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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatttctttaggcaaaaaataaaccatgcattttgcatcttgttgatgatctcatactatatacatgacagGATATTAGTCTGGGAGGATGGTTTCTGCAACTTTGCTGCCTCAACAGCCGAGATCAACTCCAGCGACTGTGTGGGCTCATCAGTCTATGGCAACTGTGAA

Basic information

species Vitis vinifera
transcript Vv01s0026g00350.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0026g00350.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA02G03740.1 (Glycine max), 3'ss of exon 2
-------------------------gtatatttctttaggcaaaaaataaaccatgcattttgcatcttgttg------atgatctcatactatatacatg---acagGATATTAGTCTGGGAGGATGGTTTCTGCAACTTTGCTGCCTCAACAGC---CGAGATCAACTCCAGCGACTGTGTGGGCTCATCAGTCTATGGCAACTGTGAA
                         |  | ||   ||   ||    |||   || |  | |||  |    |||      ||  | |  |  |||||| |||    ||||||||| || ||||| |||||||||||||| |||||||||||| ||||    || || |||||  | || |||     | || | |  ||||| ||||||   
gtaatgtttttcagtgttgagtgatgagtgttaacttcaacactgtatagtgcaggattattgtgttagtttggctaacatagtgtgtttatatatatatgcatgcagGATATTGGTGTGGGAAGATGGTTTCTGCAATTTTGCTGCCTCAGCAGCTCCTGAAATTAACTCAGGTGATTGTTCTACCCCACCTGCTTATGGGAACTGT---

upper sequence: Vv01s0026g00350.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA01G03940.1 (Glycine max), 3'ss of exon 2
--------------------gta-tatttctttaggcaaaaaataaaccatgcattttgcatcttgttga------tgatctcata---ctatatacatgacagGATATTAGTCTGGGAGGATGGTTTCTGCAACTTTGCTGCCTCAACAGC---CGAGATCAACTCCAGCGACTGTGTGGGCTCATCAGTCTATGGCAACTGTGAA
                    ||| | ||   ||   ||  |  ||   || |  | |||  | | ||| |      |||  | |||    ||||| |||| ||||||||| || ||||| |||||||||||||| |||||||| ||| ||||    ||  | |||||  | || |||     | || | || ||||| ||||||   
gtaatgtttttcagtgttgagtagtgttaacttcaacactagctagtgcaggattgttgtgtttggttaacagtagtgagtttataactttatatgcatg-cagGATATTGGTGTGGGAAGATGGTTTCTGCAATTTTGCTGCATCAGCAGCACCTGAAGTTAACTCTGGTGATTGTTCTACCCCACCTGTTTATGGGAACTGT---
















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|110422036|gb|EC988347.1|EC988347
EST:     GATGGCCAAGCAGGAGCCTATGATAGGTCAAGAGGAAATAGGAGGAACTG                         GATATTAGTCTGGGAGGATGGTTTCTGCAACTTTGCTGCCTCAACAGCCGA
genomic: GATGGCCAAGCAGGAGCCTATGATAGGTCAAGAGGAAATAGGAGGAACTGgtatatttct ... tacatgacagGATATTAGTCTGGGAGGATGGTTTCTGCAACTTTGCTGCCTCAACAGCCGA
EST: gi|110711993|gb|EE089106.1|EE089106
EST:     GATGGCCAAGCAGGAGCCTATGATAGGTCAAGAGGAAATAGGAGGAACTG                         GATATTAGTCTGGGAGGATGGTTTCTGCAACTTTGCTGCCTCAACAGCCGA
genomic: GATGGCCAAGCAGGAGCCTATGATAGGTCAAGAGGAAATAGGAGGAACTGgtatatttct ... tacatgacagGATATTAGTCTGGGAGGATGGTTTCTGCAACTTTGCTGCCTCAACAGCCGA
EST: gi|37187728|gb|CF607081.1|CF607081
EST:     GATGGCCAAGCAGGAGCCTATGATAGGTCAAGAGGAAATAGGAGGAACTG                         GATATTAGTCTGGGAGGATGGTTTCTGCAACTTTGCTGCCTCAACAGCCGA
genomic: GATGGCCAAGCAGGAGCCTATGATAGGTCAAGAGGAAATAGGAGGAACTGgtatatttct ... tacatgacagGATATTAGTCTGGGAGGATGGTTTCTGCAACTTTGCTGCCTCAACAGCCGA
EST: gi|71866843|gb|DT015898.1|DT015898
EST:     GATGGCCAAGCAGGAGCCTATGATAGGTCAAGAGGAAATAGGAGGAACTG                         GATATTAGTCTGGGAGGATGGTTTCTGCAACTTTGCTGCCTCAACAGCCGA
genomic: GATGGCCAAGCAGGAGCCTATGATAGGTCAAGAGGAAATAGGAGGAACTGgtatatttct ... tacatgacagGATATTAGTCTGGGAGGATGGTTTCTGCAACTTTGCTGCCTCAACAGCCGA
EST: gi|77581829|gb|DV219868.1|DV219868
EST:     GATGGCCAAGCAGGAGCCTATGATAGGTCAAGAGGAAATAGGAGGAACTG                         GATATTAGTCTGGGAGGATGGTTTCTGCAACTTTGCTGCCTCAACAGCCGA
genomic: GATGGCCAAGCAGGAGCCTATGATAGGTCAAGAGGAAATAGGAGGAACTGgtatatttct ... tacatgacagGATATTAGTCTGGGAGGATGGTTTCTGCAACTTTGCTGCCTCAACAGCCGA
EST: gi|71860639|gb|DT009694.1|DT009694
EST:     GATGGCCAAGCAGGAGCCTATGATAGGTCAAGAGGAAATAGGAGGAACTG                         GATATTAGTCTGGGAGGATGGTTTCTGCAACTTTGCTGCCTCAACAGCCGA
genomic: GATGGCCAAGCAGGAGCCTATGATAGGTCAAGAGGAAATAGGAGGAACTGgtatatttct ... tacatgacagGATATTAGTCTGGGAGGATGGTTTCTGCAACTTTGCTGCCTCAACAGCCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaataaaccatgcattttgcatcttgttgatgatctcatactatatacatgacagGATATTAGTCTGGGAGGATGGTTTCTGCAACTTTGCTGCCTCAACAGCCGAGATCAACTCCAGCGACTGTGTGGGCTCATCAGTCTATGGCAACTGTGAA
                        tgttgat  putative branch site (score: 4)
                                     atactatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatttctttaggcaaaaaataaaccatgcattttgcatcttgttgatgatctcatactatatacatgacagGATATTAGTCTGGGAGGATGGTTTCTGCAACTTTGCTGCCTCAACAGCCGAGATCAACTCCAGCGACTGTGTGGGCTCATCAGTCTATGGCAACTGTGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA