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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatacatgtatcataaaaattgtgtctttatttgataaaaaaaaataataataaaatgtttgtctttgtatgccctattttgaaatgtctgctgatttctctccttatgccacttacatttgcagTTGGTACTTCGTTTTGCAAATCGCATGTTTTTGCCCCTCTGGAACCGTGACAACATTGATAATGTACAG

Basic information

species Vitis vinifera
transcript Vv14s0171g00490.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: LOC_Os04g40874.1 (Oryza sativa), 3'ss of exon 6
gtaatacatgtatcataaaaattgtgtctttatttgataaaaaaaaataataataaaatgtttgtctttgtatgccctattttgaaatgtctgctgatttctctccttatgccacttacattt-gcagTTGGTACTTCGTTTTGCAAATCGCATGTTTTTGCCCCTCTGGAACCGTGACAACATTGATAATGTACAG
                                          ||     |||||    |        | | |||   |  |  |||   |   || | | || |   |    || |  |||||  ||| | || ||||||||||| || ||| |||| ||||| || |||||||||||||| ||||||||| |||||
----------------------------------------gtaatggctataattttgtcaagaatgtgggatgatttcctccgaatacttgactaactacttt---tgaaacaatcgcatttcacagCTTGTGCTTCGTTTTGCCAACCGCTTGTTCTTGCCTCTTTGGAACCGTGACAATATTGATAATATACAG

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GRMZM2G031107_T01 (Zea mays), 3'ss of exon 6
gtaatacatgtatcataaaaattgtgtctttatttgataaaaaaaaataataataaaatgtttgtctttgtatgccctattttgaaatgtctgctgatttctctccttatgccacttacatttgcagTTGGTACTTCGTTTTGCAAATCGCATGTTTTTGCCCCTCTGGAACCGTGACAACATTGATAATGTACAG
                                                  |||||   |||  | | | ||   |  ||| | |   | | |    |  | | || |||| |  |  |  ||||||| | || |||||||||||||| ||| | |||||||| |||||||||||||| ||||| | ||| ||||||
-------------------------------------------------gtaatatg-tgtgagccatagtgaactgtatat-gctttatatatgcaactgtttc-ttatactgcc-atgtttgcagCTTGTGCTTCGTTTTGCAAACCGCTTATTTTTGCCTCTCTGGAACCGTGATAACATAGCTAACGTACAG

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA19G24250.2 (Glycine max), 3'ss of exon 6
gtaatacatgtatcataaaaattgtgtctttatttgataaaaaaaaataataataaaatgtttgtctttgtatgccctattttgaaatgtctgctgatttctctccttatgcc--acttacatttgcagTTGGTACTTCGTTTTGCAAATCGCATGTTTTTGCCCCTCTGGAACCGTGACAACATTGATAATGTACAG
                                         || |||| || ||| ||||  |   | | | |  | |   ||    || ||  |||||  || | |||      ||||| ||| ||||||||||||||| |||||||||||  | || ||||| || |||||||| ||||||||||| |||||||||
---------------------------------------gtaataaatgattatacaatggcttcttgtttgtttcatgaattt---tgcctaatgattaatccctttacatttaacttatattggcagTTGGTACTTCGCTTTGCAAATCGGTTTTTCTTGCCACTTTGGAACCGCGACAACATTGACAATGTACAG

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA16G06850.1 (Glycine max), 3'ss of exon 6
gtaatacatgtatcataaaaattgtgtctttatttgataaaaaaaaataataataaaatgtttgtctttgtatgccctattttgaaatgtctgctgatttctctccttatgcc--acttacatttgcagTTGGTACTTCGTTTTGCAAATCGCATGTTTTTGCCCCTCTGGAACCGTGACAACATTGATAATGTACAG
                                         || |||| || ||| ||||  | ||||||| ||    ||   |   || ||  |||||  || | |||      ||||| ||| ||||||||||||||| |||||||||||  | || ||||| || |||||||| ||||||||||| || ||||||
---------------------------------------gtaataaatgattatacaatggct-tctttgtttgtttcatga-gttttgcctaatgattaatccctttacatttaacttatattggcagTTGGTACTTCGCTTTGCAAATCGGTTTTTCTTGCCACTTTGGAACCGCGACAACATTGACAACGTACAG

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA19G22690.1 (Glycine max), 3'ss of exon 6
gtaatacatgtatcataaaaattgtgtctttatttgataaaaaaaaataataataaaatgtttgtctttgtatgccctattttg-aaatgtctgctgatttctctccttatgccacttacatttgcagTTGGTACTTCGTTTTGCAAATCGCATGTTTTTGCCCCTCTGGAACCGTGACAACATTGATAATGTACAG
                                            |   ||| ||    | || |   |  |||  | |  ||   |||  |   || ||  |||||| | ||  ||||  |||  ||||| ||||||||||||||||| ||  | ||  |||| || ||||||||||||||||||| |||||| |||
------------------------------------------gtagtaaatgattgcttattggctctcatattgcttgcttcataaacttggcctaatccctctccatttg--acttgtattaccagTTAGTACTTCGTTTTGCAAACCGATTATTCATGCCTCTATGGAACCGTGACAACATTGCTAATGTGCAG

upper sequence: Vv14s0171g00490.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT5G40760.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaatacatgtatcataaaaattgtgtctttatttgataaaaaaaaataataataaaatgtttgtctttgtatgccctattttgaaatgtctgctgatttctctccttatgccacttacatttgcagTTGGTACTTCGTTTTGCAAATCGCATGTTTTTGCCCCTCTGGAACCGTGACAACATTGATAATGTACAG
                                     |||          || |||  | |   || |   ||  | |  |||  | | || |    | | |   ||  ||| | ||    ||||||||||| || || |||||||||||| | || ||||| || |||||||||||||| || || || || |||
------------------------------------gtaacctgcttctctattaatgtctaaatcatca-atctctttctttagactatcagtgattattttatctcgtgc-attt---cttgcagTTGGTCCTCCGGTTTGCAAATCGCTTTTTCTTGCCACTTTGGAACCGTGACAATATCGAGAACGTGCAG

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|30299156|gb|CB975950.1|CB975950
EST:     AGATTTACCGTATTGATCACTACCTGGGAAAGGAACTCGTGCAGAATTTG                         TTGGTACTTCGTTTTGCAAATCGCATGTTTTTGCCCCTCTGGAACCGTGAC
genomic: AGATTTACCGTATTGATCACTATCTGGGAAAGGAACTCGTGCAGAATTTGgtaatacatg ... acatttgcagTTGGTACTTCGTTTTGCAAATCGCATGTTTTTGCCCCTCTGGAACCGTGAC
EST: gi|110686452|gb|EE064108.1|EE064108
EST:     GATTTACCGTATTGATCCCTATCTGGGAACAGGA-CTCGTGCACAATTTG                         TTGGTTCTTCGTTTTGCAAATCGCATGATTTTGCCCCT
genomic: GATTTACCGTATTGATCACTATCTGGGAA-AGGAACTCGTGCAGAATTTGgtaatacatg ... acatttgcagTTGGTACTTCGTTTTGCAAATCGCATGTTTTTGCCCCT
EST: gi|161717585|gb|FC065623.1|FC065623
EST:     AGATTTACCGTATTGATCACTACCTGGGAAAGGAACTCGTGCAGAATTTG                         TTGGTACTTCGTTTTGCAA-TCGCATGTTTTTGCCCCTCTGGAAC
genomic: AGATTTACCGTATTGATCACTATCTGGGAAAGGAACTCGTGCAGAATTTGgtaatacatg ... acatttgcagTTGGTACTTCGTTTTGCAAATCGCATGTTTTTGCCCCTCTGGAAC
EST: gi|110364929|gb|EC928538.1|EC928538
EST:     AGATTTACCGTATTGATCACTACCTGGGAAAGGAACTCGTGCAGAATTTG                         TTGGTACTTCGTTTTGCAAATCGCATGTTTTTGCCCCTCTGGAACCGTGAC
genomic: AGATTTACCGTATTGATCACTATCTGGGAAAGGAACTCGTGCAGAATTTGgtaatacatg ... acatttgcagTTGGTACTTCGTTTTGCAAATCGCATGTTTTTGCCCCTCTGGAACCGTGAC
EST: gi|161719304|gb|FC068268.1|FC068268
EST:     AGATTTACCGTATTGATCACTACCTGGGAAAGGAACTCGTGCAGAATTTG                         TTGGTACTTCGTTTTGCAAATCGCATGTTTTTGCCCCTCTGG
genomic: AGATTTACCGTATTGATCACTATCTGGGAAAGGAACTCGTGCAGAATTTGgtaatacatg ... acatttgcagTTGGTACTTCGTTTTGCAAATCGCATGTTTTTGCCCCTCTGG
EST: gi|110372969|gb|EC937167.1|EC937167
EST:     AGATTTACCGTATTGATCACTACCTGGGAAAGGAACTCGTGCAGAATTTG                         TTGGTACTTCGTTTTGCAAATCGCATGTTTTTGCCCCTCTGGAACCGTGAC
genomic: AGATTTACCGTATTGATCACTATCTGGGAAAGGAACTCGTGCAGAATTTGgtaatacatg ... acatttgcagTTGGTACTTCGTTTTGCAAATCGCATGTTTTTGCCCCTCTGGAACCGTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgccctattttgaaatgtctgctgatttctctccttatgccacttacatttgcagTTGGTACTTCGTTTTGCAAATCGCATGTTTTTGCCCCTCTGGAACCGTGACAACATTGATAATGTACAG
                                        cacttac  putative branch site (score: 2)
     tattttgaaat  TA-rich tract