcagattattatgcgccatattgaattgatcattccatcaatgaattaatgtctctggtttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCTCCACAAGATGTTGCTACCTATGGTGGTCTTTGTGCACTTGCAAGCTTTG
||   |||  | |  ||||   |   |  | |      ||  |    |||||   |      ||   |||| |||| |    | | ||  || |   |||||||| ||        | ||||| || ||   ||| |  ||||| |||||||| |||||| |||| ||||||||||| || ||||| || ||||||||||
gtctgttgttttcc-catatttgctcatgtgtttatggatcctat-tcatatcctaactgaaatctaatcattgaacttgaatat-tgtcttgt--gcagTTCTTAGATGTTAACCCAGAACTTGGAAATTCCTATAATGAAGTCATTGCTCCTCAAGATATTGCCACCTATGGTGGACTCTGTGCCCTGGCAAGCTTTG

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:     CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAG                         TTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
genomic: CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAGgtttgtcagc ... ttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
EST: gi|351052819|gb|FQ456547.1|FQ456547
EST:     CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAG                         TTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
genomic: CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAGgtttgtcagc ... ttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
EST: gi|351038425|gb|FQ461117.1|FQ461117
EST:     CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAG                         TTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
genomic: CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAGgtttgtcagc ... ttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
EST: gi|110718443|gb|EE095284.1|EE095284
EST:     CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAG                         TTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
genomic: CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAGgtttgtcagc ... ttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
EST: gi|110723714|gb|EE101344.1|EE101344
EST:     CAGGATTGGCTCATTTGGAAGCTAAAA-GTACAAGCTTGCTGCTCGCAAG                         TTCNTGGAAACAGGTGCTGAACTGGGGA-CAACTACCCAGAAGTGATTGCT
genomic: CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAGgtttgtcagc ... ttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
EST: gi|349814204|gb|FQ414823.1|FQ414823
EST:     CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAG                         TTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
genomic: CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAGgtttgtcagc ... ttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
EST: gi|352786554|gb|FQ479761.1|FQ479761
EST:     CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAG                         TTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
genomic: CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAGgtttgtcagc ... ttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
EST: gi|351044672|gb|FQ443203.1|FQ443203
EST:     CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAG                         TTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
genomic: CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAGgtttgtcagc ... ttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
EST: gi|351034216|gb|FQ463150.1|FQ463150
EST:     CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAG                         TTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
genomic: CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAGgtttgtcagc ... ttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
EST: gi|351053350|gb|FQ455686.1|FQ455686
EST:     CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAG                         TTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
genomic: CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAGgtttgtcagc ... ttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
EST: gi|351033986|gb|FQ463041.1|FQ463041
EST:     CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAG                         TTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
genomic: CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAGgtttgtcagc ... ttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
EST: gi|351035868|gb|FQ463713.1|FQ463713
EST:     CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAG                         TTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
genomic: CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAGgtttgtcagc ... ttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
EST: gi|349828231|gb|FQ416184.1|FQ416184
EST:     AGGATTGGCTCATTTGGAAGCTAAAAAAGTACAAGCTTGCTGCTCGCAAG                         TTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
genomic: AGGATTGGCTCATTTGGAAGCTAAAAA-GTACAAGCTTGCTGCTCGCAAGgtttgtcagc ... ttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
EST: gi|110418008|gb|EC984114.1|EC984114
EST:     CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAG                         TTCTTGGAAACAGGTGCTGAACT-GGGAACAACTACACAGAAGTGATTGCT
genomic: CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAGgtttgtcagc ... ttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
EST: gi|351045624|gb|FQ440809.1|FQ440809
EST:     CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAG                         TTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
genomic: CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAGgtttgtcagc ... ttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
EST: gi|352798742|gb|FQ478377.1|FQ478377
EST:     CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAG                         TTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
genomic: CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAGgtttgtcagc ... ttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
EST: gi|352791446|gb|FQ481025.1|FQ481025
EST:     CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAG                         TTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
genomic: CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAGgtttgtcagc ... ttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
EST: gi|351038112|gb|FQ465229.1|FQ465229
EST:     CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAG                         TTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
genomic: CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAGgtttgtcagc ... ttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
EST: gi|351048369|gb|FQ449461.1|FQ449461
EST:     CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAG                         TTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
genomic: CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAGgtttgtcagc ... ttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
EST: gi|349823325|gb|FQ402524.1|FQ402524
EST:     CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAG                         TTCTTGGAAACAGGTGCTGAACTGGAGAACAACTACACAGAAGTGATTGCT
genomic: CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAGgtttgtcagc ... ttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
EST: gi|352794164|gb|FQ479406.1|FQ479406
EST:     CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAG                         TTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
genomic: CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAGgtttgtcagc ... ttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
EST: gi|351045527|gb|FQ440712.1|FQ440712
EST:     CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAG                         TTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
genomic: CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAGgtttgtcagc ... ttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
EST: gi|351051967|gb|FQ450658.1|FQ450658
EST:     CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAG                         TTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
genomic: CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAGgtttgtcagc ... ttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
EST: gi|351054564|gb|FQ462671.1|FQ462671
EST:     CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAG                         TTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
genomic: CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAGgtttgtcagc ... ttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
EST: gi|351052534|gb|FQ456382.1|FQ456382
EST:     CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAG                         TTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
genomic: CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAGgtttgtcagc ... ttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
EST: gi|349820411|gb|FQ406967.1|FQ406967
EST:     CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAG                         TTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
genomic: CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAGgtttgtcagc ... ttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
EST: gi|351056545|gb|FQ442373.1|FQ442373
EST:     CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAG                         TTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
genomic: CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAGgtttgtcagc ... ttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
EST: gi|349821444|gb|FQ411065.1|FQ411065
EST:     CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAG                         TTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
genomic: CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAGgtttgtcagc ... ttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
EST: gi|351047650|gb|FQ455047.1|FQ455047
EST:     CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAG                         TTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
genomic: CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAGgtttgtcagc ... ttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
EST: gi|110367302|gb|EC931231.1|EC931231
EST:     CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAG                         TTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
genomic: CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAGgtttgtcagc ... ttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
EST: gi|351023589|gb|FQ432972.1|FQ432972
EST:     CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAG                         TTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT
genomic: CAGGATTGGCTCATTTGGAAGCTAAAAAGTACAAGCTTGCTGCTCGCAAGgtttgtcagc ... ttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccatattgaattgatcattccatcaatgaattaatgtctctggtttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCTCCACAAGATGTTGCTACCTATGGTGGTCTTTGTGCACTTGCAAGCTTTG
                             aattaat  putative branch site (score: 3)
                                            tttattc  putative PPT
                      atcaatgaattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttacttggatgcaacatagaagagaaattttcagattattatgcgccatattgaattgatcattccatcaatgaattaatgtctctggtttattcacagTTCTTGGAAACAGGTGCTGAACTGGGGAACAACTACACAGAAGTGATTGCTCCACAAGATGTTGCTACCTATGGTGGTCTTTGTGCACTTGCAAGCTTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - -ggatgca
- - - - - - - - - - aagagaa
- - - - - - - - - - - - - - - - - - - - tatgcgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtctct