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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttaacatgtcaaaagtattgtccccgcagctctttgcttagtttgtttaacttgtaacaacattccatagcttatctgtatggtttcttgttggttcttatccattttgcattcccattgaacaagATTCAATTGAAATCTTTGGCCGAGGAAATGCAAGCTGTGAGTAAAGGTCTTGAAAAGGTTGAGCAAGAACTCACTGCCTCGGTGAATGATGGTGCTATCT

Basic information

species Vitis vinifera
transcript Vv02s0033g01360.t01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0033g01360.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA09G34830.1 (Glycine max), 3'ss of exon 14
gtatgcttaacatgtcaaaagtattgtcc-ccgcagctctttgcttagtttgt-ttaacttgtaacaacattccatagcttatctgtatggtttcttgttggttcttatccattttgcattcccattgaacaagATTCAATTGAAATCTTTGGCCGAGGAAATGCAAGCTGTGAGTAAAGGTCTTGAAAAGGTTGAGCAAGAACTCACTGCCTCGGTGAATGATGGTGCTATCT
                    ||||| ||   | |   | ||| | | |||  | || |  | | |||       ||   || | |||| | || |||  || || | ||   | ||   |  ||| | | | |||||||| | ||| | ||||| || |||||||||||||||||||||||| | || || ||||||||||||||| |||| || |  |||||||||||||| |
--------------------gtattctctgtcactaatgttttcattgttgatattgatgtattacag------atgattt-tatgtaagattactt--tgcttatgattggtattctctgtccaat-atctagATTCAACTAAAAGCATTGGCTGAAGAAATGCAAGCTGTGAGTAAAGGTTTAGAGAAAGTTGAGCAAGAACTCGCTGCTTCTGAAAATGATGGTGCTATAT

upper sequence: Vv02s0033g01360.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: GLYMA04G14770.1 (Glycine max), 3'ss of exon 14
gtatgcttaacatgtcaaaagtattgtccccgcagctctttgcttagtttgtttaacttgtaacaacattccatagcttatct-gtatggtttcttgttggttct-tatccattttgcattcccattgaacaagATTCAATTGAAATCTTTGGCCGAGGAAATGCAAGCTGTGAGTAAAGGTCTTGAAAAGGTTGAGCAAGAACTCACTGCCTCGGTGAATGATGGTGCTATCT
                                    |  | ||| | |||   | | |  ||   |  |   | || | || |  | |    |  | ||| || | |||  || ||   |  ||| | | | |||||||| | ||| | ||||| || |||||||||||||||||||||||| | || || ||||||||||||||  |||| || |  |||||||||||||| |
-----------------------------gtattctttgtcgctaatttttcattattgatatagatgtattacaggtgattttatgtaagattattttgcttatgtattgatgttctctgtccaat-atctagATTCAACTAAAAGCATTGGCTGAAGAAATGCAAGCTGTGAGTAAAGGTTTAGAGAAAGTTGAGCAAGAACTTGCTGCTTCTGAAAATGATGGTGCTATAT

upper sequence: Vv02s0033g01360.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: AT1G31810.1 (Arabidopsis thaliana), 3'ss of exon 14
gtatgcttaacatgtcaaaagtattgtccccgcagctctttgcttagtttgtttaacttgtaacaacattccatagcttatctgtatggtttcttgttggttcttatccattttgcattcccattgaacaagATTCAATTGAAATCTTTGGCCGAGGAAATGCAAGCTGTGAGTAAAGGTCTTGAAAAGGTTGAGCAAGAACTCACTGCCTCGGTGAATGATGGTGCTATCT
                                           |  | |||||  | |  |    || |     |||||  |    |  ||  || |||   ||  |  ||| |   |||  |   |   ||||| |||||||| | ||||| || ||||||||||| | || |||||| |||||||||||||||||||||||||  || || |  ||||||||||| || |
------------------------------------------gtatgcttgtt--attcatggttacttctgtgagctt--ccaccttcttgtttattgcacctgctttattctt--ttcttaaaaatgcagATTGAATTGAAAACGTTGGCTGAAGAAATGCAAGCGGCGACTAAAGGCCTTGAAAAGGTTGAGCAAGAACTCATGGCTTCAGAAAATGATGGTGCAATTT

upper sequence: Vv02s0033g01360.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: EFJ38305 (Selaginella moellendorffii), 3'ss of exon 10
gtatgcttaacatgtcaaaagtattgtccccgcagctctttgcttagtttgtttaacttgtaacaacattccatagcttatctgtatggtttcttgttggttcttatccattttgcattcccattgaacaagATTCAATTGAAATCTTTGGCCGAGGAAATGCAAGCTGTGAGTAAAGGTCTTGAAAAGGTTGAGCAAGAACTCACTGCCTCGGTGAATGATGGTGCTATCT
                                                                           | |  | | | |  |       |  || |    |  ||| |   ||  |   ||| ||||||||||||| || | || || ||||||||||| || || ||||| || |||||||||||||| ||| | || || || |  || ||||| ||  |||
---------------------------------------------------------------------------gttcttatatttcatactccagtatttgtgtctcggttttctgacctgtgttaca-gATTCAATTGAAAGCTCTTGCAGAAGAAATGCAAGCCGTAAGCAAAGGCCTGGAAAAGGTTGAGCAGGAATTGACAGCGTCTGAAAACGATGGAGCCGTCT

upper sequence: Vv02s0033g01360.t01 (Vitis vinifera), 3'ss of exon 14
lower sequence: EFJ15040 (Selaginella moellendorffii), 3'ss of exon 13
gtatgcttaacatgtcaaaagtattgtccccgcagctctttgcttagtttgtttaacttgtaacaacattccatagcttatctgtatggtttcttgttggttcttatccattttgcattcccattgaacaagATTCAATTGAAATCTTTGGCCGAGGAAATGCAAGCTGTGAGTAAAGGTCTTGAAAAGGTTGAGCAAGAACTCACTGCCTCGGTGAATGATGGTGCTATCT
                                                                           | |  | | | |  |       |  || |       ||| |   ||  |   ||| ||||||||||||| || | || || ||||||||||| || || ||||| || |||||||||||||| ||| | || || || |  || ||||| ||  |||
---------------------------------------------------------------------------gttcttatatttcatactccagtatttgtgtcttggttttctgacctgtgttaca-gATTCAATTGAAAGCTCTTGCAGAAGAAATGCAAGCCGTAAGCAAAGGCCTGGAAAAGGTTGAGCAGGAATTGACAGCGTCTGAAAACGATGGAGCCGTCT

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|22010858|gb|BQ795892.1|BQ795892
EST:     GTTCATTTGGAAGCAGCGTCTAAG                         ATTCAATTGAAATCTTTGGCCGAGGAAATGCAAGCTGTGAGTAAAGGTCTT
genomic: GTTCATTTGGAAGCAGCGTCTAAGgtatgcttaa ... attgaacaagATTCAATTGAAATCTTTGGCCGAGGAAATGCAAGCTGTGAGTAAAGGTCTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatctgtatggtttcttgttggttcttatccattttgcattcccattgaacaagATTCAATTGAAATCTTTGGCCGAGGAAATGCAAGCTGTGAGTAAAGGTCTTGAAAAGGTTGAGCAAGAACTCACTGCCTCGGTGAATGATGGTGCTATCT
                                        ttcccatt  CT-rich tract
                       ttcttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcttaacatgtcaaaagtattgtccccgcagctctttgcttagtttgtttaacttgtaacaacattccatagcttatctgtatggtttcttgttggttcttatccattttgcattcccattgaacaagATTCAATTGAAATCTTTGGCCGAGGAAATGCAAGCTGTGAGTAAAGGTCTTGAAAAGGTTGAGCAAGAACTCACTGCCTCGGTGAATGATGGTGCTATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC