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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtaaagtccgcgggtaacttctttccatggtcacttttccggtggggtttataacatgagaatatatatatgtttttgaattttgtggcagGTGAGCACTAAATTTGGGGATGTGTTCGCATTTAGTGGGCCGGCACCGGAGAGGATCAACGGCAGGCTTGCCATGGTAGGCTTTGTTGCGGCAATGGGTG

Basic information

species Vitis vinifera
transcript Vv05s0020g04110.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g04110.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA20G28890.1 (Glycine max), 3'ss of exon 2
-----gtatgtaaagtccgcgggtaacttctttccatggtcacttttccggtggggtttataacatgagaatatatatat-gtttttgaattttgtggcagGTGAGCACTAAATTTGGGGATGTGTTCGCATTTAGTGGGCCGGCACCGGAGAGGATCAACGGCAGGCTTGCCATGGTAGGCTTTGTTGCGGCAATGGGTG
             || |  |   ||| |||||    |   ||  | |    |  | |    || |||    | | | ||| | | |     ||  ||||||||||||||||| |||   |||||||| ||||| |||||||| ||||| ||||||||||| || ||| | |||||| | || ||||| || |||||||  |
tgatgacgatccgagactactaataatttcttagt-tatgcaaatgtgaattttgataagcaatatgtccctctctctattgatatcatggttaatggcagGTGAGCACTAAGTTTTCTGATGTGTTGGCATTCAGTGGGCCAGCACCTGAGAGGATCAATGGAAGGTTGGCCATGATTGGGTTTGTGGCTGCAATGGCAG

upper sequence: Vv05s0020g04110.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA10G38910.1 (Glycine max), 3'ss of exon 2
----gta-tgtaaagtccgcgggtaacttctttc--catg---gtcacttttccggtggggtttataacatgagaatatatatatgtttttgaattttgtggcagGTGAGCACTAAATTTGGGGATGTGTTCGCATTTAGTGGGCCGGCACCGGAGAGGATCAACGGCAGGCTTGCCATGGTAGGCTTTGTTGCGGCAATGGGTG
    ||  ||  ||  |      ||| |||||    |||    |  | | |     ||    || | ||| |    |||  | ||| |  | |||     ||||||||||||| || |||   |||||||| || || |||||||| ||||| ||||||||||| || ||| | |||||| | || ||||| |  |||||||  |
gttggtggtgctaaaccatataataatttcttctatcatataagcaattatgtaaatgtcaattttgacaagcctctattgacatgatggttaat-----ggcagGTGAGCACCAAGTTTTCTGATGTGTTGGCGTTCAGTGGGCCAGCACCTGAGAGGATCAATGGAAGGTTGGCCATGATTGGGTTTGTGGGTGCAATGGCAG
















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|33403991|gb|CF209618.1|CF209618
EST:     CACAGTCACGTCAACCGATCCCTCCACCTCCTCCTCCTCCTGCGCCTAAG                         GTGAGCACCAAATTTGGGGATGTGTTCGCACTTAGTGGGCCGGCACCGGAG
genomic: CACAGTCACGTCAACCGATCCCTCCTCCTCCTCCTCCTCCTGCGCCTAAGgtatgtaaag ... tttgtggcagGTGAGCACTAAATTTGGGGATGTGTTCGCATTTAGTGGGCCGGCACCGGAG
EST: gi|71883247|gb|DT032302.1|DT032302
EST:     CACAGTCACGTCAACCGATCCCTCTTCCTCCTCCTCCTCCTGCGCCTAAG                         GTGAGCACCAAATTTGGGGATGTGTTCGCATTTAGTGGGCCGGCACCGGAG
genomic: CACAGTCACGTCAACCGATCCCTCCTCCTCCTCCTCCTCCTGCGCCTAAGgtatgtaaag ... tttgtggcagGTGAGCACTAAATTTGGGGATGTGTTCGCATTTAGTGGGCCGGCACCGGAG
EST: gi|26259639|gb|CA810702.1|CA810702
EST:     CTCCTCCTCCTGCGCCTAAG                         GTGACCACCAAATTTGGGAATGTGTTCGCATTTAGTGGGCCGCCACCGGAG
genomic: CTCCTCCTCCTGCGCCTAAGgtatgtaaag ... tttgtggcagGTGAGCACTAAATTTGGGGATGTGTTCGCATTTAGTGGGCCGGCACCGGAG
EST: gi|33403907|gb|CF209534.1|CF209534
EST:     CACAGTCACGTCAACCGATCCCTCCACCTCCTCCTCCTCCTGCGCCTAAG                         GTGAGCACCAAATTTGGGGATGTGTTCGCACTTAGTGGGCCGGCACCGGAG
genomic: CACAGTCACGTCAACCGATCCCTCCTCCTCCTCCTCCTCCTGCGCCTAAGgtatgtaaag ... tttgtggcagGTGAGCACTAAATTTGGGGATGTGTTCGCATTTAGTGGGCCGGCACCGGAG
EST: gi|26262271|gb|CA813334.1|CA813334
EST:     CACAGTCACGTCAACCGATCCCTCCTCCTTCTCCTCCTCCTGCGCCTAAG                         GTGAGCACCAAATTTGGGGATGTGTNCGCATTTAGTGGGCCGGCACCGGAG
genomic: CACAGTCACGTCAACCGATCCCTCCTCCTCCTCCTCCTCCTGCGCCTAAGgtatgtaaag ... tttgtggcagGTGAGCACTAAATTTGGGGATGTGTTCGCATTTAGTGGGCCGGCACCGGAG
EST: gi|26259546|gb|CA810609.1|CA810609
EST:     CACAGTCACGTCAACCGATCCCTCCTCCTCCTTCTCCTCCTGCGCCTAAG                         GTGAGCACCAAATTTGGGGATGTGTTCGCATTTAGTGGGCCGGCACCGGAG
genomic: CACAGTCACGTCAACCGATCCCTCCTCCTCCTCCTCCTCCTGCGCCTAAGgtatgtaaag ... tttgtggcagGTGAGCACTAAATTTGGGGATGTGTTCGCATTTAGTGGGCCGGCACCGGAG
EST: gi|26261429|gb|CA812492.1|CA812492
EST:     CACAGTCACGTCAACCGATCCCTCCT--T-CTCCTCCTCCTGCGCCCAAG                         GTGAGCACCAAATTTGGGGATGTGTTCGCGTTTAGTGGGCCGGCACCGGAG
genomic: CACAGTCACGTCAACCGATCCCTCCTCCTCCTCCTCCTCCTGCGCCTAAGgtatgtaaag ... tttgtggcagGTGAGCACTAAATTTGGGGATGTGTTCGCATTTAGTGGGCCGGCACCGGAG
EST: gi|26263344|gb|CA814407.1|CA814407
EST:     CTCCTCCTGCGCCTAAG                         GTGAGCACCAAATTTGGGGATCTGTTCGCATTTACTGGGCCGGCACCGGAG
genomic: CTCCTCCTGCGCCTAAGgtatgtaaag ... tttgtggcagGTGAGCACTAAATTTGGGGATGTGTTCGCATTTAGTGGGCCGGCACCGGAG
EST: gi|46919777|gb|CN549106.1|CN549106
EST:     CTCCTCCTCCTGCGCCCAAG                         GTGAGCACCAAATTTGGGGATGTGTTCGCGTTTAGTGGGCCGGCACCGGAG
genomic: CTCCTCCTCCTGCGCCTAAGgtatgtaaag ... tttgtggcagGTGAGCACTAAATTTGGGGATGTGTTCGCATTTAGTGGGCCGGCACCGGAG
EST: gi|45771394|gb|CN007246.1|CN007246
EST:     CACAGTCAGGTCAACCGAT--C-CCTCCTCCTCCTCCTCGTGCGCCCAAG                         GTGAGCACCAAATTTGGGGATGTGTTCGCGTTTAGTGGGCCGGCACCGGAG
genomic: CACAGTCACGTCAACCGATCCCTCCTCCTCCTCCTCCTCCTGCGCCTAAGgtatgtaaag ... tttgtggcagGTGAGCACTAAATTTGGGGATGTGTTCGCATTTAGTGGGCCGGCACCGGAG
EST: gi|28961187|gb|CB340604.1|CB340604
EST:     CACAGTCACGTCAACCGA----T-C-CCTCCTCCTCCTCCTGCGCCTAAG                         GTGAGCACCAAATCTGGGGATGTGTTCGCATTTAGTGGGCCGGCACCGGAG
genomic: CACAGTCACGTCAACCGATCCCTCCTCCTCCTCCTCCTCCTGCGCCTAAGgtatgtaaag ... tttgtggcagGTGAGCACTAAATTTGGGGATGTGTTCGCATTTAGTGGGCCGGCACCGGAG
EST: gi|27584341|gb|CB007036.1|CB007036
EST:     CACAGTCACGTCAACCGATCCCTCCTCCTTCTCCTCCTCCTGCGCCCAAG                         GTGAGCACCAAATTTGGGGATGTGTTCGCGTTTAGTGGGCCGGCACCGGAG
genomic: CACAGTCACGTCAACCGATCCCTCCTCCTCCTCCTCCTCCTGCGCCTAAGgtatgtaaag ... tttgtggcagGTGAGCACTAAATTTGGGGATGTGTTCGCATTTAGTGGGCCGGCACCGGAG
EST: gi|26263523|gb|CA814586.1|CA814586
EST:     CCTCCTCCTCCTCTTCCTGCGCCCAAG                         GTGAGCACCACATTTGGGGATGTGTTCGCGTTTCGTGGGCCGGCACCGGAG
genomic: CCTCCTCCTCCTCCTCCTGCGCCTAAGgtatgtaaag ... tttgtggcagGTGAGCACTAAATTTGGGGATGTGTTCGCATTTAGTGGGCCGGCACCGGAG
EST: gi|33407797|gb|CF213424.1|CF213424
EST:     CACAGTCACGTCAACCGATCCCTCCTCCTCCTCCTGCTCCTGCGCCTAAG                         GTGAGCACCAAATTTGGGGACGTGTTCGCATTTAGTGGGCCGGCACCGGAG
genomic: CACAGTCACGTCAACCGATCCCTCCTCCTCCTCCTCCTCCTGCGCCTAAGgtatgtaaag ... tttgtggcagGTGAGCACTAAATTTGGGGATGTGTTCGCATTTAGTGGGCCGGCACCGGAG
EST: gi|71888395|gb|DT037450.1|DT037450
EST:     CACAGTCACGTCAACCGATCCCTCTTCCTCCTCCTCCTCCTGCGCCTAAG                         GTGAGCACCAAATTTGGGGATGTGTTCGCATTTAGTGGGCCGGCACCGGAG
genomic: CACAGTCACGTCAACCGATCCCTCCTCCTCCTCCTCCTCCTGCGCCTAAGgtatgtaaag ... tttgtggcagGTGAGCACTAAATTTGGGGATGTGTTCGCATTTAGTGGGCCGGCACCGGAG
EST: gi|28961367|gb|CB340693.1|CB340693
EST:     CACAGTCACGTCAACCGA----T-C-CCTCCTCCTCCTCCTGCGCCTAAG                         GTGAGCACCAAATCTGGGGATGTGTTCGCATTTAGTGGGCCGGCACCGGAG
genomic: CACAGTCACGTCAACCGATCCCTCCTCCTCCTCCTCCTCCTGCGCCTAAGgtatgtaaag ... tttgtggcagGTGAGCACTAAATTTGGGGATGTGTTCGCATTTAGTGGGCCGGCACCGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccggtggggtttataacatgagaatatatatatgtttttgaattttgtggcagGTGAGCACTAAATTTGGGGATGTGTTCGCATTTAGTGGGCCGGCACCGGAGAGGATCAACGGCAGGCTTGCCATGGTAGGCTTTGTTGCGGCAATGGGTG
            ttataac  putative branch site (score: 2)
           tttataacatgagaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtaaagtccgcgggtaacttctttccatggtcacttttccggtggggtttataacatgagaatatatatatgtttttgaattttgtggcagGTGAGCACTAAATTTGGGGATGTGTTCGCATTTAGTGGGCCGGCACCGGAGAGGATCAACGGCAGGCTTGCCATGGTAGGCTTTGTTGCGGCAATGGGTG

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