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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgatagtactcttattttcaatttcattgtttgtttgtaaattgcatgtgcaacatattattattcttctttctcagcttattctttcattggcaacagTTCAGGTACATTTATTAGTGCATCAGAAGACAAAACTGGGATTCTGGACTTTGTTGAGCGAAAAATTGCAAAGGCTACAATGATTCCAAGAAGCCATGGA

Basic information

species Vitis vinifera
transcript Vv03s0091g00520.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0091g00520.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA20G26800.1 (Glycine max), 3'ss of exon 2
atgatagtactcttattttcaatttcattgtttgtttgtaaattgca--tgtgcaacatattattattcttctttctcagc-ttattctttcattggcaacagTTCAGGTACATTTATTAGTGCATCAGAAGACAAAACTGGGATTCTGGACTTTGTTGAGCGAAAAATTGCAAAGGCTACAATGATTCCAAGAAGCCATGGA
   ||  | |   | |       |  | || |||   || |     |    |      |  | | ||   |     |||    || | ||    ||||||||||||||||||||| || || ||||||||||||||| |||| ||  | ||||| |||||| | |||||||| || | ||||||||||||||| | |||||| 
---atgttgcatatgtaagagcatatagtgattgacggtgatcgagagccatttgtgctgctgtcatatatgaagttcaatgctaattttaagctggcaacagTTCAGGTACATTCATCAGCGCATCAGAAGACAAATCTGGCATCTTAGACTTCGTTGAGAGGAAAATTGCTAAAGTTACAATGATTCCAAGGACCCATGGG

upper sequence: Vv03s0091g00520.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G40520.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------------------------------------atgatagtactcttattttcaatttcattgtt--tgtttgtaaattgcatgtgcaacatattattattcttctttctcagcttattctttcattggcaacagTTCAGGTACATTTATTAGTGCATCAGAAGACAAAACTGGGATTCTGGACTTTGTTGAGCGAAAAATTGCAAAGGCTACAATGATTCCAAGAAGCCATGGA
                                                                               || | |  | | || | |    |      | |  || ||| ||||     | |  |||  || |  | || || | |     || | | |   || |||||||||||| ||||| || || ||||||||||||||| |||| ||  | ||||| |||||| | || ||||| || | ||||||||||||||| | |||||| 
gtactttaatgagcaaggtatttaaaatcaatttcacaaacggttacccatatacacacttagtttctggttttgaaagataaaaacaatgttgtatatgttagagcagatagtgattgaaaatgatgggagagacac-ttgtgttgctgctatatgtagctaatttatagctgacaacagTTCAGGCACATTCATCAGCGCATCAGAAGACAAATCTGGCATCTTAGACTTGGTTGAGAGGAAGATTGCTAAAGTTACAATGATTCCAAGGACCCATGGG
















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|71868121|gb|DT017176.1|DT017176
EST:     GCTTTGCGGCAGGGAGAAACTGATGAGAGCACGAAGGGAACAAGAACTAG                         TTCAGGTACATTTATTAGTGCATCAGAAGACAAAACTGGGATTCTGGACTT
genomic: GCTTTGCGGCAGGGAGAAACTGATGAGAGCACGAAGGGAACAAGAACTAGgtaccttttt ... ttggcaacagTTCAGGTACATTTATTAGTGCATCAGAAGACAAAACTGGGATTCTGGACTT
EST: gi|77585486|gb|DV221831.1|DV221831
EST:     GCTTTGCGGCAGGGAGAAACTGATGAGAGCACGAAGGGAACAAGAACTAG                         TTCAGGTACATTTATTAGTGCATCAGAAGACAAAACTGGGATTCTGGACTT
genomic: GCTTTGCGGCAGGGAGAAACTGATGAGAGCACGAAGGGAACAAGAACTAGgtaccttttt ... ttggcaacagTTCAGGTACATTTATTAGTGCATCAGAAGACAAAACTGGGATTCTGGACTT
EST: gi|30252901|gb|CB970452.1|CB970452
EST:     GCTTTGCGGCAGGGAGAAACTGATGAGAGCACCAAGGGAACAAGAACTAG                         TTCAGGTACATTTATTAGTGCATCAGAAGACAAAACTGGGATTCTGGACTT
genomic: GCTTTGCGGCAGGGAGAAACTGATGAGAGCACGAAGGGAACAAGAACTAGgtaccttttt ... ttggcaacagTTCAGGTACATTTATTAGTGCATCAGAAGACAAAACTGGGATTCTGGACTT
EST: gi|30134078|gb|CB919416.1|CB919416
EST:     GCTTTGCGGCAGGGAGAAACTGATGAGAGCACGAAGGGAACAAGAACTAG                         TTCAGGTACATTTATTAGTGCATCAGAAGACAAAACTGGGATTCTGGACTT
genomic: GCTTTGCGGCAGGGAGAAACTGATGAGAGCACGAAGGGAACAAGAACTAGgtaccttttt ... ttggcaacagTTCAGGTACATTTATTAGTGCATCAGAAGACAAAACTGGGATTCTGGACTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgtgcaacatattattattcttctttctcagcttattctttcattggcaacagTTCAGGTACATTTATTAGTGCATCAGAAGACAAAACTGGGATTCTGGACTTTGTTGAGCGAAAAATTGCAAAGGCTACAATGATTCCAAGAAGCCATGGA
                   ttcttctttctcagct  CT-rich tract
       aacatattattattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgatagtactcttattttcaatttcattgtttgtttgtaaattgcatgtgcaacatattattattcttctttctcagcttattctttcattggcaacagTTCAGGTACATTTATTAGTGCATCAGAAGACAAAACTGGGATTCTGGACTTTGTTGAGCGAAAAATTGCAAAGGCTACAATGATTCCAAGAAGCCATGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - -catgtgc