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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atctatataattctgtggagagatgaagatatatattcttaatgtgataaatatgcttataattacctaatatacgatgttcctttccatgttcactcagGACATTGTCATAGGTACTCCTGGACGTTTGAAGGATCTAATTGAAATGGGTGTGTGTTGCCTTACAGAGGTATCTTTTGTG

Basic information

species Vitis vinifera
transcript Vv02s0109g00380.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0109g00380.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA01G01390.1 (Glycine max), 3'ss of exon 3
---------------------------------atctatat---aattctg--tggagagatgaagatatatattctta-atgtgataaatatgcttataattacctaatatacga-----tgttccttt-------ccatgttcactcagGACATTGTCATAGGTACTCCTGGACGTTTGAAGGATCTAATTGAAATGGGTGTGTGTTGCCTTACAGAGGTATCTTTTGTG
                                    | |||   ||| |    || ||  |      | |  | |   | ||    | | | |  || | | |   | ||| ||       ||||| |||       |  | | || ||||||||||||||| || || ||||| ||| |  ||||||| |||||||||||| | |||||||| | ||| ||||||||||||
gtaagttatcaagttcttctgttcctttggatggcttgtattcaaatgccagttgaagtcacatgcttgttcacttccatattgagtgagtttttttgttacttttttataaacatcaaattgttcttttaatcctactttttccattcagGACATTGTCATTGGAACCCCTGGTCGTATCCAGGATCTGATTGAAATGGGTATCTGTTGCCTAAAAGAAGTATCTTTTGTG

upper sequence: Vv02s0109g00380.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G34390.1 (Glycine max), 3'ss of exon 3
-----------atctatataattctgtggagagatgaagatatatattcttaatgtgataaatatgcttataattacctaatatac-gatgttcctttccatgttcactcagGACATTGTCATAGGTACTCCTGGACGTTTGAAGGATCTAATTGAAATGGGTGTGTGTTGCCTTACAGAGGTATCTTTTGTG
           |  | |    |||  | |   | |    ||  | || |    ||   | |  |||||| || | |  | || |    ||  | ||||     | || |||||||||| |||| || |||||||| ||| |  ||||||| |||||||||||| | |||||||| | ||| ||||||||||||
gtaagttatcaagttcttctgttcctttggatggtttgtattcaaatgccagttgaagtca-catgcttgtattcaattgatcttttaatactacttttt---tccattcagGACATTATCATTGGAACTCCTGGTCGTATCCAGGATCTGATTGAAATGGGTATCTGTTGCCTAAAAGAAGTATCTTTTGTG
















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|71862644|gb|DT011699.1|DT011699
EST:     ATGGAGGAACTTCTAAAGGACCTCAAATAAGTTCCCTGAAGTCTGGTGTT                         GACATTGTCATAGGTACTCCTGGACGTTTGAAGGATCTAATTGAAATGGGT
genomic: ATGGAGGAACTTCTAAAGGACCTCAAATAAGTTCCCTGAAGTCTGGTGTTgtatgatatt ... gttcactcagGACATTGTCATAGGTACTCCTGGACGTTTGAAGGATCTAATTGAAATGGGT
EST: gi|27586192|gb|CB008887.1|CB008887
EST:     ATGGAGGAACTTCTAAAGGACCTCAAATAAGTTCCCTGAAGTCTGGTGTT                         GACATTGTCATAGGTACTCCTGGACGTTTGAAGGATCTAATTGAAATGGGT
genomic: ATGGAGGAACTTCTAAAGGACCTCAAATAAGTTCCCTGAAGTCTGGTGTTgtatgatatt ... gttcactcagGACATTGTCATAGGTACTCCTGGACGTTTGAAGGATCTAATTGAAATGGGT
EST: gi|110410371|gb|EC976052.1|EC976052
EST:     ATGGAGGAACTTCTAAAGGACCTCAAATAAGTTCCCTGAAGTCTGGTGTT                         GACATTGTCATAGGTACTCCTGGACGTTTGAAGGATCTAATTGAAATGGGT
genomic: ATGGAGGAACTTCTAAAGGACCTCAAATAAGTTCCCTGAAGTCTGGTGTTgtatgatatt ... gttcactcagGACATTGTCATAGGTACTCCTGGACGTTTGAAGGATCTAATTGAAATGGGT
EST: gi|161717360|gb|FC065275.1|FC065275
EST:     ATGGAGGAACTTCTAAAGGACCTCAAATAAGTTCCCTGAAGTCTGGTGTT                         GACATTGTCATAGGTACTCCTGGACGTTTGAAGGATCTAATTGAAATGGGT
genomic: ATGGAGGAACTTCTAAAGGACCTCAAATAAGTTCCCTGAAGTCTGGTGTTgtatgatatt ... gttcactcagGACATTGTCATAGGTACTCCTGGACGTTTGAAGGATCTAATTGAAATGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gataaatatgcttataattacctaatatacgatgttcctttccatgttcactcagGACATTGTCATAGGTACTCCTGGACGTTTGAAGGATCTAATTGAAATGGGTGTGTGTTGCCTTACAGAGGTATCTTTTGTG
                   acctaat  putative branch site (score: 3)
                                  ttcctttccatgttc  putative PPT
           ttataattacctaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atctatataattctgtggagagatgaagatatatattcttaatgtgataaatatgcttataattacctaatatacgatgttcctttccatgttcactcagGACATTGTCATAGGTACTCCTGGACGTTTGAAGGATCTAATTGAAATGGGTGTGTGTTGCCTTACAGAGGTATCTTTTGTG

- - - - - - - - - - - - - - - - - - - - - - - ataaata