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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttaatgttgtttcagcaataatcttcatttctcacctgtatttgtattttaaacaagtactttgatgctaattttgttctagtgtttctatctgtgcagCTTTCATTTCAGATGTGGACCAATCAAATGCAGGAGACCTTGAATTCCAAGAAGCATGGAGATACCGCTTTCCGAGCTAAGGATTTCACAACTGCCATTG

Basic information

species Vitis vinifera
transcript Vv08s0007g01520.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g01520.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA01G26690.2 (Glycine max), 3'ss of exon 5
gttaatgttgtttcagcaataatcttcatttctcacctgtatttgtattttaaacaagtactttgatgctaattttgttctagtgtttctatctgtgcagCTTTCATTTCAGATGTGGACCAATCAAATGCAGGAGACCTTGAATTCCAAGAAGCATGGAGATACCGCTTTCCGAGCTAAGGATTTCACAACTGCCATTG
         ||||       |     || || || ||| ||||| |||| | | |||   || | ||| | ||  | |  || | ||   ||   |||||||||| |||||  |||||||||  ||||||||||||||||||||||  ||||||||||||||||| |||||  |||||||||| || |  ||||||||||
---------gttttgtttgca-----cacttttc-cctctatttttattgttaccaa---ctctaatgttgatcct-tcttaattttgaaat---tgcagCTTTCCTTTCAATTGTGGACCAGCCAAATGCAGGAGACCTTGAATTTGAAGAAGCATGGAGATACTGCTTTTAGAGCTAAGGACTTTATCACTGCCATTG

upper sequence: Vv08s0007g01520.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA03G15830.1 (Glycine max), 3'ss of exon 8
gttaatgttgtttcagcaataatcttcatttctcacctgtatttgtattttaaacaagtactttgatgctaattttgttctagtgtttctatctgtgcagCTTTCATTTCAGATGTGGACCAATCAAATGCAGGAGACCTTGAATTCCAAGAAGCATGGAGATACCGCTTTCCGAGCTAAGGATTTCACAACTGCCATTG
               |      |   || || |  ||| ||||| |||| | | |||   || | ||| | ||  | |  || ||||   |    |||||||||| |||||  ||||||||| ||||||||| |||||||||||||  ||||||||||||||||| |||||  |||||||||| ||    ||||||||||
---------------gtttgcttacacactttttccctctatttttattgttaccaa---ctctaatgttgatcct-tcttaatgttgaaac---tgcagCTTTCCTTTCAATTGTGGACCAGTCAAATGCAAGAGACCTTGAATTTGAAGAAGCATGGAGATACTGCTTTTAGAGCTAAGGACTTTGTTACTGCCATTG
















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|110425902|gb|EC992297.1|EC992297
EST:     AAATCTTGGACAAGATTGGATACAAGGATGATGAAGGGATTGCCAATGAG                         CTTTCATTTCAGATGTGGACCAATCAAATGCAGGAGACCTTGAATTCCAAG
genomic: AAATCTTGGACAAGATTGGATACAAGGATGATGAAGGGATTGCCAATGAGgtttgctact ... atctgtgcagCTTTCATTTCAGATGTGGACCAATCAAATGCAGGAGACCTTGAATTCCAAG
EST: gi|34363245|gb|CF404830.1|CF404830
EST:     GATGATGAAGGGATTGCCAATGAG                         CTTTCATTTCAGATGTGGACCAATCAAATGCAGGAGACCTTGAATTCCAAG
genomic: GATGATGAAGGGATTGCCAATGAGgtttgctact ... atctgtgcagCTTTCATTTCAGATGTGGACCAATCAAATGCAGGAGACCTTGAATTCCAAG
EST: gi|33410051|gb|CF215678.1|CF215678
EST:     AAATCTTGGACAAGATTGGATACAAGGATGATGAAGGGATTGCCAATGAG                         CTTTCATTTCAGATGTGGACCAATCAAATGCAGGAGACCTTGAATTCCAAG
genomic: AAATCTTGGACAAGATTGGATACAAGGATGATGAAGGGATTGCCAATGAGgtttgctact ... atctgtgcagCTTTCATTTCAGATGTGGACCAATCAAATGCAGGAGACCTTGAATTCCAAG
EST: gi|110364306|gb|EC923835.1|EC923835
EST:     AAATCTTGGACAAGATTGGATACAAGGATGATGAAGGGATTGCCAATGAG                         CTTTCATTTCAGATGTGGACCAATCAAATGCAGGAGACCTTGAATTCCAAG
genomic: AAATCTTGGACAAGATTGGATACAAGGATGATGAAGGGATTGCCAATGAGgtttgctact ... atctgtgcagCTTTCATTTCAGATGTGGACCAATCAAATGCAGGAGACCTTGAATTCCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttaaacaagtactttgatgctaattttgttctagtgtttctatctgtgcagCTTTCATTTCAGATGTGGACCAATCAAATGCAGGAGACCTTGAATTCCAAGAAGCATGGAGATACCGCTTTCCGAGCTAAGGATTTCACAACTGCCATTG
                     tgctaat  putative branch site (score: 2)
                                        tttctatct  putative PPT
                        taattttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaatgttgtttcagcaataatcttcatttctcacctgtatttgtattttaaacaagtactttgatgctaattttgttctagtgtttctatctgtgcagCTTTCATTTCAGATGTGGACCAATCAAATGCAGGAGACCTTGAATTCCAAGAAGCATGGAGATACCGCTTTCCGAGCTAAGGATTTCACAACTGCCATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - tcagcaa
- - - - - - - - - - - - - - - - -cacctgt
- - - - - - - - - - - - - - - - - - - - - - - - - taaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgct