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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatacttaggatattcatttggaaataactaaataacttgcttgatctgtaatttgcttcaaattttaccacttataatctttaccttgtttcggcagGCTGTAATGCAGATATCCATGTCATTGTTAAAATTGAAAGTGCCGACTCCATTCCCAATCTACATTCAATTATTACCGCATCTGATGGG

Basic information

species Vitis vinifera
transcript Vv16s0050g02180.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0050g02180.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g47080.1 (Oryza sativa), 3'ss of exon 5
gtaaatacttaggatattcatttggaaataactaaataacttgcttgatctgtaatttgcttcaaattttaccacttataatctttaccttgtttcggcagGCTGTAATGCAGATATCCATGTCATTGTTAAAATTGAAAGTGCCGACTCCATTCCCAATCTACATTCAATTATTACCGCATCTGATGGG
              || | |||    |    ||| || |      | |||    | ||  |   || | |   | |  |    |||   ||| |||  ||||||  ||||| ||||| ||||| ||||| || ||||||||||| || |||||||| || ||||| ||||| || || ||||| ||||||
-------------gtaataatt----atcccctacattatgaaaattatccagcacttattc--aactgtcttaatagtgtgttttgttttgattct-cagGCTCCAATGCCGATATACATGTAATTGTAAAGATTGAAAGTGCAGATTCCATTCCAAACCTACACTCAATCATCACAGCATCGGATGGG

upper sequence: Vv16s0050g02180.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 5
gtaaatacttaggatattcatttggaaataactaaataacttgcttgatc-tgtaatttgcttcaaattttaccacttataatctttaccttgtttcggcagGCTGTAATGCAGATATCCATGTCATTGTTAAAATTGAAAGTGCCGACTCCATTCCCAATCTACATTCAATTATTACCGCATCTGATGGG
              || ||  ||  |   ||||   |||        ||| || |  ||  || | | |||||       | |||  |   | ||    |||| || ||||| || || ||||| || || ||||| |||||||| |||||||| |||||  |||||||||| || || ||||||||||||
-------------gtaatc--ttcaacccaactttgtaaaaaatcatatcatgcacctttttttacaatttactgagctcattct--attctattct--cagGTTGCAATGCTGACATACATGTTATCGTAAAAATAGAAAGTGCAGACTCCATCCCCAACTTACATTCAATCATCACAGCATCTGATGGG

upper sequence: Vv16s0050g02180.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G37210.1 (Glycine max), 3'ss of exon 5
gtaaatacttaggatattcatttggaaataactaaataacttgcttgatctgtaatttgcttcaaattttaccacttataatctttaccttgtttcggcagGCTGTAATGCAGATATCCATGTCATTGTTAAAATTGAAAGTGCCGACTCCATTCCCAATCTACATTCAATTATTACCGCATCTGATGGG
||||||  | | |||| |  |    |  |   ||| ||  | |  ||||   |   |    | |  ||  |  |     |||  |   ||     | ||||||||| |||| ||||| ||||||||||| |||||||||||||| ||||| || || ||  | |||||||||||||| || |||||||||
gtaaattttcaagatacttgt---aatttttttaattagttcgtctgattaatttctctaattattttaaagtatgataaattgtccactcaacactgcagGCTGTGATGCTGATATACATGTCATTGTAAAAATTGAAAGTGCAGACTCTATACCAAACTTGCATTCAATTATTACAGCGTCTGATGGG

upper sequence: Vv16s0050g02180.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G30430.1 (Glycine max), 3'ss of exon 5
gtaaatacttaggatattcat-ttggaaataactaaataacttgcttgatctgta-atttgcttcaaattttaccacttataatctttaccttgtttcggcagGCTGTAATGCAGATATCCATGTCATTGTTAAAATTGAAAGTGCCGACTCCATTCCCAATCTACATTCAATTATTACCGCATCTGATGGG
||||||| | | |||| |  | ||     ||| ||    |  || || || | |  | ||  |||||| | |   |     |||  |   ||     | ||||||||| |||| ||||| || |||||||| |||||||||||||| ||||| || || ||  | |||||||||||||| || |||||||||
gtaaatattcaagatacttgtattttttttaattagtccatctgattaatttctctaattatttcaaaatgtgata-----aattgtccactcaacgctgcagGCTGTGATGCTGATATACACGTCATTGTAAAAATTGAAAGTGCAGACTCTATACCAAACTTGCATTCAATTATTACAGCGTCTGATGGG

upper sequence: Vv16s0050g02180.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA16G28980.1 (Glycine max), 3'ss of exon 5
gtaaatacttaggatattcatttggaaataactaa-ataacttgcttgatctgtaat-ttgc---ttcaaattttaccacttataatctttac-cttgtttcggcagGCTGTAATGCAGATATCCATGTCATTGTTAAAATTGAAAGTGCCGACTCCATTCCCAATCTACATTCAATTATTACCGCATCTGATGGG
|||||||  ||  |||||   ||  |||||  |   | || ||    |||  ||  |  |||   || | ||| ||    | ||||  ||| | |||| | | ||||||||   ||| ||||| |||||||| || |||||||||||||| ||||| || || ||| | ||||||||||| || ||||||||||||
gtaaatatctaaaatatt---ttaaaaatactttttaaaatttatccgattagttttgctgcatatttagattataaatatgataaattttccacttgatactgcagGCTGCGGTGCTGATATACATGTCATCGTAAAAATTGAAAGTGCAGACTCTATACCAAATTTGCATTCAATTATCACTGCATCTGATGGG

upper sequence: Vv16s0050g02180.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA09G23150.1 (Glycine max), 3'ss of exon 5
gtaaatacttaggatattcatttggaaataactaaa--taacttgcttgatctgtaatttgcttcaaattttaccacttataatctttaccttgtttcggcagGCTGTAATGCAGATATCCATGTCATTGTTAAAATTGAAAGTGCCGACTCCATTCCCAATCTACATTCAATTATTACCGCATCTGATGGG
|||||||  ||  |||||        | |   |||   | |     ||  | ||     |   |  | | | |  |     ||| ||    ||| | | |||||||||  ||| ||||| |||||||| || ||||| |||||||| ||||| || || ||| | ||||||||||| || || |||||||||
gtaaatatctaaaatattttaaaaatactttttaacatttatccaattagtttgctgcatatattgattataaatatgataaattttccatttggtactgcagGCTGTGGTGCTGATATACATGTCATCGTAAAAATCGAAAGTGCAGACTCTATACCAAATTTGCATTCAATTATCACTGCGTCTGATGGG

upper sequence: Vv16s0050g02180.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: PP1S318_21V6.1 (Physcomitrella patens), 3'ss of exon 4
gtaaatacttaggatattcatttggaaataactaaata-acttgcttgatctgtaat-ttgcttcaaattttaccacttataatct--ttaccttgtttcggcagGCTGTAATGCAGATATCCATGTCATTGTTAAAATTGAAAGTGCCGACTCCATTCCCAATCTACATTCAATTATTACCGCATCTGATGGG
      |  |  | |||   |||    || |||   |  || ||| | ||    | | |   |   | | |||  | |  ||||    |    |     | ||||        || || || ||||||||||| || ||||||||||| || || |||||||||||||| || ||| |    ||| ||||||| 
-----aatcttcgttatctttttaacgatgactctgtttacatgcatcattatcattatcattattactattattattattaattgaatagtgtgagcgctgcagAGAAGTCAGCTGACATTCATGTCATTGTGAAGATTGAAAGTGCGGATTCGATTCCCAATCTACAATCCATTCTGGATGCAGCTGATGGT

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|110688927|gb|EE068039.1|EE068039
EST:     CTTTGTTAAAGATGCGAAAGTAGTCCATGAATTGAAGAACTATCTGAAAA                         GCTGTAATGCAGATATCCATGTCATTGTTAAAATTTGAA-GTGCCGACTCC
genomic: CTTTGTTAAAGATGCAAAAGTAGTCCATGAATTGAAGAACTATCTGAAAAgtaaatactt ... gtttcggcagGCTGTAATGCAGATATCCATGTCATTGTTAAAATT-GAAAGTGCCGACTCC
EST: gi|110698146|gb|EE075377.1|EE075377
EST:     CTTTGTTAAAGATGCGAAAGTAGTCCATGAATTGAAGAACTATCTGAAAA                         GCTGTAATGCAGATATCCATGTCATTGTTAAAATTGAAAGTGCCGACTCCA
genomic: CTTTGTTAAAGATGCAAAAGTAGTCCATGAATTGAAGAACTATCTGAAAAgtaaatactt ... gtttcggcagGCTGTAATGCAGATATCCATGTCATTGTTAAAATTGAAAGTGCCGACTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatctgtaatttgcttcaaattttaccacttataatctttaccttgtttcggcagGCTGTAATGCAGATATCCATGTCATTGTTAAAATTGAAAGTGCCGACTCCATTCCCAATCTACATTCAATTATTACCGCATCTGATGGG
 gcttgat  putative branch site (score: 5)
                                   tctttaccttgtttc  putative PPT
                           acttataatcttta  TA-rich tract