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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagattctagtcttgaatgttaaatctgttttgtttgctgaaccatacaacagaggcgttgttgttcatctgggcacatccttccctttgtgtagGTCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGAGGCACTTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCA

Basic information

species Vitis vinifera
transcript Vv15s0048g00370.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv15s0048g00370.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os06g04270.1 (Oryza sativa), 3'ss of exon 2
gttagattctagtcttgaatgttaaatctgttttgtttgctgaaccatacaacagaggcgttgttgttcatctgggcacatcct----tccctttgtgtagGTCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGAGGCACTTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCA
||  |          ||||  | | | |   |||   |    |  | |  || | |  |     ||    | | ||    |  |    |  | || |||||| |||||||||||||||||||| ||||| |||||  |||| ||||| |||| |||| |||||||||| |||||||| || ||||  ||||||||||||||
gtctgtcatctcaactgaagctcatagcacctttaagtttctatgcttg-aatacatacagaactgaatgtttcggtttcttgtttggtttcgttctgtagGACCTCTTGGTCAGGGTATTGCAAATGCAGTTGGGCTGGCCCTTGCTGAGAAGCACCTGGCTGCTCGTTTCAACAAGCCCGACAGCGAGATTGTTGATCA

upper sequence: Vv15s0048g00370.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G033208_T01 (Zea mays), 3'ss of exon 2
----gttagattctagtcttgaatgttaaat--ctgttttgtttgctgaaccatacaacagaggcgttgttgttcatctgggcacatccttccctttgtgtagGTCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGAGGCACTTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCA
    |||   ||||    | |  ||| || |  | ||     ||||||  |  || || |  |     |||  |    |    | ||  || |   |||| ||| ||||||||||||||||| |||||||| ||||| ||||| ||||| |||| |||| ||||||| || |||||||| || |||| |||||| || || ||
gtctgttttcttctctattgggctgtgaattagccgtgccccttgctgtgctgtataaaactgagaaagtt--tgggtttcctatatggttgc---tgtgcagGGCCTCTTGGTCAGGGTATCGCCAATGCCGTTGGGTTGGCACTTGCTGAGAAGCACCTGGCTGCCCGCTTCAACAAGCCTGACAGTGAGATCGTCGACCA

upper sequence: Vv15s0048g00370.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G010494_T01 (Zea mays), 3'ss of exon 2
gttagattctagtcttgaatgttaaatctgttttg--tttgctgaaccatacaacagaggcgttgttgttcatctgggcacatccttccctttgtgtagGTCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGAGGCACTTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCA
              |||   | | || |  |||    ||||||   || | |  | ||  | |   |    ||||    || |   |       ||||||||||||||| |||||| |||| |||||||||||  | || ||||| ||||  ||  | ||| | || ||||||||  | ||||   |  | || || ||
-------------gttgccagctgaaacattttaaattttgctttgcctt-cttctgatacttaaattgatatctaa--acttttctgatgccatgtagGTCCTCTTGGGCAGGGTTTTGCAAATGCTGTTGGACTAGCACTTGCTGAGAAACATCTAGCTTCACGTTTCAACAAGACTGACATGAAAGTCGTGGACCA

upper sequence: Vv15s0048g00370.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT2G45290.1 (Arabidopsis thaliana), 3'ss of exon 2
----gttagattctagtcttgaatgttaaatctgttttgtttgctgaaccatacaacagaggcgttgttgttcatctgggcacatccttccctttgtgtagGTCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGAGGCACTTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCA
    |||||||| |     ||  | ||   | ||||||  ||| ||            ||    ||||  |  | |   ||   |  || ||    || |||||||||||| || |||||||| ||||||||||| || ||||||||||||| ||| ||||||||| |||| |||||||| ||||||||||||||||| ||
gttagttagatttt--ctctgcttcttttgtgtgttttagttgatg----------ttgatcttttgtaatatagcattgcttgtatttgccaacatgcagGTCCTCTTGGACAAGGTATTGCAAATGCTGTTGGTTTAGCTCTTGCGGAGAAGCATTTGGCTGCTAGATTTAACAAACCTGACAATGAGATTGTTGACCA

upper sequence: Vv15s0048g00370.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: AT3G60750.1 (Arabidopsis thaliana), 3'ss of exon 2
--gttagattctagtcttgaatgttaaatctgttttgtttgctgaaccatacaacagaggcgttgttgttcatctgggcacatccttccctttg-------tgtagGTCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGAGGCACTTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCA
   | ||||| |  |  |    | | |   || ||  | ||      || | ||   |    |   |||   |           ||   |||||       || |||||||||||| || || || || ||||||||||| || |||||||| |||| ||| ||||||||| ||||||||||||| ||   |||  | || || ||
gtttgagattttgcttcttttggctta---tggttcatgtgaaatttcacagaaactatctataactgtatttacaattgtgctctctgctttggctgctatgcagGTCCTCTTGGACAAGGAATCGCTAATGCTGTTGGTTTAGCTCTTGCTGAGAAGCATTTGGCTGCTAGATTCAACAAACCTGATGCTGAAGTAGTCGACCA

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|110689991|gb|EE066698.1|EE066698
EST:     ACCTGGTCACCCAGAAAATTTTGAGACACCTGGTGTTGAAGTCACTACTG                         GTCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGA
genomic: ACCTGGTCACCCAGAAAATTTTGAGACACCTGGTGTTGAAGTCACTACTGgttagattct ... ctttgtgtagGTCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGA
EST: gi|351013311|gb|FQ425016.1|FQ425016
EST:     ACCTGGTCACCCAGAAAATTTTGAGACACCTGGTGTTGAAGTCACTACTG                         GTCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGA
genomic: ACCTGGTCACCCAGAAAATTTTGAGACACCTGGTGTTGAAGTCACTACTGgttagattct ... ctttgtgtagGTCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGA
EST: gi|161705830|gb|FC057107.1|FC057107
EST:     ACCTGGTCACCCAGAAAATTTTGAGACACCTGGTGTTGAAGTCACTACTG                         GCCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGA
genomic: ACCTGGTCACCCAGAAAATTTTGAGACACCTGGTGTTGAAGTCACTACTGgttagattct ... ctttgtgtagGTCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGA
EST: gi|110689389|gb|EE065571.1|EE065571
EST:     ACCTGGTCACCCAGAAAATTTTGAGACACCTGGTGTTGAAGTCACTACTG                         GTCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGA
genomic: ACCTGGTCACCCAGAAAATTTTGAGACACCTGGTGTTGAAGTCACTACTGgttagattct ... ctttgtgtagGTCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGA
EST: gi|110687702|gb|EE065414.1|EE065414
EST:     ACCTGGTCACCCAGAAAATTTTGAGACACCTGGTGTTGAAGTCACTACTG                         GTCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGA
genomic: ACCTGGTCACCCAGAAAATTTTGAGACACCTGGTGTTGAAGTCACTACTGgttagattct ... ctttgtgtagGTCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGA
EST: gi|110700650|gb|EE077489.1|EE077489
EST:     ACCTGGTCACCCAGAAAATTTTGAGACACCTGGTGTTGAAGTCACTACTG                         GTCCTCTTGGTCAGGNTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGA
genomic: ACCTGGTCACCCAGAAAATTTTGAGACACCTGGTGTTGAAGTCACTACTGgttagattct ... ctttgtgtagGTCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGA
EST: gi|110686000|gb|EE063214.1|EE063214
EST:     ACCTGGTCACCCAGAAAATTTTGAGACACCTGGTGTTGAAGTCACTACTG                         GTCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGA
genomic: ACCTGGTCACCCAGAAAATTTTGAGACACCTGGTGTTGAAGTCACTACTGgttagattct ... ctttgtgtagGTCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGA
EST: gi|77579456|gb|DV218569.1|DV218569
EST:     ACCTGGTCACCCAGAAAATTTTGAGACGCCTGGTGTTGAAGTCACTACTG                         GTCCTCTTGGTCA
genomic: ACCTGGTCACCCAGAAAATTTTGAGACACCTGGTGTTGAAGTCACTACTGgttagattct ... ctttgtgtagGTCCTCTTGGTCA
EST: gi|161713434|gb|FC063712.1|FC063712
EST:     ACCTGGTCACCCAGAAAATTTTGAGACACCTGGTGTTGAAGTCACTACTG                         GCCCTCTTGGTCAGGGTATTGC
genomic: ACCTGGTCACCCAGAAAATTTTGAGACACCTGGTGTTGAAGTCACTACTGgttagattct ... ctttgtgtagGTCCTCTTGGTCAGGGTATTGC
EST: gi|34548489|gb|CF516721.1|CF516721
EST:     ACCTGGTCACCCAGAAAATTTTGAGACACCTGGTGTTGAAGTCACTACTG                         GCCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGA
genomic: ACCTGGTCACCCAGAAAATTTTGAGACACCTGGTGTTGAAGTCACTACTGgttagattct ... ctttgtgtagGTCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGA
EST: gi|110689357|gb|EE065511.1|EE065511
EST:     ACCTGGTCACCCAGAAAATTTTGAGACACCTGGTGTTGAAGTCACTACTG                         GTCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGA
genomic: ACCTGGTCACCCAGAAAATTTTGAGACACCTGGTGTTGAAGTCACTACTGgttagattct ... ctttgtgtagGTCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaccatacaacagaggcgttgttgttcatctgggcacatccttccctttgtgtagGTCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGAGGCACTTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCA
                                  cacatccttcccttt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagattctagtcttgaatgttaaatctgttttgtttgctgaaccatacaacagaggcgttgttgttcatctgggcacatccttccctttgtgtagGTCCTCTTGGTCAGGGTATTGCCAATGCTGTTGGCTTGGCTCTTGCGGAGAGGCACTTGGCTGCTCGATTCAACAAACCAGACAATGAGATTGTTGATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT