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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagaacctttcttagtcttgcatacttatggtgctatggtcatttaaccctgttgctacctgtggcataatgggctacccttttgcctctgtatggcttatgtgctgacatagtttttttgtgtttccaagGTTGCAATTAGGCGGATAGCAGGGGGCAAGTGGGCAAGCAATAATGGACAAGCCTGCATTGCTCCTGATTATATTGTCACAACAAAAGACTTTGCTCCAA

Basic information

species Vitis vinifera
transcript Vv18s0001g02440.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g02440.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA14G24140.1 (Glycine max), 3'ss of exon 5
gtaaagaacctttcttagtcttgcatacttatggtgctatggtcatttaaccctgttgctacctgtggcata--atgggctacccttttgcctctgtatggcttatgtgctgacatagtttt---tttgtgtttccaagGTTGCAATTAGGCGGATAGCAGGGGGCAAGTGGGCAAGCAATAATGGACAAGCCTGCATTGCTCCTGATTATATTGTCACAACAAAAGACTTTGCTCCAA
                                 ||  ||   |  |   ||  | ||  || |  |  | |   ||     |||  ||||| |||      ||| ||  || | ||   |||   ||||  ||  |||||| ||||  || || |||   |  || |||||||     ||||||||||||||||||||| |||| ||||||||| | ||||| ||||||| |||||| |
---------------------------------gta-tacctttgtcccactttatttttatcaattacttgccatcactgacctctttgcatctc----acttttgaccttaaattaatttgaatttgaattggcaagGTAGCAACAAGACGAATAATTGCAGGAAAGTGGGGTTCTAATAATGGACAAGCCTGCATTTCTCCAGATTATATTATAACAACTAAAGACTATGCTCCCA

upper sequence: Vv18s0001g02440.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA04G42740.1 (Glycine max), 3'ss of exon 5
gtaaagaacctttcttagtcttgcatacttatggtgctatggtcatttaaccctgttgctacctgtggcataatgggctacc-cttttgcctctgtatggcttatgtgctgacatagtttttttgtgtttccaagGTTGCAATTAGGCGGATAGCAGGGGGCAAGTGGGCAAGCAATAATGGACAAGCCTGCATTGCTCCTGATTATATTGTCACAACAAAAGACTTTGCTCCAA
                         ||||  |  |||    |  |   | || | ||| |  |      || |   ||||   | ||  ||||| |  | || ||   || |    |||  | ||| ||| || ||| |||  ||| || |||   |  |||||||||| |   || |||||||||||||||||| |||| |||||| || | ||||||||||||| |||||| |
------------------------gtactactattgcctaagcta---agcctttttgttttccca---attacttgctattaccttaacctctttcagactcatt--cttat---gttaatatgtatttgca-gGTAGCAGCTAGACGAATAATTGCTGGCAAGTGGGGATTGAACAATGGACAAGCCTGCATTTCTCCCGATTATGTTATAACAACAAAAGACTATGCTCCCA

upper sequence: Vv18s0001g02440.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA06G12010.1 (Glycine max), 3'ss of exon 5
gtaaagaacctttcttagtcttgcatacttatggtgctatggtcatttaaccctgttgctacctgtggcataatgggctacccttttgcctctgtatggcttatgtgctgacatagtttttttgtgtttccaagGTTGCAATTAGGCGGATAGCAGGGGGCAAGTGGGCAAGCAATAATGGACAAGCCTGCATTGCTCCTGATTATATTGTCACAACAAAAGACTTTGCTCCAA
                                          |    ||| ||| ||| |   |     |   |    |||  | ||  || |  ||  | ||| |      | | ||  ||||| ||  || | | |||  |||||| |||      |||||||||| |   ||||||||||||||||||||| |||| |||||| || | ||||||||||| | |||||| |
---------------------------------------gtattgcctaagcctcttggtttttcaattactttttattactttattctctttcaatttcatattttact-taaaattaatttgtattcaca-gATAGCAGCTAGGCGAATAATTTCTGGCAAGTGGGGATTGAATAATGGACAAGCCTGCATTTCTCCAGATTATGTTATAACAACAAAAGATTGTGCTCCCA

upper sequence: Vv18s0001g02440.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GLYMA02G26390.1 (Glycine max), 3'ss of exon 5
gtaaagaacctttcttagtcttgcatacttatggtgctatggtcatttaaccctgttgctacctgtggcataatgggctacccttttgcctctgtatggcttatgtgctgacatagtttt--tttgtgtttccaagGTTGCAATTAGGCGGATAGCAGGGGGCAAGTGGGCAAGCAATAATGGACAAGCCTGCATTGCTCCTGATTATATTGTCACAACAAAAGACTTTGCTCCAA
                      | |||| | || | || |  | ||||    |  || ||  |  |  | | ||    | |  | |  | | |     | |||  |       ||||||   ||||  ||  |||||| ||||  || || |||   |  || |||||||     |||||||| |||||||||||| |||| ||||||||| | ||||| ||||||| |||||| |
----------------------gtatacctttg-tcctgtt-ttattttcatcaattactttccatcac-tgatctcttgcaatctcactttta---agattaaat-------tagtttgaatttgaattggcaagGTAGCAACAAGACGAATAATTGCAGGAAAGTGGGGTTCTAATAATGGGCAAGCCTGCATTTCTCCAGATTATATTATAACAACTAAAGACTATGCTCCCA

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|110361747|gb|EC925243.1|EC925243
EST:     GACATTAATTTACCC                         GTTGCAATTAGGCGGATAGCAGGGGGCAAGTGGGCAAGCAATAATGGACAA
genomic: GACATTAATTTACCTgtaaagaacc ... tgtttccaagGTTGCAATTAGGCGGATAGCAGGGGGCAAGTGGGCAAGCAATAATGGACAA
EST: gi|110387056|gb|EC951696.1|EC951696
EST:     AGCTTGGGGGGAAATGTCCAGTTGTCGTTGATTCAGACATTAATTTACCC                         GTTGNCA-TTAGGCGGATAGCAGGGGGCAAGTGGGCAAGCAATAATGGACA
genomic: AGCTTGGGGGGAAATGTCCAGTTGTCGTTGATTCAGACATTAATTTACCTgtaaagaacc ... tgtttccaagGTTG-CAATTAGGCGGATAGCAGGGGGCAAGTGGGCAAGCAATAATGGACA
EST: gi|33405976|gb|CF211603.1|CF211603
EST:     AGCTTGGGGGGAAATGTCCAGTTGTCGTTGATTCAGACATTAATTTACCC                         GTTGCAATTAGGCGGATAGCAGGGGGCAAGTGGGCAAGCAATAATGGACAA
genomic: AGCTTGGGGGGAAATGTCCAGTTGTCGTTGATTCAGACATTAATTTACCTgtaaagaacc ... tgtttccaagGTTGCAATTAGGCGGATAGCAGGGGGCAAGTGGGCAAGCAATAATGGACAA
EST: gi|33406064|gb|CF211691.1|CF211691
EST:     AGCTTGGGGGGAAATGTCCAGTTGTCGTTGATTCAGACATTAATTTACCC                         GTTGCAATTAGGCGGATAGCAGGGGGCAAGTGGGCAAGCAATAATGGACAA
genomic: AGCTTGGGGGGAAATGTCCAGTTGTCGTTGATTCAGACATTAATTTACCTgtaaagaacc ... tgtttccaagGTTGCAATTAGGCGGATAGCAGGGGGCAAGTGGGCAAGCAATAATGGACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acccttttgcctctgtatggcttatgtgctgacatagtttttttgtgtttccaagGTTGCAATTAGGCGGATAGCAGGGGGCAAGTGGGCAAGCAATAATGGACAAGCCTGCATTGCTCCTGATTATATTGTCACAACAAAAGACTTTGCTCCAA
                          tgctgac  putative branch site (score: 2)
                                     tttttttgtgtttcc  putative PPT
                                 atagttttttt  TA-rich tract