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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttctccttgtcatgctgatataattggcttttttgggctttgcgtaaatgttaatgttcattagaaatcttataaaatcataatggttttttgtgcagATACAATGATGAAATTTGCTTCTTTTGAGACTATTGTTGAGATGCTTTACAAGTATGCCATTCCTACTCCGAAGGACCAGTGCAGTAAAACTCTGCAGCT

Basic information

species Vitis vinifera
transcript Vv14s0068g01260.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0068g01260.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G118208_T01 (Zea mays), 3'ss of exon 3
-gtttctccttgtcatgctgatataattggcttttttgggctttgcgtaaatgttaatgttcattagaaatcttataaaatcataatggttttttgtgcagATACAATGATGAAATTTGCTTCTTTTGAGACTATTGTTGAGATGCTTTACAAGTATGCCATTCCTACTCCGAAGGACCAGTGCAGTAAAACTCTGCAGCT
   ||     ||    |   || ||      |  | ||  |         |||||||  |        ||     |||   | |  ||  || |  | |||| || ||||||||||||||||  ||||| ||||||||||||||| | |||||| ||||  |||| |  ||||| ||||| ||||||||  | || || ||
aactttgaggtgctgggtc-atgtagagatataatctgcacagaagccttatgttaacctgtgcacccaagtccctaattactttctgtgttatcctacagACACTATGATGAAATTTGCTTGCTTTGAAACTATTGTTGAGATGGTCTACAAGCATGCTGTTCCGAAACCGAAAGACCAATGCAGTAAGCCACTACAACT

upper sequence: Vv14s0068g01260.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G14040.1 (Arabidopsis thaliana), 3'ss of exon 3
----------gtttctccttgtcatgctgatata-attggcttttttgggctttgcgtaaatgttaatgtt-cattagaaatcttataaaatca--------taatggttttt------tgtgcagATACAATGATGAAATTTGCTTCTTTTGAGACTATTGTTGAGATGCTTTACAAGTATGCCATTCCTACTCCGAAGGACCAGTGCAGTAAAACTCTGCAGCT
          |  |||  ||  ||  ||| |  | | |   ||||||    |||   |   | || |||   |||  | | |  | ||||| ||        | ||| | | |      | | |||| || |||||||| |||||||| |||||||| |||||||||||| |||||||||| || || || |  || |||    ||||||| |||  |||||| ||
gtaagttctggcctctattttgcaacctgttgcacaatctttttttttttttttttttgtttattgatgaaacatatgtagttctttaaaagcaaaaggtggtgatgatatctatgaattttacagACACTATGATGAAGTTTGCTTCCTTTGAGACCATTGTTGAGATGATTTACAAGTACGCAATCCCCAACCCAAAGAGTGAGTGCAGCAAAGGTCTGCAACT
















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|33402024|gb|CF207651.1|CF207651
EST:     ATTGTACAAGGGCATTGTTCCTCTCTGGGGACGTCAGATTCCAT                         ATACAATGATGAAATTTGATTCTTTTGAGACTATTGTTGAGATGCTTTACA
genomic: ATTGTACAAGGGCATTGTTCCTCTCTGGGGACGTCAGATTCCATgtaagttgag ... ttttgtgcagATACAATGATGAAATTTGCTTCTTTTGAGACTATTGTTGAGATGCTTTACA
EST: gi|110366072|gb|EC929727.1|EC929727
EST:     ATTGTACAAGGGCATTGTTCCTCTCTGGGGACGTCAGATTCCAT                         ATACAATGATGAAATTTGCTTCTTTTGAGACTATTGTTGAGATGCTTTACA
genomic: ATTGTACAAGGGCATTGTTCCTCTCTGGGGACGTCAGATTCCATgtaagttgag ... ttttgtgcagATACAATGATGAAATTTGCTTCTTTTGAGACTATTGTTGAGATGCTTTACA
EST: gi|110707594|gb|EE084171.1|EE084171
EST:     ATTGTACAAGGGCATTGTTCCTCTCTGGGGACGTCCGATTCCCT                         ATACAATGATGAAATTTGCTTCCTTTTGA
genomic: ATTGTACAAGGGCATTGTTCCTCTCTGGGGACGTCAGATTCCATgtaagttgag ... ttttgtgcagATACAATGATGAAATTTGCTTC-TTTTGA
EST: gi|71865829|gb|DT014884.1|DT014884
EST:     ATTGTACAAGGGCATTGTTCCTCTCTGGGGACGTCAGATTCCAT                         ATACAATGATGAAATTTGCTTCTTTTGAGACTAT
genomic: ATTGTACAAGGGCATTGTTCCTCTCTGGGGACGTCAGATTCCATgtaagttgag ... ttttgtgcagATACAATGATGAAATTTGCTTCTTTTGAGACTAT
EST: gi|110685233|gb|EE063420.1|EE063420
EST:     ATTGTACAAGGGCATTGTTCCTCTCTGGGGACGTCAGATTCCAT                         ATACAATGATGAAATTTGCTTCTTTTGAGACTATTGTTGAGATGCTTTACA
genomic: ATTGTACAAGGGCATTGTTCCTCTCTGGGGACGTCAGATTCCATgtaagttgag ... ttttgtgcagATACAATGATGAAATTTGCTTCTTTTGAGACTATTGTTGAGATGCTTTACA
EST: gi|110379440|gb|EC944634.1|EC944634
EST:     ATTGTACAAGGGCATTGTTCCTCTCTGGGGACGTCAGATTCCAT                         ATACAATGATGAAATTTGCTTCTTTTGAGACTATTGTTGAGATGCTTTACA
genomic: ATTGTACAAGGGCATTGTTCCTCTCTGGGGACGTCAGATTCCATgtaagttgag ... ttttgtgcagATACAATGATGAAATTTGCTTCTTTTGAGACTATTGTTGAGATGCTTTACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaatgttaatgttcattagaaatcttataaaatcataatggttttttgtgcagATACAATGATGAAATTTGCTTCTTTTGAGACTATTGTTGAGATGCTTTACAAGTATGCCATTCCTACTCCGAAGGACCAGTGCAGTAAAACTCTGCAGCT
     tgttaat  putative branch site (score: 3)
                                           ttttttgt  putative PPT
       ttaatgttcattagaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttctccttgtcatgctgatataattggcttttttgggctttgcgtaaatgttaatgttcattagaaatcttataaaatcataatggttttttgtgcagATACAATGATGAAATTTGCTTCTTTTGAGACTATTGTTGAGATGCTTTACAAGTATGCCATTCCTACTCCGAAGGACCAGTGCAGTAAAACTCTGCAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - ctccttg
- - - - - -tcatgct
- - - - - - - - - - - - - - - - ttttggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaatca