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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgacttttaatctactgaaatacattgtgaagttacaagcatttgatgaatttgtgttgttttgatatgtttgaattttttatctcatcgaacagATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTTGATCTTGCTTGTGGCAAG

Basic information

species Vitis vinifera
transcript Vv19s0014g04740.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0014g04740.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA06G41190.1 (Glycine max), 3'ss of exon 2
gtatgacttttaatctactgaaatacattgtgaagttacaagcatttgatgaatttgtgttgttttgatatgtttgaattttttatctcatcgaacagATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTTGATCTTGCTTGTGGCAAG
|||||  ||  | |||     |||| ||  |    || | |     |  |   |    | || ||   | | ||    ||  || | ||||  |||||||||| || ||| | ||||||||||||||||| ||||| ||||| || ||||| || || |||||||||
gtatgtgttgcattcttt---aatatatgatttgtttcccatggagtattatgtgatcgctgattaattgtatt---gttaattttgtcatttaacagATTAAAAGCGTCTTAATTCAGCTTTATGCTCGTCGAGGAGATGCAGTACTTGACCTCGCCTGTGGCAAG

upper sequence: Vv19s0014g04740.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G22390.1 (Glycine max), 3'ss of exon 2
gtatgacttttaatctactgaaataca--ttgtgaagttacaagcatttgatgaatttgtgttgttttgatatgtttgaattttttatctcatcgaacagATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTTGATCTTGCTTGTGGCAAG
|||||  || || |||  | | |||    ||||      |   | |||  |||| ||  || |   ||| | |||   ||||| | || |     ||||||||||||| ||| | |||||||||||||||||  |||| ||||| || || || || || |||||||||
gtatgtgttgtattct-ttaatatatgatttgtttcccaaggggtattacatga-ttgctgattaattgctttgtc-aaatttgtcattt-----aacagATTAAGAGCGTCTTAATTCAGCTTTATGCTCGTAGAGGAGATGCAGTACTCGACCTCGCCTGTGGCAAG
















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|71882642|gb|DT031697.1|DT031697
EST:     AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGG                         ATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
genomic: AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGGgtatgacttt ... catcgaacagATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
EST: gi|351017257|gb|FQ435609.1|FQ435609
EST:     AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGG                         ATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
genomic: AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGGgtatgacttt ... catcgaacagATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
EST: gi|351029176|gb|FQ435376.1|FQ435376
EST:     AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGG                         ATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
genomic: AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGGgtatgacttt ... catcgaacagATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
EST: gi|352786282|gb|FQ478893.1|FQ478893
EST:     AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGG                         ATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
genomic: AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGGgtatgacttt ... catcgaacagATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
EST: gi|71889110|gb|DT038165.1|DT038165
EST:     AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGG                         ATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
genomic: AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGGgtatgacttt ... catcgaacagATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
EST: gi|71887602|gb|DT036657.1|DT036657
EST:     AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGG                         ATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
genomic: AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGGgtatgacttt ... catcgaacagATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
EST: gi|349809402|gb|FQ411900.1|FQ411900
EST:     AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGG                         ATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
genomic: AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGGgtatgacttt ... catcgaacagATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
EST: gi|349829213|gb|FQ419745.1|FQ419745
EST:     AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGG                         ATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
genomic: AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGGgtatgacttt ... catcgaacagATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
EST: gi|349814559|gb|FQ399199.1|FQ399199
EST:     AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGG                         ATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
genomic: AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGGgtatgacttt ... catcgaacagATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
EST: gi|351041305|gb|FQ447432.1|FQ447432
EST:     AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGG                         ATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
genomic: AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGGgtatgacttt ... catcgaacagATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
EST: gi|349823220|gb|FQ400199.1|FQ400199
EST:     AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGG                         ATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
genomic: AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGGgtatgacttt ... catcgaacagATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
EST: gi|71888703|gb|DT037758.1|DT037758
EST:     AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGG                         ATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
genomic: AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGGgtatgacttt ... catcgaacagATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
EST: gi|71884044|gb|DT033099.1|DT033099
EST:     AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGG                         ATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
genomic: AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGGgtatgacttt ... catcgaacagATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
EST: gi|351046268|gb|FQ442646.1|FQ442646
EST:     AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGG                         ATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
genomic: AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGGgtatgacttt ... catcgaacagATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
EST: gi|349809129|gb|FQ398926.1|FQ398926
EST:     AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGG                         ATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
genomic: AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGGgtatgacttt ... catcgaacagATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
EST: gi|349824512|gb|FQ413179.1|FQ413179
EST:     AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGG                         ATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
genomic: AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGGgtatgacttt ... catcgaacagATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
EST: gi|161710854|gb|FC058160.1|FC058160
EST:     AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGG                         ATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
genomic: AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGGgtatgacttt ... catcgaacagATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
EST: gi|351056793|gb|FQ443420.1|FQ443420
EST:     AAGAACGAGAAGCAAGTCCAATCATTCATTTGGAGAAACTAAACAACTGG                         ATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
genomic: AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGGgtatgacttt ... catcgaacagATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
EST: gi|351038453|gb|FQ464319.1|FQ464319
EST:     AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGG                         ATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT
genomic: AAGAACGAGAAGCAAGTCCAATCATTCATTTGAAGAAACTAAACAACTGGgtatgacttt ... catcgaacagATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgatgaatttgtgttgttttgatatgtttgaattttttatctcatcgaacagATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTTGATCTTGCTTGTGGCAAG
                   ttttgat  putative branch site (score: 4)
                                   ttttttatctcatc  putative PPT
                ttgttttgatatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgacttttaatctactgaaatacattgtgaagttacaagcatttgatgaatttgtgttgttttgatatgtttgaattttttatctcatcgaacagATTAAGAGTGTCCTCATTCAGCTTTATGCTCGCCGAGGGGATGCTGTTCTTGATCTTGCTTGTGGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT