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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttagatgctatcttctctgcctgtcttttttttttttttttccttttactctttagctctacattcagcgagctaattgatttcatctggtctgttcagAGTTGTCAGAAGAAGAATCTGATTATGAAATTGAGTATGAAATCCTCTCTGCTGGTTCAGCTGAGCCATGGGATGACACAGACGAGGTATGGGTGTCTGC

Basic information

species Vitis vinifera
transcript Vv07s0031g02260.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g02260.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT5G65960.1 (Arabidopsis thaliana), 3'ss of exon 5
-------------------------------------------------------------------------------gttttagatgctatcttctctgcct--gtcttttttttttttttttccttttactctttagctctacattcag-cgagctaattgatttcatctggtctgttcagAGTTGTCAGAAGAAGAATCTGATTATGAAATTGAGTATGAAATCCTCTCTGCTGGTTCAGCTGAGCCATGGGATGACACAGACGAGGTATGGGTGTCTGC
                                                                               |     || |   |   |     ||    |    |      |  |       ||  || |  || || |  |  |  | | ||||  |        ||   |||||||||||||||||||||||||| |||||| | ||||||||| | || || || || |||| ||| ||||||||| | |  || ||   |||||| |||||
gttaattgtttcttccactttcctctcccatatatgtatgagttcctgaaatgtcctttcccggttagagtttctgttcgaccaggaagtggtagaccgaaactcgacccagataagaaatcctggtgaggacatttcatttccacttggattcatgttgattgggtcttatatttcctctcagAGTTGTCAGAAGAAGAATCTGAATATGAATTGGAGTATGAAGTGCTATCAGCAGGCTCAGGTGATCCATGGGATAATATTGAAGAAAGATGGGTTTCTGC
















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|110375495|gb|EC940484.1|EC940484
EST:     CCTGAAATCTGGTGATAAGATAATGGAACCATCATTGCCTGAAAACCAAG                         AGTTGTCAGAAGAAGAATCTGATTATGAAATTGAGTATGAAATCCTCTCTG
genomic: CCTGAAATCTGGTGATAAGATAATGGAACCATCATTGCCTGAAAACCAAGgttttagatg ... gtctgttcagAGTTGTCAGAAGAAGAATCTGATTATGAAATTGAGTATGAAATCCTCTCTG
EST: gi|30302965|gb|CB979759.1|CB979759
EST:     CCTGAAATCTGGTGATAAGATAATGGAACCATCATTACCTGAAAACCAAG                         AGTTGTCAGAAGAAGAATCTGATTATGAAATTGAGTATGAAATCCTCTCTG
genomic: CCTGAAATCTGGTGATAAGATAATGGAACCATCATTGCCTGAAAACCAAGgttttagatg ... gtctgttcagAGTTGTCAGAAGAAGAATCTGATTATGAAATTGAGTATGAAATCCTCTCTG
EST: gi|110728911|gb|EE104893.1|EE104893
EST:     CCTGAAATCTGGTGATAAGATAATGGAACCATCATTGCCTGAAAACCAAG                         AGTTGTCAGAAGAAGAATCTGATTATGAAATTGAGTATGAAATCCTCTCTG
genomic: CCTGAAATCTGGTGATAAGATAATGGAACCATCATTGCCTGAAAACCAAGgttttagatg ... gtctgttcagAGTTGTCAGAAGAAGAATCTGATTATGAAATTGAGTATGAAATCCTCTCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttactctttagctctacattcagcgagctaattgatttcatctggtctgttcagAGTTGTCAGAAGAAGAATCTGATTATGAAATTGAGTATGAAATCCTCTCTGCTGGTTCAGCTGAGCCATGGGATGACACAGACGAGGTATGGGTGTCTGC
                                              tctgttc  CT-rich tract
                             taattgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttagatgctatcttctctgcctgtcttttttttttttttttccttttactctttagctctacattcagcgagctaattgatttcatctggtctgttcagAGTTGTCAGAAGAAGAATCTGATTATGAAATTGAGTATGAAATCCTCTCTGCTGGTTCAGCTGAGCCATGGGATGACACAGACGAGGTATGGGTGTCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA