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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttcattctcaaaataatttcaaagagatcttactttatcctatgtaactagaataatgacttcagctgcttttttccaatatcttgctgtaccttcttgatttcattttcatgattttggcagCTGTTGAATTTCTTAGACATGTACCTGAAGGGAAGTATGATGCAATTATTGTTGATTCATCAGATCCTGTGG

Basic information

species Vitis vinifera
transcript Vv16s0050g02670.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g02670.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os06g33710.1 (Oryza sativa), 3'ss of exon 7
gtatgttcattctcaaaataatttcaaagagatcttactttatcctatgtaactagaataatgacttcagctgcttttttccaatatcttgctgtaccttcttgatttcattttcatgattttggcagCTGTTGAATTTCTTAGACATGTACCTGAAGGGAAGTATGATGCAATTATTGTTGATTCATCAGATCCTGTGG
                  ||  ||    | | ||||| | | |  |   |   || | |  || |||  | |    |||   | |  |||  | || |||| | ||     |    | |||||| ||||||| || ||  | ||| |||  ||||||||||| |||||||| || |||||||||||||| || ||  | |
------------------tatctt--gcgtgttcttaatcttttttgcatgcatata-tggtggctttggat----tttaaaattgcctt--tatatcttcataatagacctgcttttattttg-cagCTGTGGATTTCTTGAGAAATGCCCCTGAAGGGAAATATGATGCTATCATTGTTGATTCATCTGACCCAATTG

upper sequence: Vv16s0050g02670.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os02g15550.1 (Oryza sativa), 3'ss of exon 7
gtatgttcattctcaaaataatttcaaagagatcttactttatcctatgtaactagaataatgacttcagctgcttttttccaatatcttgctgtaccttcttgatttcattttcatgattttggcagCTGTTGAATTTCTTAGACATGTACCTGAAGGGAAGTATGATGCAATTATTGTTGATTCATCAGATCCTGTGG
||| |||||   |||| || |  |        | | ||| |     |  ||  |   ||    | || || |||   |||| |||   ||| | |    | || ||  |  |   ||  | ||  ||||||| || ||  | ||  |||  ||||||||||  |||||||| |||||||| ||||||||||| ||  | |
gtacgttcacaatcaatattacct-----gtttataactgtgaaaaaaatatatcctatttgcaatttagatgcacctttc-aattctttggtttgtaattttcataactgtcctattttattt-cagCTGTGGAGTTCTTAAGGAATGCTCCTGAAGGGACATATGATGCTATTATTGTCGATTCATCAGACCCGATTG

upper sequence: Vv16s0050g02670.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G047867_T01 (Zea mays), 3'ss of exon 7
gtatgttca--------ttctcaaaataatttcaaagagatcttac----tttatcctatgtaactagaata-atgacttcagctgcttttttccaat--atcttgctgtacc-ttcttgatttcattttcatgattttg-gcagCTGTTGAATTTCTTAGACATGTACCTGAAGGGAAGTATGATGCAATTATTGTTGATTCATCAGATCCTGTGG
|||||||||        | |        | || | |    | | ||    | ||   ||||  ||||   |  ||  | ||||   |||| || |      ||||| | |    |  || ||   ||  |    |||||  ||||||||||| || || ||  ||   || ||||| || |||||||| |||||||| ||||||||||||||  | |
gtatgttcaaaagctggtacctggtggtactttatatgactgtgacaggctgtaggatatgccactattgtttatagcctcaggcactttgtttctgctggtcttgatctcttatagttcatagtatacttgctattttttgcagCTGTTGATTTCCTGAGGAATTCTCCCGAAGGAAAATATGATGCTATTATTGTAGATTCATCAGATCCAATTG

upper sequence: Vv16s0050g02670.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA06G13210.2 (Glycine max), 3'ss of exon 7
gtatgttcattctcaaaataatttcaaagagatcttactttatcctatgtaactagaataatgacttcagctgcttttttccaatatcttgctgtaccttcttgatttcattttcatg-attttggcagCTGTTGAATTTCTTAGACATGTACCTGAAGGGAAGTATGATGCAATTATTGTTGATTCATCAGATCCTGTGG
                                   ||  |  |  | ||    |    |  ||| ||    ||  || |  |  | | | ||| ||  || |||||||  ||| ||   ||||||||||||||||| ||||||| |   |  |||||||||||||||||||| || ||||||||||| |||||||| ||||
----------------------------------gtatatatttatctgctggtcttgttttgaatttgtatgagttgtctct-tctgtggctttagtttgttgattttttttccacccattttggcagCTGTTGATTTTCTTAAATCCGCTCCTGAAGGGAAGTATGATGCCATAATTGTTGATTCCTCAGATCCAGTGG

upper sequence: Vv16s0050g02670.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA04G41600.1 (Glycine max), 3'ss of exon 7
gtatgttcattctcaaaataatttcaaagagatcttactttatcctatgtaactagaataatgacttcagctgcttttttccaatatcttgctgtaccttcttgatttcatttt-catgattttggcagCTGTTGAATTTCTTAGACATGTACCTGAAGGGAAGTATGATGCAATTATTGTTGATTCATCAGATCCTGTGG
                             | || ||  | |        |   |  |||  |   || || ||| | ||      |      | ||  || || ||||  ||   |    ||||| |||||||||||||||||| |  ||    |||||||||||||||||| || ||||||||||| |||||||| ||||
---------------------------gtatatatttatctgctggtcttgttttaaat--ttgtttgagttgcctcttctgtgcag---aatttagtttgttaatttttttccacccatttttgacagCTGTTGAATTTCTTAAATCTGCTTGTGAAGGGAAGTATGATGCCATAATTGTTGATTCCTCAGATCCCGTGG

upper sequence: Vv16s0050g02670.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: AT5G53120.4 (Arabidopsis thaliana), 3'ss of exon 8
gtatgttcattctcaaaataatttcaaagagatcttactttatcctatgtaactagaataatgacttcagctgcttttttccaatatcttgctgtaccttcttgatttcattttcatgattttggcagCTGTTGAATTTCTTAGACATGTACCTGAAGGGAAGTATGATGCAATTATTGTTGATTCATCAGATCCTGTGG
                            |  ||    | || | |||  |           |   ||||       |  || || || |   |||      ||||| ||| ||||     | ||||||||| ||| || ||  |  |    |||||||||||||||||||| || ||||||||||| |||||||| || |
----------------------------gtaattaagcattcttctacttgttc-------tctgttcacaaaacgtagtcaaaaatttgcttgtg-----ttgatatcactttc----ctctggcagCTGCTGAGTTCCTCCGTAAATCCCCTGAAGGGAAGTATGATGCCATCATTGTTGATTCTTCAGATCCCGTAG

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|110686791|gb|EE064831.1|EE064831
EST:     TTATACGTTGGGGTTTGAAGACCCTCGTGTCCAGCTTCATGTTGGGGATG                         CTGTTGAATTTC
genomic: TTATACGTTGGG-TTTGAAGACCCTCGTGTCCAGCTTCATGTTGGGGATGgtatgttcat ... attttggcagCTGTTGAATTTC
EST: gi|110687699|gb|EE065403.1|EE065403
EST:     GTTATACGTTGGGTTTGAAGACCCTCGTGTCCAGC-TCATGTTGGGGATG                         CTGTTGAATTTCTTAGACATGTACCTGAAGGGAAGTATGATGCAATTATTG
genomic: GTTATACGTTGGGTTTGAAGACCCTCGTGTCCAGCTTCATGTTGGGGATGgtatgttcat ... attttggcagCTGTTGAATTTCTTAGACATGTACCTGAAGGGAAGTATGATGCAATTATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttttccaatatcttgctgtaccttcttgatttcattttcatgattttggcagCTGTTGAATTTCTTAGACATGTACCTGAAGGGAAGTATGATGCAATTATTGTTGATTCATCAGATCCTGTGG
                          tcttgat  putative branch site (score: 4)
                                    attttcatgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttcattctcaaaataatttcaaagagatcttactttatcctatgtaactagaataatgacttcagctgcttttttccaatatcttgctgtaccttcttgatttcattttcatgattttggcagCTGTTGAATTTCTTAGACATGTACCTGAAGGGAAGTATGATGCAATTATTGTTGATTCATCAGATCCTGTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG