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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgttcctctctcctgatgtctagccctaatttttgtcatgtctttgtgatttgtggtgttttctaggaaattttgctctggtgattttcaggcacttggcaagattgcttgcaaattgatttttctcatctggttgtattgtgatttgtggtgttttcaagGCACTTAGCAAAATCGCTTGCAATCGGCTCCAGAAAGAGCTTGTTGAGTGGCAGGTCAATCCACCCGCCGGTTTCAAACACAAAGTCACCGACAATCTTC

Basic information

species Vitis vinifera
transcript Vv04s0023g02620.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0023g02620.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os03g47770.1 (Oryza sativa), 3'ss of exon 1
gtctgttcctctctcctgatgtctagccctaatttttgtcatgtctttgtgatttgtggtgttttctaggaaattttgctctggtgattttcaggcacttggcaagattgcttgcaaattgatttttctcatctggttgtattgtgatttgtggtgttttcaagGCACTTAGCAAAATCGCTTGCAATCGGCTCCAGAAAGAGCTTGTTGAGTGGCAGGTCAATCCACCCGCCGGTTTCAAACACAAAGTCACCGACAATCTTC
             | |  |   ||| ||||||       |         | ||       |  | | |       |    |    ||||  | |  | |||    |   | ||     |   | | ||| | ||| |||| |     | ||||   |  |  |||  || ||||| ||||| ||||| ||||| ||||| ||||| |  |||||||||||||| || ||| |||| ||||| ||||| |||||||||||||| |
------------gtaccaaaccctaaccctaaccccctcctctctaccctcatcccctccggatcccatctcccctccgccc--cgattcgccgtaatttgttttgggggtttttttctctctctctctgagctgtttgtgtgtgtgtatgtgtgttcgtgcagGTGCTGAGCAAGATCGCGTGCAACCGGCTGCAGAAGGAGCTCGCGGAGTGGCAGGTCAACCCTCCCTCCGGCTTCAAGCACAAGGTCACCGACAATCTCC

upper sequence: Vv04s0023g02620.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os12g44000.2 (Oryza sativa), 3'ss of exon 1
gtctgttcctctctcctgatgtctagccctaatttttgtcatgtctttgtgatttgtggtgtttt-ctaggaaattttgctctggtgattttcaggcacttggcaagattgcttgcaaattgatttttctcatctggttgtattgtgatttgtggtgttttcaagGCACTTAGCAAAATCGCTTGCAATCGGCTCCAGAAAGAGCTTGTTGAGTGGCAGGTCAATCCACCCGCCGGTTTCAAACACAAAGTCACCGACAATCTTC
                                                       ||  | || | ||      | |  |||         || |   || |       |   ||  ||    ||  ||| || |       || |  |||||          |||| || ||||| ||||||||||||||||| ||||| ||||| |  |||||||||||||  || ||| |||| |||||  |||  ||| |||| || || |
-------------------------------------------------------gtattattctactccttcctctctctccccaatccgtctgattctcg------ctatctgtgaacgttttggtctaatttccccccctttttttttgtacctgcgcgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAGGAGCTCGCCGAGTGGCAGGTCAGCCCTCCCTCCGGGTTCAAGTACAGGGTCTCCGATAACCTCC

upper sequence: Vv04s0023g02620.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G007381_T01 (Zea mays), 3'ss of exon 1
gtctgttcctctctcctgatgtctagccctaatttttgtcatgtctttgtgatttgtggtgttttctaggaaattttgctctggtgattttcaggcacttggcaagattgcttgcaaattgatttttctcatctggttgtattgtgatttgtggtgttttcaagGCACTTAGCAAAATCGCTTGCAATCGGCTCCAGAAAGAGCTTGTTGAGTGGCAGGTCAATCCACCCGCCGGTTTCAAACACAAAGTCACCGACAATCTTC
                                        | ||  |  |  |         |   | |||      || | ||       |||||  ||||         || |     ||||   || |     ||  || |     | |     | |  |||| || ||||| ||||||||||||||||| ||||||||||| |  |||||||||   || || |||| ||| ||||| ||||| ||| |||| || || |
--------------------------------------gtacgtgctc-tcctcccccccaatccatcggattcgccgcccggggagcgcccaggcggttggt-------tttccgtcccgattcggctaac--aattcgatcgatcccttttcgcctgtgcagGCGCTGAGCAAGATCGCTTGCAATCGGCTGCAGAAAGAGCTCGCCGAGTGGCAGCAAAACCCCCCCGTCGGGTTCAAGCACAAGGTCTCCGATAACCTCC

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|71861276|gb|DT010331.1|DT010331
EST:     CCGTAGCCATTGAAGCAAGCATGACCAGCTCCTCCGCCACCTCTCGCAAG                         GCACTTAGCAAAATCGCTTGCAATCGGCTCCAGAAAGAGCTTGTTGAGTGG
genomic: CCGTAGCCATTGAAGCAAGCATGACCAGCTCCTCCGCCACCTCTCGCAAGgtctgttcct ... tgttttcaagGCACTTAGCAAAATCGCTTGCAATCGGCTCCAGAAAGAGCTTGTTGAGTGG
EST: gi|30297123|gb|CB973917.1|CB973917
EST:     CCGTAGCCATTGAAGCAAGCATGACCAGCTCCTCCGCCACCTCTCGCAAG                         GCACTTAGCAAAATCGCTTGCAATCGGCTCCAGAAAGAGCTTGTTGAGTGG
genomic: CCGTAGCCATTGAAGCAAGCATGACCAGCTCCTCCGCCACCTCTCGCAAGgtctgttcct ... tgttttcaagGCACTTAGCAAAATCGCTTGCAATCGGCTCCAGAAAGAGCTTGTTGAGTGG
EST: gi|37183496|gb|CF602850.1|CF602850
EST:     CCGTAGCCATTGAAGCAAGCATGACCAGCTCCTCCGCCACCTCTCGCAAG                         GCACTTAGCAAAATCGCTTGCAATCGGCTCCAGAAAGAGCTTGTTGAGTGG
genomic: CCGTAGCCATTGAAGCAAGCATGACCAGCTCCTCCGCCACCTCTCGCAAGgtctgttcct ... tgttttcaagGCACTTAGCAAAATCGCTTGCAATCGGCTCCAGAAAGAGCTTGTTGAGTGG
EST: gi|26262225|gb|CA813288.1|CA813288
EST:     CCGTAGCCATTGAAGCAAGCATGACCAGCTCCTCCGCCACCTCTCGCAAG                         GCACTTAGCAAAATCGCTTGCAATCGGCTCCAGAAAGAGCTTGTTGAGTGG
genomic: CCGTAGCCATTGAAGCAAGCATGACCAGCTCCTCCGCCACCTCTCGCAAGgtctgttcct ... tgttttcaagGCACTTAGCAAAATCGCTTGCAATCGGCTCCAGAAAGAGCTTGTTGAGTGG
EST: gi|26262347|gb|CA813410.1|CA813410
EST:     CCGTAGCCATTGAAGCAAGCATGACCAGCTCCTCCGCCACCTCTCGCAAG                         GCACTTAGCAAAATCGCTTGCAATCGGCTCCAGAAAGAGCTTGTTGAGTGG
genomic: CCGTAGCCATTGAAGCAAGCATGACCAGCTCCTCCGCCACCTCTCGCAAGgtctgttcct ... tgttttcaagGCACTTAGCAAAATCGCTTGCAATCGGCTCCAGAAAGAGCTTGTTGAGTGG
EST: gi|26262237|gb|CA813300.1|CA813300
EST:     CCGTAGCCATTGAAGCAAGCATGACCAGCTCCTCCGCCACCTCTCGCAAG                         GCAGTTAGCAAAATCGCTTGCAATCGGCTCCAGAAAGAGCTTGTTGAGTGG
genomic: CCGTAGCCATTGAAGCAAGCATGACCAGCTCCTCCGCCACCTCTCGCAAGgtctgttcct ... tgttttcaagGCACTTAGCAAAATCGCTTGCAATCGGCTCCAGAAAGAGCTTGTTGAGTGG
EST: gi|30305051|gb|CB981845.1|CB981845
EST:     CCGTAGCCATTGAAGCAAGCATGACCAGCTCCTCCGCCACCTCTCGCAAG                         GCACTTAGCAAAATCGCTTGCAATCGGCTCCAGAAAGAGCTTGTTGAGTGG
genomic: CCGTAGCCATTGAAGCAAGCATGACCAGCTCCTCCGCCACCTCTCGCAAGgtctgttcct ... tgttttcaagGCACTTAGCAAAATCGCTTGCAATCGGCTCCAGAAAGAGCTTGTTGAGTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttgcaaattgatttttctcatctggttgtattgtgatttgtggtgttttcaagGCACTTAGCAAAATCGCTTGCAATCGGCTCCAGAAAGAGCTTGTTGAGTGGCAGGTCAATCCACCCGCCGGTTTCAAACACAAAGTCACCGACAATCTTC
       aattgat  putative branch site (score: 4)
                                             tgttttc  putative PPT
      aaattgatttttct  TA-rich tract