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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtggtgaaatgccttcatctgattcacaaatctagctctaaatgaatgctcctgaactgttctgctgctgaatgattttcagGCTTTTGTCAGTGAGTATGCTGTGACAGGTAAAGATGCTGGTTCAGGAACTCTTTTGGCAGCATTGGCTGAAGCTGCATTCCTCATTGGGGTGGAAAAGA

Basic information

species Vitis vinifera
transcript Vv08s0040g00320.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA03G27460.2 (Glycine max), 3'ss of exon 12
----------gtgtggtgaaatgccttcatctgattcacaaatc-tagctctaaatgaatgctcctgaactgttctgctgctgaatgattttcagGCTTTTGTCAGTGAGTATGCTGTGACAGGTAAAGATGCTGGTTCAGGAACTCTTTTGGCAGCATTGGCTGAAGCTGCATTCCTCATTGGGGTGGAAAAGA
           ||   |  |      || |||| || |  | |  | |   ||      || || | | || || ||    || |   ||| ||||||||||| ||||||||||||||||| || |||||||||||  ||||||  || ||||||||  | ||||||||||  ||||| |||||  |||||||||
gttttattttatgatctctatcaaagtcctctgttttattagttattggcatatccatttgttcttaatctattttg----tggacactttacagGCTTTTGTAAGTGAGTATGCTGTGACTGGAAAAGATGCTGGGACAGGAAGCCTCTTGGCAGCCCTAGCTGAAGCTGGGTTCCTTATTGGACTGGAAAAGA

upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA19G30450.1 (Glycine max), 3'ss of exon 13
gtgtggtgaaatgccttcatctgattcacaaatctagctctaaatgaatgctcctgaactgt-tctgctgc-tgaatgattttcagGCTTTTGTCAGTGAGTATGCTGTGACAGGTAAAGATGCTGGTTCAGGAACTCTTTTGGCAGCATTGGCTGAAGCTGCATTCCTCATTGGGGTGGAAAAGA
|| |  |||  |   |  | |   |         ||| | |      || |   || |  |  |||  |   || |   ||| ||||||||||| ||||||||||| ||||| || |||||||||||  ||||||  || ||||||||  | ||||||||||  ||||| |||||  |||||||||
gttttatgatctctatcaaacacctctgttttattagttattggcatatccatttgtatggaatctattttgtggacactttacagGCTTTTGTAAGTGAGTATGCCGTGACTGGAAAAGATGCTGGGACAGGAAGCCTCTTGGCAGCCCTAGCTGAAGCTGGCTTCCTAATTGGACTGGAAAAGA

upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA19G30150.1 (Glycine max), 3'ss of exon 13
--------gtgtggtgaaatgccttcatctgattcacaaatctagctctaaatgaatgctcctgaact--gttctgctgctgaatgattttcagGCTTTTGTCAGTGAGTATGCTGTGACAGGTAAAGATGCTGGTTCAGGAACTCTTTTGGCAGCATTGGCTGAAGCTGCATTCCTCATTGGGGTGGAAAAGA
         | |  | |  |  | |||  | ||  |   | |||    ||  |  ||       | ||  | | || | ||   || | |  |||| ||||| || |||||||||||        | ||||||||    |||||||||||||| ||  ||||||||||||||||||| |||||  | ||||  |
gtttgattatttaatcatttttcatcaaattatctatgta-ctatgattatcttcataggtagaagctcagctttgattctatttggtctatagGCGTTTGTTAGCGAGTATGCTGTTTGGAAGGATGATGCTGGAAATGGAACTCTTTTGGCTGCCGTGGCTGAAGCTGCATTCCTTATTGGACTAGAAAGAA

upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: AT3G10740.1 (Arabidopsis thaliana), 3'ss of exon 13
gtgtggtgaaatgccttcatctgattca--caaatctagctctaaatgaatgctcctgaactgttct-gctgctgaa--tgattttcagGCTTTTGTCAGTGAGTATGCTGTGACAGGTAAAGATGCTGGTTCAGGAACTCTTTTGGCAGCATTGGCTGAAGCTGCATTCCTCATTGGGGTGGAAAAGA
||| ||| | |     | |    | | |     | | | | | | |||||   | | |   | | ||  ||  ||||  |  ||| ||||||||||||||||| |||||||| || || |||||||||||| ||||||  ||| | ||  |  | || |||||||| || ||||||||  | |||||||
gtgcggtaatagattataacaaaacttaattccaacaaacacaagatgaagctttcagcgttttactcactcgtgaactttgtttacagGCTTTTGTCAGTGAATATGCTGTTACTGGAAAAGATGCTGGTACAGGAAGCCTTCTTGCCTCTCTTGCAGAAGCTGCGTTTCTCATTGGTCTTGAAAAGA

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|33406071|gb|CF211698.1|CF211698
EST:     TGTATAGTATGGCTCATCAATTTGATCGCACATCACGTGATGCTCCAAAG                         GCTTTTGTCAGTGAGTATGCTGTGACAGGTAAAGATGCTGGTTCAGGAACT
genomic: TGTATAGTATGGCTCATCAATTTGATCGCACATCACGTGATGCTCCAAAGgtgtggtgaa ... tgattttcagGCTTTTGTCAGTGAGTATGCTGTGACAGGTAAAGATGCTGGTTCAGGAACT
EST: gi|161713404|gb|FC062796.1|FC062796
EST:     TGTATAGTATGGCTCATCAATTTGATCGCACATCACGTGATGCTCCAAAG                         GCTTTTGTCAGTGAGTATGCTGTGACAGGTAAAGATGCTGGTTCAGGAACT
genomic: TGTATAGTATGGCTCATCAATTTGATCGCACATCACGTGATGCTCCAAAGgtgtggtgaa ... tgattttcagGCTTTTGTCAGTGAGTATGCTGTGACAGGTAAAGATGCTGGTTCAGGAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatctagctctaaatgaatgctcctgaactgttctgctgctgaatgattttcagGCTTTTGTCAGTGAGTATGCTGTGACAGGTAAAGATGCTGGTTCAGGAACTCTTTTGGCAGCATTGGCTGAAGCTGCATTCCTCATTGGGGTGGAAAAGA
        ctctaaa  putative branch site (score: 3)
                                                ttttc  putative PPT
           taaatgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtggtgaaatgccttcatctgattcacaaatctagctctaaatgaatgctcctgaactgttctgctgctgaatgattttcagGCTTTTGTCAGTGAGTATGCTGTGACAGGTAAAGATGCTGGTTCAGGAACTCTTTTGGCAGCATTGGCTGAAGCTGCATTCCTCATTGGGGTGGAAAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA