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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGGTGATCTAATCAAATGGGACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCGgtaaactgctaatatacttctttctgtttcttgaaactctctttctgttggactttgacgtggatgaaattataattaatgcatgaactggaggccattt...

Basic information

species Vitis vinifera
transcript Vv19s0014g04740.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0014g04740.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA06G41190.1 (Glycine max), 5'ss of exon 4
GGTGGTGATCTAATCAAATGGGACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCGgtaa--actgctaatatacttctttctgtttcttgaaactctctttctgttggactttgacgtggatgaaattataattaatgcatgaactggaggccattt-
||||||||||| ||||||||||||||||| || |||||||| |||||||| || || |||||||||||||||||||  | | |       | |  ||   |     |    ||  | |||||| |  |      |  ||   || |  ||| || | | |  || ||   | |  
GGTGGTGATCTTATCAAATGGGACAAGGCCAAAATTGGATATTATGTTGGTATTGACATTGCTGAAGGCTCGgtaagtattacgtgctgccataattggctgcaccggttttccttatctgtttgtgtccataatcaattccatca--attcatac-taagatgcagttgactaa

upper sequence: Vv19s0014g04740.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA08G22390.1 (Glycine max), 5'ss of exon 4
GGTGGTGATCTAATCAAATGGGACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCGgtaaactgctaatatacttctttctgtttcttgaaactctctttctgttggactttgacgtggatgaaattat-aattaatgcatgaactggaggccattt-
||||||||||| ||||||||||||||||| || |||||||| |||||||| || || |||||||||||||| ||||       || |  |  |   ||| |        | || || |  ||  | ||  | | |        || || | || | | |  || ||   | |  
GGTGGTGATCTTATCAAATGGGACAAGGCCAAAATTGGATATTATGTTGGTATTGACATTGCTGAAGGCTCAgtaagtattacatcttgtcataattgtctgcactggttttcctttt-ctgatcatttccttagtcacttccatcaaatcatac-taagatgcagttgaatct

upper sequence: Vv19s0014g04740.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA12G17220.1 (Glycine max), 5'ss of exon 5
GGTGGTGATCTAATCAAATGGGACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCGgtaaactgctaatatacttctttctgtttcttgaaactctctttctgttggactttgacgtggatgaaattata----attaatgcatgaactggaggccattt
||||||||||| |||||||||||| |||| || |||||||| |||||||| || || ||||||||||||||||||     |   | |     |   || ||     |  ||  | |||||| |  |      |  ||   || |||    | |||                 ||||
GGTGGTGATCTTATCAAATGGGACTAGGCCAAAATTGGATATTATGTTGGTATTGACATTGCTGAAGGCTCGGTATgtatcatgttttgccataattggttgcaccagttccttatctgtttgtttccataatcaattccatcatatcatactaagatgcagttgactaaggattt

upper sequence: Vv19s0014g04740.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: AT3G20650.2 (Arabidopsis thaliana), 5'ss of exon 4
GGTGGTGATCTAATCAAATGGGACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCGgtaaact-gctaatatacttctttctgtttcttgaaactctctttctgttggactttgacgtggatgaaattataattaatgcatgaactggaggccattt
||||||||| | ||||| ||||| ||||| |  || || ||||||||||| || |||||||||||||| |||||||  |  ||     | |  |  |||| |||| |   |   | | ||||  |  |  |       ||| |  |  |  |||  || |||  |   ||   
GGTGGTGATTTGATCAAGTGGGATAAGGCGAGAATCGGGTACTATGTTGGAATTGATATTGCTGAAGGGTCGgtaagtttactggctgaatgatagctgtatctttattttgcatatatgttttatctctatacctgagaagtgct--tctatgt-tgtacttaataacag--

