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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtactgaagtattaaatatgttgcttttggtcaaatttttctgtctgtttgtttactttagtatttattccagatggcatacgacttaacttcttacagaatctaacttccatttttatcaattaaaatcagAATGCAGTTTCTTTAGAGAAAAGCCATAACTCTAGCTGGGCTCCTATTTTTATTAGGCCATCAAATTTCAAATTACCTGTTGATCCTTTGACTCCAATTA

Basic information

species Vitis vinifera
transcript Vv18s0001g07630.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g07630.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA06G10180.2 (Glycine max), 3'ss of exon 13
-----------------gtagtactgaagtattaaata--tgttgcttttggtcaaa---tttttctgtctgtttgtt-tactt-tagtatttatt-----ccagatggcatacgacttaac---ttcttacagaatctaacttccatttttatcaattaaaatcagAATGCAGTTTCTTTAGAGAAAAGCCATAACTCTAGCTGGGCTCCTATTTTTATTAGGCCATCAAATTTCAAATTACCTGTTGATCCTTTGACTCCAATTA
                  ||    || | | |||      |||| | ||   |   |   ||||| |  |   ||||  | |||    | || ||      ||    ||   |  || |||    ||  |   |  | ||||||  || | | |    ||  ||||||||||  || | ||||| ||||| |   ||| |||||||||||||||||||||||||||||||||||||||  |||| ||||||| ||  | ||| ||||
gtagctctatgcaattgatacacttgcaatcttatgctcctgtttcattatcttggactcttttttttccaacttgtcatgcttgcgattttcatctctccccgaggggtgcaatacctaatcagtttatgttgtttttaacttaaatctctct----tatgatcagAATGCTATTCCCTTAGAAAAAAGTCCCGACTGTAGCTGGGCTCCTATTTTTATTAGGCCATCAAATTTCAAGCTACCAGTTGATCATTCAATTCCTATTA

upper sequence: Vv18s0001g07630.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA04G10200.1 (Glycine max), 3'ss of exon 13
------------------------------gtagtactgaagtattaaatatgttgcttttggtcaaatttttctgtctgtt-tgttt---actttagtatttattccaga--tggcatacgacttaacttcttacagaatctaacttccatttttatcaattaaaatcagAATGCAGTTTCTTTAGAGAAAAGCCATAACTCTAGCTGGGCTCCTATTTTTATTAGGCCATCAAATTTCAAATTACCTGTTGATCCTTTGACTCCAATTA
                              | | |  |    |  |   |      | ||   ||   ||||||    |||  || ||   | |||  | | |   | ||   ||  ||||    | | ||  |   |  ||||||||  || | | |    ||  | ||||||||  || | ||||| ||||| |   ||| | |||||||||||||||||||||||||||| ||||||||  |||| ||||||| ||  | ||| ||||
gtagcaatatgcaattgatacacttcacttgcaatcttatgctcctgtttcaaaatccttgactctcttttttcaacttgtcatgcttgtgattttcatctctccccgaggggtgcaatacctaatcattttatgttgtttctaacttaaatctctct----tatgaccagAATGCTATTCCCTTAGAAAAAAGTCCCGACTGTTGCTGGGCTCCTATTTTTATTAGGCCATCGAATTTCAAGCTACCAGTTGATCATTCAATTCCTATTA

upper sequence: Vv18s0001g07630.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA14G36070.1 (Glycine max), 3'ss of exon 13
----gtagtactgaagtattaaatatgtt-------gcttttggtcaaatttttctgtctgtttgttta---ctttagtatttattccagatggcatacgactt--aacttcttacagaatctaactt----ccatttttatcaattaaa--atcagAATGCAGTTTCTTTAGAGAAAAGCCATAACTCTAGCTGGGCTCCTATTTTTATTAGGCCATCAAATTTCAAATTACCTGTTGATCCTTTGACTCCAATTA
      | |  ||| | ||| | | ||||         | ||| |  ||  | |  | || ||| || |     || || |  ||| |      |  |   ||   || | || |   |   | | |       |  |  |||  | |||  ||||||||||  || | ||||||||||||| | ||| ||| ||||||||||||||||| ||  ||||||| ||||| ||||| | ||||| ||  | ||| ||||
gtatcaacttttgatggattcattttgttctatcaaattcttgtttcaacgtcttggactcttttttcataatctttgtgtgaatttcccccttctgagtgctcgcaattgctaatcaagctttattatatgtaacctgaatctctcaaattatcagAATGCCATTCCCTTAGAGAAAAGCCGTGACTGTAGTTGGGCTCCTATTTTTATCAGAACATCAAACTTCAAGTTACCAGCTGATCATTCCATTCCTATTA

upper sequence: Vv18s0001g07630.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA02G37850.1 (Glycine max), 3'ss of exon 13
----gtagtactgaagtattaaatatgttgcttttgg--tcaaatttttctgtctgtttgtttactttagtatttattccagatggcatacgacttaacttcttacagaatctaacttccatttttatcaattaaaatcagAATGCAGTTTCTTTAGAGAAAAGCCATAACTCTAGCTGGGCTCCTATTTTTATTAGGCCATCAAATTTCAAATTACCTGTTGATCCTTTGACTCCAATTA
      | |  ||| | ||| | | ||| ||| |     ||   |||   |||||     | |  |||  || |  ||  |         | | | ||  | |||    |||| || |  || | |   |||||   |||||||||  || | ||||||||||||  | ||| ||| ||||||||||||||||| ||  ||||||| ||||| ||||| | ||||| ||    | | ||||
gtatcaacttttgatggattcactttgt-gctatcaaattcttgtttcaatgtcttggactcttttttcataatctttgtatgaatttccccaatcaagct-ttattatatctgacctgaatctct-caaatta---tcagAATGCCATTCCCTTAGAGAAAAGCTGTGACTGTAGTTGGGCTCCTATTTTTATCAGAACATCAAACTTCAAGTTACCAGCTGATCATTCCGTTGCTATTA

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|27584661|gb|CB007356.1|CB007356
EST:     CAAGTCCCACAGGCAGAATTCACAAAGGGGTGTGTTCAACCTGGATGAAG                         AATGCAGTTTCTTTAGAGAAAAGCCATAACTCTAGCTGGGCTCCTATTTTT
genomic: CAAGTCCCACAGGCAGAATTCACAAAGGGGTGTGTTCAACCTGGATGAAGgtagtactga ... ttaaaatcagAATGCAGTTTCTTTAGAGAAAAGCCATAACTCTAGCTGGGCTCCTATTTTT
EST: gi|30125286|gb|CB910625.1|CB910625
EST:     GTTCAACCTGGATGAAG                         AATGCAGTTTCTTTAGAGAAAAGCCATAACTCTAGCTGGGCTCCTATTTTT
genomic: GTTCAACCTGGATGAAGgtagtactga ... ttaaaatcagAATGCAGTTTCTTTAGAGAAAAGCCATAACTCTAGCTGGGCTCCTATTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catacgacttaacttcttacagaatctaacttccatttttatcaattaaaatcagAATGCAGTTTCTTTAGAGAAAAGCCATAACTCTAGCTGGGCTCCTATTTTTATTAGGCCATCAAATTTCAAATTACCTGTTGATCCTTTGACTCCAATTA
                       atctaac  putative branch site (score: 2)
                              ttccatttttatcaat  TA-rich tract