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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcatgttcccaacaatttgggtcaatttgaaatttattcgtgccttccattgcttatttttcagattgtagttctaattgaaatcaattgtagtggcacctattatgttccttgtatgcaccattaatcagagaatacaaatgttttatagGCTTTGGCTGACATGAAATCCATCAACCTTTTTGGGGTTCAGCAGATATGTCGGAATTCAATTGCATTGGAACAG

Basic information

species Vitis vinifera
transcript Vv13s0019g04770.t01
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g04770.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA20G32370.1 (Glycine max), 3'ss of exon 23
gtttgcatgttcccaacaatttgggtcaatttgaaatttattcgtgccttccattgcttatttttcagattgtagttctaattgaaatcaattgtagtggcacctattatgttccttgtatgcaccattaatcagagaatac----aaatgttttatagGCTTTGGCTGACATGAAATCCATCAACCTTTTTGGGGTTCAGCAGATATGTCGGAATTCAATTGCATTGGAACAG
                             | |||   || || |    ||    |  | || |||     |||| ||  | || |||||| ||          |||| |  ||||||   | |||   |||| | ||| | |    |  |  ||  ||||||||||| || ||||||||||| || |||||||| ||||| || || ||||| ||| | |||||||||||||||
----------------------------gtgtgattcttttttggagttttttct-ttaatgtttggagctgtattttcagtt-aaatcattt----------ctatcac-ttcctttctttcactgctaatgatagagtgctcttatttacttattagGCTTTGGCAGATATGAAATCCATAAATCTTTTTGGCGTTCAACAAATTTGTCGAAATGCTATTGCATTGGAACAG

upper sequence: Vv13s0019g04770.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: GLYMA10G35190.2 (Glycine max), 3'ss of exon 20
gtttgcatgttcccaacaatttgggtcaatttgaaatttattcgtgccttccattgcttatttttcagattgtagttctaattgaaatcaattgtagtggcacctattatgttccttgtatgcaccattaatcagagaatacaaatgtttt----atagGCTTTGGCTGACATGAAATCCATCAACCTTTTTGGGGTTCAGCAGATATGTCGGAATTCAATTGCATTGGAACAG
                               ||  |||  ||  |    |   |   | || |||     |||| || | | | |||||| ||          |||| |  ||||||   |  ||   |||| | ||| | |   | ||||     ||||||||||| || ||||||||||| || |||||||| |||||||| || ||||| ||| | |||||||| ||||||
------------------------------gtgtgattcttttttagagtttttctttaatgtttggagctgtatttttcagttaaatcattt----------ctatcac-ttcctttcttttactgctaatgatagagtgctcttattttcttattagGCTTTGGCGGATATGAAATCCATAAATCTTTTTGGTGTTCAGCAAATTTGTCGAAATGCTATTGCATTAGAACAG

upper sequence: Vv13s0019g04770.t01 (Vitis vinifera), 3'ss of exon 21
lower sequence: AT3G10380.1 (Arabidopsis thaliana), 3'ss of exon 23
gtttgcatgttcccaacaatttgggtcaatttgaaatttattcgtgccttccattgcttatttttcagattgtagttctaattgaaatcaattgtagtggcacctattatgttccttgtatgcaccatta-atcagagaatacaaatgttttatagGCTTTGGCTGACATGAAATCCATCAACCTTTTTGGGGTTCAGCAGATATGTCGGAATTCAATTGCATTGGAACAG
                       |  ||| |     ||  ||  |  |||   |  ||| |  |||| |||  | |      |   || | | |   |   |    ||||     |  | |  ||  | | |  |   | ||| ||  |||| ||||||||||||||||||| ||| ||||||||||| |||||||| || |||||||||||  | |||||| ||||||||
-----------------------gtacaactc----ttcctttctatctttggt-acttctagttcaaatttgaatataccatactataattcgatatccaataggttatcacaatcttctaaactgtgacagtatttattacgaa-attttctagGCTTTGGCTGACATGAGATCAATCAACCTTTTCGGGGTTCAACAAATATGTCGGAACACTATTGCAGTGGAACAG

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|110363229|gb|EC926805.1|EC926805
EST:     ATTATATATTTGGCGGGATATGTAGTATTGCAGCGAATGCATCAATGAAG                         GCTTTGGCTGACATGAAATCCATCAACCTTTTTGGGGTTCAGCAGATATGT
genomic: ATTATATATTTGGCGGGATATGTAGTATTGCAGCGAATGCATCAATGAAGgtttgcatgt ... tgttttatagGCTTTGGCTGACATGAAATCCATCAACCTTTTTGGGGTTCAGCAGATATGT
EST: gi|110717691|gb|EE093767.1|EE093767
EST:     ATTATATATTTGGCGGGATATGTAGTATTGCAGCGAATGCATCAATGAAG                         GCTTTGGCTGACATGAAATCCATCAACCTTTTTGGGGTTCAGCAGATATGT
genomic: ATTATATATTTGGCGGGATATGTAGTATTGCAGCGAATGCATCAATGAAGgtttgcatgt ... tgttttatagGCTTTGGCTGACATGAAATCCATCAACCTTTTTGGGGTTCAGCAGATATGT
EST: gi|30303826|gb|CB980620.1|CB980620
EST:     ATTATATATTTGGCGGGATATGTAGTATTGCAGCGAATGCATCAATGAAG                         GCTTTGGCTGACATGAAATCCATCAACCTTTTTGGGGTTCAGCAGATATGT
genomic: ATTATATATTTGGCGGGATATGTAGTATTGCAGCGAATGCATCAATGAAGgtttgcatgt ... tgttttatagGCTTTGGCTGACATGAAATCCATCAACCTTTTTGGGGTTCAGCAGATATGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacctattatgttccttgtatgcaccattaatcagagaatacaaatgttttatagGCTTTGGCTGACATGAAATCCATCAACCTTTTTGGGGTTCAGCAGATATGTCGGAATTCAATTGCATTGGAACAG
                         cattaat  putative branch site (score: 3)
                                     aatacaaatgttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgcatgttcccaacaatttgggtcaatttgaaatttattcgtgccttccattgcttatttttcagattgtagttctaattgaaatcaattgtagtggcacctattatgttccttgtatgcaccattaatcagagaatacaaatgttttatagGCTTTGGCTGACATGAAATCCATCAACCTTTTTGGGGTTCAGCAGATATGTCGGAATTCAATTGCATTGGAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT