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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatatccttctggtttttgagtcttgtggttgaaccataccgtttgtcagtgtgctttaagattgggaatttgactttgtagttgttaacattttcttgcctgggcttgtttgaccgtttctttttcctactttatagGAGGTCAAGCGAAGACCCTTATGTTTGTACAGCTTAATCCTGATGTGGATTCCTACTCCGAAACTATAAGTACCTTGAAGTTTGCCGAGAGAGTCTCTGG

Basic information

species Vitis vinifera
transcript Vv02s0025g03480.t01
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0025g03480.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GRMZM2G173700_T01 (Zea mays), 3'ss of exon 14
gtacatatccttctggtttttgagtcttgtggttgaaccataccgtttgtcagtgtgctttaagattgggaatttgactttgtagttgttaacattttcttgcctgggcttgtttgaccgtttctttttcctactttatagGAGGTCAAGCGAAGACCCTTATGTTTGTACAGCTTAATCCTGATGTGGATTCCTACTCCGAAACTATAAGTACCTTGAAGTTTGCCGAGAGAGTCTCTGG
                                                || |       || |  ||   |  | ||  ||  |  | ||||  |||   | ||     || | | ||| ||| ||||       ||  ||| || ||||| || || || |||||||| ||| | ||||||||||| || || || || |||||||||||||| || |||||||| || || || |||||
------------------------------------------------gtaatcaaatatttat-ttactacctagatgttaaatatattaatgtttatcttccaaattttatgt-accttttattttc------ttccagGTGGACAAGCAAAAACTCTAATGTTTGTTCAGATAAATCCTGATGTTGAGTCATATTCAGAAACTATAAGTACTTTAAAGTTTGCTGAAAGGGTGTCTGG

upper sequence: Vv02s0025g03480.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA08G01800.1 (Glycine max), 3'ss of exon 18
gtacatatccttctggtttttga-gtcttgtggttgaaccataccgtttgtcagtgtgctttaagattgggaatttgactttgtagttgttaacattttcttgcctgggcttgtttgaccgtttctttttcctactttatagGAGGTCAAGCGAAGACCCTTATGTTTGTACAGCTTAATCCTGATGTGGATTCCTACTCCGAAACTATAAGTACCTTGAAGTTTGCCGAGAGAGTCTCTGG
|||  | |     |  ||  |      ||   |||     |||     | ||| | || ||  |  |||   |||| |   | | |  || |    || ||    ||   | | ||    ||  ||| |    | |||||||| ||||||||||| |||||||||||||||||||||||||||||||| | ||| || || |||||| |||| |||||||||||||| ||| | || || ||
gtaattgttgccattattggtatcaatttacagttttgttatatttggtttcatt-tgtttgcattttg---atttaagcatattgcagtcatggcttactaaattgcaatagctt---tgtcccttgta---attttatagGTGGTCAAGCGAAAACCCTTATGTTTGTACAGCTTAATCCTGATGTTGCTTCATATTCTGAAACTGTAAGCACCTTGAAGTTTGCTGAGCGGGTTTCCGG

upper sequence: Vv02s0025g03480.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: GLYMA05G37800.1 (Glycine max), 3'ss of exon 17
gtacatatccttctggtttttgagtcttgtggttgaaccataccgtttgtcagtgtgctttaagattgggaatttgactttgtagttgttaacattttcttgcctgggcttgtttgaccgtttctttttcctactttatagGAGGTCAAGCGAAGACCCTTATGTTTGTACAGCTTAATCCTGATGTGGATTCCTACTCCGAAACTATAAGTACCTTGAAGTTTGCCGAGAGAGTCTCTGG
    |  |  | |   | || |  ||   |    | |   |    ||||      |   ||   |||  || ||| |   | | |  || |    || ||    ||   | | ||       | |   |  ||  | ||||| ||||||||||| |||||||||||||||||||||||||||||||| | ||| || || |||||| |||| |||||||||||||| ||  | || |||||
--gtaattgttgccattattggtatcaatttacagtattgttatatttggtttcatttgtttgcattttga-tttaagcatattgcagtcatggcttactaaattgcaatagctt-------tgtccgttgtatatgatagGTGGTCAAGCGAAAACCCTTATGTTTGTACAGCTTAATCCTGATGTTGCTTCATATTCTGAAACTGTAAGCACCTTGAAGTTTGCTGAACGGGTTTCTGG

upper sequence: Vv02s0025g03480.t01 (Vitis vinifera), 3'ss of exon 18
lower sequence: AT5G41310.1 (Arabidopsis thaliana), 3'ss of exon 15
gtacatatccttctggtttttgagtcttgtggttgaaccataccgtttgtcagtgtgctttaagattgggaatttgactttgtagttgttaacattttcttgcctgggcttgtttgaccgtttctttttcctactttatagGAGGTCAAGCGAAGACCCTTATGTTTGTACAGCTTAATCCTGATGTGGATTCCTACTCCGAAACTATAAGTACCTTGAAGTTTGCCGAGAGAGTCTCTGG
                                                      || || ||||||   || ||  |      |  | ||| | |  | |||     ||||| ||      | || |||   | ||| ||||||| |||||||| || ||||||||||| ||  ||||||||||||  ||||| ||  | || ||| ||||||| ||||| ||||| || ||||| |||||
------------------------------------------------------gtactataagat--agacttcaataaaaaaaatatta-cttgatattgtt---gcttgcttctttactcctctttttaattttttagGAGGGCAAGCGAAAACTCTTATGTTTGTTCAAATTAATCCTGATGAAGATTCATATGCTGAGACTGTAAGTACTTTGAAATTTGCGGAAAGAGTTTCTGG

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|351015024|gb|FQ444313.1|FQ444313
EST:     TGTGCCATACAGAAATAGCAAACTAACTCAAGTCCTTCAAAGCTCTTTGG                         GAGGTCAAGCGAAGACCCTTATGTTTGTACAGCTTAATCCTGATGTGGATT
genomic: TGTGCCATACAGAAATAGCAAACTAACTCAAGTCCTTCAAAGCTCTTTGGgtacatatcc ... tactttatagGAGGTCAAGCGAAGACCCTTATGTTTGTACAGCTTAATCCTGATGTGGATT
EST: gi|37187741|gb|CF607094.1|CF607094
EST:     TGTGCCATACAGAAATAGCAAACTAACTCAAGTCCTTCAAAGCTCTTTGG                         GAGGTCAAGCGAAGACCCTTATGTTTGTACAGCTTAATCCTGATGTGGATT
genomic: TGTGCCATACAGAAATAGCAAACTAACTCAAGTCCTTCAAAGCTCTTTGGgtacatatcc ... tactttatagGAGGTCAAGCGAAGACCCTTATGTTTGTACAGCTTAATCCTGATGTGGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttaacattttcttgcctgggcttgtttgaccgtttctttttcctactttatagGAGGTCAAGCGAAGACCCTTATGTTTGTACAGCTTAATCCTGATGTGGATTCCTACTCCGAAACTATAAGTACCTTGAAGTTTGCCGAGAGAGTCTCTGG
                               ccgtttctttttccta  CT-rich tract
                                  tttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacatatccttctggtttttgagtcttgtggttgaaccataccgtttgtcagtgtgctttaagattgggaatttgactttgtagttgttaacattttcttgcctgggcttgtttgaccgtttctttttcctactttatagGAGGTCAAGCGAAGACCCTTATGTTTGTACAGCTTAATCCTGATGTGGATTCCTACTCCGAAACTATAAGTACCTTGAAGTTTGCCGAGAGAGTCTCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG