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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtgtattacaatagattttccttttttaaaaattttatcttgactgtgaaattgattaaaattgatactctgatggacagAGATACTACTTTGCCTCTGCAAAAGAGTTGATGCGGATCAATGGTACGACCAAGTCTTTGGTGGCAAACCATCTGGCTGAGTCTATAGCAGGAGCCATGA

Basic information

species Vitis vinifera
transcript Vv16s0050g02480.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g02480.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os12g37580.1 (Oryza sativa), 3'ss of exon 6
-gtagtgtattacaatagattttccttttttaaaaatttta----tcttgactgtgaaattgattaaaatt-----gatactctgatggacagAGATACTACTTTGCCTCTGCAAAAGAGTTGATGCGGATCAATGGTACGACCAAGTCTTTGGTGGCAAACCATCTGGCTGAGTCTATAGCAGGAGCCATGA
   ||| | || |||||  | ||  | ||  |  |||||        || | |||    ||  | | | ||     || ||  ||     ||||||||||| |  |||||| ||||||| ||||||||||||||||| || || || ||| | || || || || || || || || ||  |||||||  | |
gtcagtctgtt-caatacttgtttttcttggatgaatttagaaatcttttattgttttcttattaatagttttgatgaaacattgtactgcagAGATACTATTCAGCCTCTTCAAAAGAATTGATGCGGATCAATGGCACTACAAAATCTCTTGTTGCCAATCACCTTGCAGAATCAATTTCAGGAGCAGTTA
















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|110713048|gb|EE088630.1|EE088630
EST:     AAGTCCTGTTTGTCTCCATACCGATGATCTATGTGGCTATTCGCTTACAG                         AGATACTACTTTGCCTCTGCAAA
genomic: AAGTCCTGTTTGTCTCCATACCGATGATCTATGTGGCTATTCGCTTACAGgtagtgtatt ... tgatggacagAGATACTACTTTGCCTCTGCAAA
EST: gi|10283302|gb|BE846425.1|BE846425
EST:     AAGTCCTGTTTGTCTCCATACCGATGATCTATGTGGCTATTCGCTTACAG                         AGATACTACTTTGCCTCTGCAAAAGAGTTGATGCGGATCAATGGTACGACC
genomic: AAGTCCTGTTTGTCTCCATACCGATGATCTATGTGGCTATTCGCTTACAGgtagtgtatt ... tgatggacagAGATACTACTTTGCCTCTGCAAAAGAGTTGATGCGGATCAATGGTACGACC
EST: gi|110726701|gb|EE102715.1|EE102715
EST:     AAGTCCTGTTTGTCTCCATACCGATGATCTATGTGGCTATTCGCTTACAG                         AGATACTACTTTGCCTCTGCAAAAGAGTTGATGCGGATCAATGGTACGACC
genomic: AAGTCCTGTTTGTCTCCATACCGATGATCTATGTGGCTATTCGCTTACAGgtagtgtatt ... tgatggacagAGATACTACTTTGCCTCTGCAAAAGAGTTGATGCGGATCAATGGTACGACC
EST: gi|71860768|gb|DT009823.1|DT009823
EST:     AAGTCCTGTTTGTCTCCATACCGATGATCTATGTGGCTATTCGCTTACAG                         AGATACTACTTTGCCTCTGCAAAAGAGTTGATGCGGATCAATGGTACGACC
genomic: AAGTCCTGTTTGTCTCCATACCGATGATCTATGTGGCTATTCGCTTACAGgtagtgtatt ... tgatggacagAGATACTACTTTGCCTCTGCAAAAGAGTTGATGCGGATCAATGGTACGACC
EST: gi|161706059|gb|FC057138.1|FC057138
EST:     CGATGATCTATGTGGCTATTCGCTTACAG                         AGATACTACTTTGCCTCTGCAAAAGAGTTGATGCGGATCAATGGTACGACC
genomic: CGATGATCTATGTGGCTATTCGCTTACAGgtagtgtatt ... tgatggacagAGATACTACTTTGCCTCTGCAAAAGAGTTGATGCGGATCAATGGTACGACC
EST: gi|30300354|gb|CB977148.1|CB977148
EST:     AAGTCCTGTTTGTCTCCATACCGATGATCTATGTGGCTATTCGCTTACAG                         AGATACTACTTTGCCTCTGCAAAAGAGTTGATGCGGATCAATGGTACGACC
genomic: AAGTCCTGTTTGTCTCCATACCGATGATCTATGTGGCTATTCGCTTACAGgtagtgtatt ... tgatggacagAGATACTACTTTGCCTCTGCAAAAGAGTTGATGCGGATCAATGGTACGACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaaaattttatcttgactgtgaaattgattaaaattgatactctgatggacagAGATACTACTTTGCCTCTGCAAAAGAGTTGATGCGGATCAATGGTACGACCAAGTCTTTGGTGGCAAACCATCTGGCTGAGTCTATAGCAGGAGCCATGA
                     tgaaattgattaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagtgtattacaatagattttccttttttaaaaattttatcttgactgtgaaattgattaaaattgatactctgatggacagAGATACTACTTTGCCTCTGCAAAAGAGTTGATGCGGATCAATGGTACGACCAAGTCTTTGGTGGCAAACCATCTGGCTGAGTCTATAGCAGGAGCCATGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG