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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatccagtaggtttttaatgggatgggatatccaggaattgggggatagtcatagattaaaataattgtttaacttcgtttttatttgctcatgtacagTGGCAATCCAAAGGAAGAACCTGGTGCAATTGTTTGTAGAGTTGCTCAATCCTTTTTGCGATTTGGTTCTTACCAAATACATGCTGCTAGAGGGAAGGAG

Basic information

species Vitis vinifera
transcript Vv06s0004g01360.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g01360.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os06g21600.1 (Oryza sativa), 3'ss of exon 4
--atatccagtaggtt--tttaatgggatgggatatccaggaattgggggatagtcatagattaaaataattgtttaacttcgtttttatttgctcatgtacagTGGCAATCCAAAGGAAGAACCTGGTGCAATTGTTTGTAGAGTTGCTCAATCCTTTTTGCGATTTGGTTCTTACCAAATACATGCTGCTAGAGGGAAGGAG
   | ||||| |  ||  |||    || |    ||   | |   |      |||   | | |||  || ||   |  | |  |||| | |||    ||   |||||||||| ||||||| ||||| ||||| ||||| ||  | || || | |||||||||||| |||||||| || || ||||||||| | || |  || |||
ttttttccagaaccttccttttgaaggttttagtaattatgttgtatctattagcatttgtttatgatgataaatctaatg-gtttgtctttatatat---cagTGGCAATTCAAAGGAGGAACCAGGTGCCATTGTATGCCGTGTAGCACCATCCTTTTTGCGTTTTGGTTCATATCAGATACATGCTACAAGGGACAAAGAG

upper sequence: Vv06s0004g01360.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G158595_T02 (Zea mays), 3'ss of exon 4
atatccagt---aggtttttaatgggatgggatatccaggaattgggggatagtcatagattaaaataattgtttaacttcgtttttatttgctcatgtacagTGGCAATCCAAAGGAAGAACCTGGTGCAATTGTTTGTAGAGTTGCTCAATCCTTTTTGCGATTTGGTTCTTACCAAATACATGCTGCTAGAGGGAAGGAG
|||  | ||   | |  |    |       | | |  || || |      ||   ||   || | | | || | |   ||  |  ||  |     ||  ||||||||||| |||||||||||||||||||||| |||||| | || || |  || ||||| || |||||||| || || ||||| ||| | || || || |||
atactctgtttgaaggatcatgtttctgaaggttttgagtaaatacactgtacctat---ttgatacacttctattgtttaatcattcatcttatatacacagTGGCAATGCAAAGGAAGAACCTGGTGCAATAGTTTGTCGTGTAGCACCGTCTTTTTTACGTTTTGGTTCGTATCAGATACACGCTTCAAGGGGCAAAGAG

upper sequence: Vv06s0004g01360.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G39090.2 (Glycine max), 3'ss of exon 1
-------------------atatccagtaggtttttaatgggatgggatatccaggaattgggggat----agtcatagattaaaataattgttta-acttc--gtttttatttgctcatgtacagTGGCAATCCAAAGGAAGAACCTGGTGCAATTGTTTGTAGAGTTGCTCAATCCTTTTTGCGATTTGGTTCTTACCAAATACATGCTGCTAGAGGGAAGGAG
                   |  | || |   ||||  ||    |         |   ||||| |||       || | | ||  | | |  | ||| | |||  ||||||| |  | || |  ||| ||||||||||||||||||||||| ||||||||||| |||||||| ||||| ||| |||| ||||| || ||||||||||||||  | ||| |  | |||
gtatgctattgcttcctctactttcactt--ttttctatcatctctacctattacatattggtggacttcggatccttggttttatttaccgattacatttcctgtttttaatatcacacgcgcagCGGCAATCCAAAGGAAGAACCTGGCGCAATTGTTTGCAGAGTTGCCCAATCTTTTCTGCGGTTTGGGTCATACCAAATACATGCCTCCAGAAGTGATGAG

upper sequence: Vv06s0004g01360.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT5G13030.1 (Arabidopsis thaliana), 3'ss of exon 4
----atatccag-taggtttttaatgggatgggatatccaggaattgggggatagtcatagattaaaataattgtttaacttcgtttttatttgctcatgtacagTGGCAATCCAAAGGAAGAACCTGGTGCAATTGTTTGTAGAGTTGCTCAATCCTTTTTGCGATTTGGTTCTTACCAAATACATGCTGCTAGAGGGAAGGAG
     ||   |  || |  | || | |   |  || |      ||      |   |  ||| |     | | |  |    || ||||    |||  | | | |||||||||||| ||||||||||| || ||||| ||||| || ||| |||| || ||| | || ||||| || ||||||||||||||  ||||||| || |||
taatctactgaactaagcctctagtaga--gaaatttttgtctataaaattaggcttctaggt--ggttgactactcctatt-gtttggcattgtgcgtttgcagTGGCAATCCGAAGGAAGAACCCGGCGCAATCGTTTGCAGGGTTTCTCAGTCATTTCTACGCTTTGGGTCATACCAAATACATGCCTCTAGAGGAAAAGAG

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|71873134|gb|DT022189.1|DT022189
EST:     CTTTGTCTTGTGACGACTGGGAAGTATGTCACCCGGGACATGTTTTATGA                         TGGCAATCCAAAGGAAGAACCTGGTGCAATTGTTTGTAGAGTTGCTCAATC
genomic: CTTTGTCTTGTGACGACTGGGAAGTATGTCACCCGGGACATGTTTTATGAgtacgttctt ... tcatgtacagTGGCAATCCAAAGGAAGAACCTGGTGCAATTGTTTGTAGAGTTGCTCAATC
EST: gi|71862025|gb|DT011080.1|DT011080
EST:     CTTTGTCTTGTGACGACTGGGAAATATGTCACCCGGGACATGTTTTATGA                         TGGCAATCCAAAGGAAGAACCTGGTGCAATCGTTTGTAGAGTTGCTCAATC
genomic: CTTTGTCTTGTGACGACTGGGAAGTATGTCACCCGGGACATGTTTTATGAgtacgttctt ... tcatgtacagTGGCAATCCAAAGGAAGAACCTGGTGCAATTGTTTGTAGAGTTGCTCAATC
EST: gi|161712103|gb|FC061475.1|FC061475
EST:     CTTTGTCTTGTGACGACTGGGAAGTATGTCACCCGGGACATGTTTTATGA                         TGGCAATCCAAAGGAAGAACCTGGTGCAATTGTTTGTAGAGTTGCTCAATC
genomic: CTTTGTCTTGTGACGACTGGGAAGTATGTCACCCGGGACATGTTTTATGAgtacgttctt ... tcatgtacagTGGCAATCCAAAGGAAGAACCTGGTGCAATTGTTTGTAGAGTTGCTCAATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatagtcatagattaaaataattgtttaacttcgtttttatttgctcatgtacagTGGCAATCCAAAGGAAGAACCTGGTGCAATTGTTTGTAGAGTTGCTCAATCCTTTTTGCGATTTGGTTCTTACCAAATACATGCTGCTAGAGGGAAGGAG
                       gtttaac  putative branch site (score: 3)
                                        tttgctc  putative PPT
       atagattaaaataatt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatccagtaggtttttaatgggatgggatatccaggaattgggggatagtcatagattaaaataattgtttaacttcgtttttatttgctcatgtacagTGGCAATCCAAAGGAAGAACCTGGTGCAATTGTTTGTAGAGTTGCTCAATCCTTTTTGCGATTTGGTTCTTACCAAATACATGCTGCTAGAGGGAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - -ggatggg
- - - - - - - - - - - - - - - - - - - -ttggggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaataa