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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtattaaagtggcttatttatatttcctttatcatttatgtctttgattacatttttcctttttcttcttgcagTTCTATGTAAGCCATGGGGAGTTATCATGCCAAATGTACCAGCGATCTGCTGACATGGGTCTTGGTGTGCCGTTTAACATTGCATCTTATGCGCTCTTAA

Basic information

species Vitis vinifera
transcript Vv03s0038g04500.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os12g26060.1 (Oryza sativa), 3'ss of exon 6
-----------gttagtattaaagtggctt--at----ttatat-ttcctttatcatttatgtctttgattacatttttcctttttctt----cttgcagTTCTATGTAAGCCATGGGGAGTTATCATGCCAAATGTACCAGCGATCTGCTGACATGGGTCTTGGTGTGCCGTTTAACATTGCATCTTATGCGCTCTTAA
           |||  |  | || ||  ||  ||      | || | | ||| ||||||   | | | ||   | || |    | |  |        ||||| |||||     |||||||||| |||||||| |||||||| || |||||||| ||||| || |||||||| || ||||||||||| ||| | ||  | |
gacatctcttagtttttcatgaaatgattttgatgctaccagatgtgcttttctcatttgactatcttatctaacttctgtaatgtactgaaatccccagTTTTATGTTGAGAATGGGGAGTTGTCATGCCAGATGTACCAACGCTCTGCTGATATGGGGCTCGGTGTGCCATTCAACATTGCATCATATTCTCTTCTGA

upper sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os11g29390.1 (Oryza sativa), 3'ss of exon 8
----------------------------gttagtattaaagtggcttatttatatttcctttatcatttatgtctttgattacatttttcctttttcttcttgcagTTCTATGTAAGCCATGGGGAGTTATCATGCCAAATGTACCAGCGATCTGCTGACATGGGTCTTGGTGTGCCGTTTAACATTGCATCTTATGCGCTCTTAA
                              |   | |||| ||   ||   |||||| |||    |  ||  |  ||| ||||| |  |    ||||||||| ||||| |||||       |||||| |||| ||||| ||||| || || |||||||| ||||| |||||||| || || ||||||||||| ||| | ||  | |
ttctctctctctctctctccatgtgtagaattacagtaaaatgatatacaaatattttcttg--tagatagtttcttgcttacaataat----tttcttcttccagTTTTATGTTGAGAGCGGGGAGCTATCGTGCCAGATGTATCAACGCTCTGCTGATATGGGACTTGGTGTTCCATTCAACATTGCATCATATTCTCTTCTGA

upper sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA11G12280.1 (Glycine max), 3'ss of exon 7
-------gttagtattaaagtggcttattta---tatttcctttatcatttatg-----tctttgattacattttt---cctttttcttcttgcagTTCTATGTAAGCCATGGGGAGTTATCATGCCAAATGTACCAGCGATCTGCTGACATGGGTCTTGGTGTGCCGTTTAACATTGCATCTTATGCGCTCTTAA
       | || ||||   ||  ||  ||      | |  |||| ||  | |||     |  |||| | | ||||      ||||| ||| ||||||||||||||    |||||||| ||||||| |||||||| ||||||||||| |||||||| || ||||| || ||||| |||||||||||||||||| | |
gtccgcagcta-tatttgggtttctctttggaagaactctctttttctctcatgaaattttgttgacttccttttattgttttttttttcctgcagTTCTATGTAGCAAATGGGGAGCTATCATGTCAAATGTATCAGCGATCTGCCGACATGGGCCTGGGTGTCCCATTTAATATTGCATCTTATGCGCTCCTGA

upper sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA04G01240.1 (Glycine max), 3'ss of exon 8
--------gttagtattaaagtggcttatttatatt--tcctttatcatttatgtctttgatt-acatttttcctttttc-ttcttgcagTTCTATGTAAGCCATGGGGAGTTATCATGCCAAATGTACCAGCGATCTGCTGACATGGGTCTTGGTGTGCCGTTTAACATTGCATCTTATGCGCTCTTAA
         ||| |       |  |||    | |||   ||||   || ||||  |    ||| | ||||||  |||||   | |||||||| ||||||   || |||||||||||||| |||||||| |||||||||||||||||||| || || || || ||||| |||||||||||||| || || |
gtctgcagcttaattcaggtttttctttgaaaaattgccccttccacacttattccacatattgatatttttaatttttaacttttgcagTTTTATGTAGCACACGGGGAGTTATCATGTCAAATGTATCAGCGATCTGCTGACATGGGCCTGGGCGTTCCATTTAATATTGCATCTTATGCCCTTTTGA

upper sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA12G04480.1 (Glycine max), 3'ss of exon 8
------------------gttagtattaaagtggcttatttatatttcctttatcatttatgtctttgattacatttttcctttttcttcttgcagTTCTATGTAAGCCATGGGGAGTTATCATGCCAAATGTACCAGCGATCTGCTGACATGGGTCTTGGTGTGCCGTTTAACATTGCATCTTATGCGCTCTTAA
                  |||  | ||     |   | | | | ||||  | || |    | |  |  | | | ||||    |||| | | || |||||||||||    |||||||| ||||||| |||||||| ||||||||||| |||||||| || ||||| || ||||| |||||||||||||| ||| | |
gtccgcagctatatttgggtttctctttggaagagctctctctttttctctcatgaa--gttttgtcaacttccttttattgttttttccctgtagTTCTATGTAGCTAATGGGGAGCTATCATGTCAAATGTATCAGCGATCTGCCGACATGGGCCTGGGTGTCCCATTTAATATTGCATCTTATGCACTCCTGA

upper sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA06G01280.3 (Glycine max), 3'ss of exon 8
--------gttagtattaaagtggcttatttatatttcctttatcatttatgtctttgatt-acatttttcctttttc-ttcttgcagTTCTATGTAAGCCATGGGGAGTTATCATGCCAAATGTACCAGCGATCTGCTGACATGGGTCTTGGTGTGCCGTTTAACATTGCATCTTATGCGCTCTTAA
         ||| |       |  |||    | ||| ||  |  ||  |||  |    ||| | ||||||  |||||   | |||||||| ||||||   || |||||||||||||| |||||||| |||||||||||||| ||||| || ||  | || ||||| |||||||||||||| || || |
gtctgcagcttaattcaggtttttctttgaaaaattgccccttccacatattccacctattgatatttttaatttttaacttttgcagTTTTATGTAGCACACGGGGAGTTATCATGTCAAATGTATCAGCGATCTGCTGATATGGGCCTGGGCATTCCATTTAATATTGCATCTTATGCCCTTTTGA

upper sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT2G16370.1 (Arabidopsis thaliana), 3'ss of exon 8
gttagtattaaagtggcttatttatatttcctttatcattta-tgtctttgattacatttttcctttttcttcttgcagTTCTATGTAAGCCATGGGGAGTTATCATGCCAAATGTACCAGCGATCTGCTGACATGGGTCTTGGTGTGCCGTTTAACATTGCATCTTATGCGCTCTTAA
  || |   |   |  ||| |   | | |  ||| || |  | ||  ||||||||| |||||  |||||    |||||||| |||||     | |||||  | ||||| |||||||| ||||| || || || ||||| ||||||||||||||||||||||| |||||  | ||  | |
-gtaatgccactttatcttctaattctgttgtttctcctacaatgagtttgattacttttttttttttt----ttgcagTTTTATGTGGCAGAAGGGGAACTCTCATGTCAAATGTATCAGCGTTCAGCAGATATGGGCCTTGGTGTGCCGTTTAACATTGCTTCTTACTCTCTTCTTA

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|33405951|gb|CF211578.1|CF211578
EST:     CTTCTGATCTCAAATTGATGGCACTTCCACCCTGCCATATGTTTGCACAG                         TTCTATGTAAGCCATGGGGAGTTATCATGCCAAAAGTACCAGCGATCTGCT
genomic: CTTCTGATCTCAAATTGATGGCACTTCCACCCTGCCATATGTTTGCACAGgttagtatta ... cttcttgcagTTCTATGTAAGCCATGGGGAGTTATCATGCCAAATGTACCAGCGATCTGCT
EST: gi|33401638|gb|CF207265.1|CF207265
EST:     CTTCTGATCTCAAATTGATGGCACTTCCACCCTGCCATATGTTTGCACAG                         TTCTATGTAAGCCATGGGGAGTTATCATGCCAAATGTACCAGCGATCTGCT
genomic: CTTCTGATCTCAAATTGATGGCACTTCCACCCTGCCATATGTTTGCACAGgttagtatta ... cttcttgcagTTCTATGTAAGCCATGGGGAGTTATCATGCCAAATGTACCAGCGATCTGCT
EST: gi|110361466|gb|EC924940.1|EC924940
EST:     CTTCTGATCTCAAATTGATGGCACTTCCACCCTGCCATATGTTTGCACAG                         TTCTATGTAAGCCATGGGGAGTTATCATGCCAAATGTACCAGCGATCTGCT
genomic: CTTCTGATCTCAAATTGATGGCACTTCCACCCTGCCATATGTTTGCACAGgttagtatta ... cttcttgcagTTCTATGTAAGCCATGGGGAGTTATCATGCCAAATGTACCAGCGATCTGCT
EST: gi|110413975|gb|EC979795.1|EC979795
EST:     CTTCTGATCTCAAATTGATGGCACTTCCACCCTGCCATATGTTTGCACAG                         TTCTATGTAAGCCATGGGGAGTTATCATGCCAAATGTACCAGCGATCTGCT
genomic: CTTCTGATCTCAAATTGATGGCACTTCCACCCTGCCATATGTTTGCACAGgttagtatta ... cttcttgcagTTCTATGTAAGCCATGGGGAGTTATCATGCCAAATGTACCAGCGATCTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatttcctttatcatttatgtctttgattacatttttcctttttcttcttgcagTTCTATGTAAGCCATGGGGAGTTATCATGCCAAATGTACCAGCGATCTGCTGACATGGGTCTTGGTGTGCCGTTTAACATTGCATCTTATGCGCTCTTAA
                      ctttgat  putative branch site (score: 5)
                     tctttgattacatttt  CT-rich tract
                       tttgattacattttt  TA-rich tract