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:     ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCG                         ATAGAAGACTGCCGTACACGCTATAATGGTGATGCAGACCATCATCAACGG
genomic: ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCGgtaaactgct ... ctatgtacagATAGAAGACTGCCGTACACGCTATAATGGTGACGCAGACCATCATCAACGG
EST: gi|351017257|gb|FQ435609.1|FQ435609
EST:     ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCG                         ATAGAAGACTGCCGTACACGCTATAATGGTGACGCAGACCATCATCAACGG
genomic: ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCGgtaaactgct ... ctatgtacagATAGAAGACTGCCGTACACGCTATAATGGTGACGCAGACCATCATCAACGG
EST: gi|351029176|gb|FQ435376.1|FQ435376
EST:     ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCG                         ATAGAAGACTGCCGTACACGCTATAATGGTGACGCAGACCATCATCAACGG
genomic: ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCGgtaaactgct ... ctatgtacagATAGAAGACTGCCGTACACGCTATAATGGTGACGCAGACCATCATCAACGG
EST: gi|352786282|gb|FQ478893.1|FQ478893
EST:     ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCG                         ATAGAAGACTGCCGTACACGCTATAATGGTGACGCAGACCATCATCAACGG
genomic: ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCGgtaaactgct ... ctatgtacagATAGAAGACTGCCGTACACGCTATAATGGTGACGCAGACCATCATCAACGG
EST: gi|71889110|gb|DT038165.1|DT038165
EST:     ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCG                         ATAGAAGACTGCCGTACACGCTATAATGGTGATGCAGACCATCATCAACGG
genomic: ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCGgtaaactgct ... ctatgtacagATAGAAGACTGCCGTACACGCTATAATGGTGACGCAGACCATCATCAACGG
EST: gi|71887602|gb|DT036657.1|DT036657
EST:     ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCG                         ATAGAAGACTGCCGTACACGCTATAATGGTGATGCAGACCATCATCAACGG
genomic: ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCGgtaaactgct ... ctatgtacagATAGAAGACTGCCGTACACGCTATAATGGTGACGCAGACCATCATCAACGG
EST: gi|349809402|gb|FQ411900.1|FQ411900
EST:     ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCG                         ATAGAAGACTGCCGTACACGCTATAATGGTGACGCAGACCATCATCAACGG
genomic: ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCGgtaaactgct ... ctatgtacagATAGAAGACTGCCGTACACGCTATAATGGTGACGCAGACCATCATCAACGG
EST: gi|349829213|gb|FQ419745.1|FQ419745
EST:     ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCG                         ATAGAAGACTGCCGTACACGCTATAATGGTGACGCAGACCATCATCAACGG
genomic: ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCGgtaaactgct ... ctatgtacagATAGAAGACTGCCGTACACGCTATAATGGTGACGCAGACCATCATCAACGG
EST: gi|349814559|gb|FQ399199.1|FQ399199
EST:     ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCG                         ATAGAAGACTGCCGTACACGCTATAATGGTGACGCAGACCATCATCAACGG
genomic: ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCGgtaaactgct ... ctatgtacagATAGAAGACTGCCGTACACGCTATAATGGTGACGCAGACCATCATCAACGG
EST: gi|351041305|gb|FQ447432.1|FQ447432
EST:     ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCG                         ATAGAAGACTGCCGTACACGCTATAATGGTGACGCAGACCATCATCAACGG
genomic: ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCGgtaaactgct ... ctatgtacagATAGAAGACTGCCGTACACGCTATAATGGTGACGCAGACCATCATCAACGG
EST: gi|349823220|gb|FQ400199.1|FQ400199
EST:     ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCG                         ATAGAAGACTGCCGTACACGCTATAATGGTGACGCAGACCATCATCAACGG
genomic: ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCGgtaaactgct ... ctatgtacagATAGAAGACTGCCGTACACGCTATAATGGTGACGCAGACCATCATCAACGG
EST: gi|71888703|gb|DT037758.1|DT037758
EST:     ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCG                         ATAGAAGACTGCCGTACACGCTATAATGGTGATGCAGACCATCATCAACGG
genomic: ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCGgtaaactgct ... ctatgtacagATAGAAGACTGCCGTACACGCTATAATGGTGACGCAGACCATCATCAACGG
EST: gi|71884044|gb|DT033099.1|DT033099
EST:     ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCG                         ATAGAAGACTGCCGTACACGCTATAATGGTGATGCAGACCATCATCAACGG
genomic: ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCGgtaaactgct ... ctatgtacagATAGAAGACTGCCGTACACGCTATAATGGTGACGCAGACCATCATCAACGG
EST: gi|351046268|gb|FQ442646.1|FQ442646
EST:     ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCG                         ATAGAAGACTGCCGTACACGCTATAATGGTGACGCAGACCATCATCAACGG
genomic: ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCGgtaaactgct ... ctatgtacagATAGAAGACTGCCGTACACGCTATAATGGTGACGCAGACCATCATCAACGG
EST: gi|349809129|gb|FQ398926.1|FQ398926
EST:     ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCG                         ATAGAAGACTGCCGTACACGCTATAATGGTGACGCAGACCATCATCAACGG
genomic: ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCGgtaaactgct ... ctatgtacagATAGAAGACTGCCGTACACGCTATAATGGTGACGCAGACCATCATCAACGG
EST: gi|349824512|gb|FQ413179.1|FQ413179
EST:     ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCG                         ATAGAAGACTGCCGTACACGCTATAATGGTGACGCAGACCATCATCAACGG
genomic: ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCGgtaaactgct ... ctatgtacagATAGAAGACTGCCGTACACGCTATAATGGTGACGCAGACCATCATCAACGG
EST: gi|351056793|gb|FQ443420.1|FQ443420
EST:     ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCG                         ATAGAAGACTGCCGTACACGCTATAATGGTGACGCAGACCATCATCAACGG
genomic: ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCGgtaaactgct ... ctatgtacagATAGAAGACTGCCGTACACGCTATAATGGTGACGCAGACCATCATCAACGG
EST: gi|351038453|gb|FQ464319.1|FQ464319
EST:     ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCG                         ATAGAAGACTGCCGTACACGCTATAATGGTGACGCAGACCATCATCAACGG
genomic: ACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCGgtaaactgct ... ctatgtacagATAGAAGACTGCCGTACACGCTATAATGGTGACGCAGACCATCATCAACGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGGTGATCTAATCAAATGGGACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCGgtaaactgctaatatacttctttctgtttcttgaaactctctttctgttggactttgacgtggatgaaattataattaatgcatgaactggaggccattt

- - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgaaa