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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtacaaagtgcaaaggcatacttgttctgtcagtgaagatcatgaagtcataattatttgccttgtttctaggtgttcttttgatacctgtgactctttctgttaattgttagAATGCAATGCCAGCAGCTGCTGGAGCTGTTGCAGCTGCTGCTGTAGCTGATCAGATGCTTGGTCCGAAAGAGGATAGACATTTGGCAATTGTCCTG

Basic information

species Vitis vinifera
transcript Vv06s0004g06920.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os03g18310.1 (Oryza sativa), 3'ss of exon 4
gtttgtacaaagtgcaaaggcatacttgttctgtcagtgaagatcatgaagtcataattatttgccttgtttctaggtgttcttttgatacctgtgactctttctgttaattgttagAATGCAATGCCAGCAGCTGCTGGAGCTGTTGCAGCTGCTGCTGTAGCTGATCAGATGCTTGGTCCGAAAGAGGATAGACATTTGGCAATTGTCCTG
     || ||  ||  ||    |  | || |||||  |     |  |   |||| || ||| |    ||||||       | || ||  | ||     |||  | | |  |   ||| | |  |||||||||||||  |||||||||||||| || |||||||||||||| |||  ||| || || |||||| |  | ||||||||||| |||
---gctataatttgagaa----tggtggtactgtctatttttgtactt--gtcaaaaatatgt----tgtttcc------ttttctgtcatcttaagttctgacagctg-taactagcagGACATGCCAGCAGCTGAAGGAGCTGTTGCAGCAGCAGCTGTAGCTGATCAAATGTATGGCCCAAAGGAGGATCGCAAGTTGGCAATTGTGCTG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os05g07130.1 (Oryza sativa), 3'ss of exon 5
gtttgtacaaagtgcaaaggcatacttgttctgtcagtgaagatcatgaagtcataatta--tttgccttgtttctaggtgttcttttgatacctgtgactctttctgttaat-tgttagAATGCAATGCCAGCAGCTGCTGGAGCTGTTGCAGCTGCTGCTGTAGCTGATCAGATGCTTGGTCCGAAAGAGGATAGACATTTGGCAATTGTCCTG
                | ||   |  | | |  ||| | ||  |  |   || | ||  |  ||| | | |    || || |    ||||| | |       | |   || || | |||| | || ||||||| ||| || ||||||||||||||||| ||||||||||| |   ||| |||  | || |||||  || |  | || |||||  ||
---------------tatggtccatctatccattca-tcaattttctattgttaaaagaaattttccatcggaattaagtttgtacttgattctt----tcttcttaattgatgtattagCAGGCCATGCCAGAAGCAGCAGGAGCTGTTGCAGCTGCAGCTGTAGCTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os05g07130.2 (Oryza sativa), 3'ss of exon 5
gtttgtacaaagtgcaaaggcatacttgttctgtcagtgaagatcatgaagtcataatta--tttgccttgtttctaggtgttcttttgatacctgtgactctttctgttaat-tgttagAATGCAATGCCAGCAGCTGCTGGAGCTGTTGCAGCTGCTGCTGTAGCTGATCAGATGCTTGGTCCGAAAGAGGATAGACATTTGGCAATTGTCCTG
                  ||   |  | | |  ||| | ||  |  |   || | ||  |  ||| | | |    || || |    ||||| | |       | |   || || | |||| | || ||||||| ||| || ||||||||||||||||| ||||||||||| |   ||| |||  | || |||||  || |  | || |||||  ||
------------------ggtccatctatccattca-tcaattttctattgttaaaagaaattttccatcggaattaagtttgtacttgattctt----tcttcttaattgatgtattagcagGCCATGCCAGAAGCAGCAGGAGCTGTTGCAGCTGCAGCTGTAGCTGACCGATTGCATGGGTCAAAGGAGGACCGAAAACTAGCTATTGTTTTG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G021846_T02 (Zea mays), 3'ss of exon 5
gtttgtacaaagtgcaaaggcatacttgttctgtcagtgaagatc-atgaagtcataattatttgccttgtttctaggtgttcttttgatacctgtgactctttctgttaattgttagAATGCAATGCCAGCAGCTGCTGGAGCTGTTGCAGCTGCTGCTGTAGCTGATCAGATGCTTGGTCCGAAAGAGGATAGACATTTGGCAATTGTCCTG
                  |   || ||     | || ||| |||  | |  ||   |   |            | | || |   ||| | || | | ||| ||  ||  | ||  || |   ||||||||| ||| || ||||||||||||||||| |||||||||||||   ||| |||  | || |||||  |  |  |||| |||||  ||
------------------gaattaattaaatgggcattgatgattgacgtggtttgagaaaaaaaatccagaacaaagtttgtatttta-actttttactattgttgaca-ttactacag-

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM5G824405_T01 (Zea mays), 3'ss of exon 5
gtttgtacaaagtgcaaaggcatacttgttctgtcagtg-aagatcatgaagtcataattatttgccttgtttctaggtgttcttttgatacctgtgactctttctgttaattg---ttagAATGCAATGCCAGCAGCTGCTGGAGCTGTTGCAGCTGCTGCTGTAGCTGATCAGATGCTTGGTCCGAAAGAGGATAGACATTTGGCAATTGTCCTG
                      |   | |  || ||    | |||| |   || | |     |      ||    |  ||||  ||   |   ||| ||  ||||||  |  ||     || | |  ||||||||||| |  || ||||||||||| |||||||||||||||||||||  ||| || ||||||||  |  | ||||| || ||  ||
----------------------ttgatttcttgccatcctatgatcgtt--gtaacagcatctgaatccgtcaaaacttgttacttcattttttgtcacaatttctgacagctgcctccagcagGGTATGCCAGCAGCAGAAGGGGCTGTTGCAGCAGCTGCTGTAGCTGATCAGATGTATGGACCAAAAGAGGACCGCAAGTTGGCCATCGTATTG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 7
gtttgtacaaagtgcaaaggcatacttgttctgtcagtgaagatcatga--agtcataattatttgccttgtttctaggtgttcttttgata------cctgtgactctttctgttaattgttagAATGCAATGCCAGCAGCTGCTGGAGCTGTTGCAGCTGCTGCTGTAGCTGATCAGATGCTTGGTCCGAAAGAGGATAGACATTTGGCAATTGTCCTG
||||||| ||| || |    |||   |  | |||   | ||  | ||    ||||| | | | ||    ||||   ||||  ||     |||       ||||  || |  || || |||| |||||| |||||||||| ||||||||||||||||| ||||| ||||| |||||||||||||| ||||| || || |||||||||||||||||| |||||
gtttgtataaa-tg-atttccatttcttgtttgttgttcaaagttattgctagtca-actaacttattgtgttgtgaggttgtccacaaataattgtttctgttcctttgcctttttattgatagAATTCAATGCCAGCTGCTGCTGGAGCTGTTGCTGCTGCAGCTGTTGCTGATCAGATGCTGGGTCCCAAGGAAGATAGACATTTGGCAATTATCCTG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 10
gtttgtacaaagtgcaaaggcatacttgttctgtcagtgaagatcatgaagtcataattatttgccttgtttctaggtgttcttttgatacctgtgactctttctgttaattgttagAATGCAATGCCAGCAGCTGCTGGAGCTGTTGCAGCTGCTGCTGTAGCTGATCAGATGCTTGGTCCGAAAGAGGATAGACATTTGGCAATTGTCCTG-----------------
                                                                                           ||||  || |  || || |||| |||||| |||||||||| |||||||||||||| || ||||| ||||| |||||||||||||| ||||| || || |||||||||||||||||| |||||                 
-----------------------------------------------------------------------------------------gtctgttcctttacctttttattgatagaattcaatgccagCTGCTGCTGGAGCTGTCGCTGCTGCAGCTGTTGCTGATCAGATGCTGGGTCCCAAGGAAGATAGACATTTGGCAATTATCCTGGTATTTTTCTGGCATTA

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 5
---------------------gtttgtacaaagtgcaaaggcatacttgttctg--tcagtgaagatcatga-agtcataattatttgccttgtttctaggtgttcttttgatacctgtgactctttctgttaattgttagAATGCAATGCCAGCAGCTGCTGGAGCTGTTGCAGCTGCTGCTGTAGCTGATCAGATGCTTGGTCCGAAAGAGGATAGACATTTGGCAATTGTCCTG
                      ||| |    | |   ||    || ||   |||  | | |  |  |      |  | |    ||| |  || ||   |  |  |   ||     |     | ||    |||   ||  ||||| |||| ||||| ||||||||||||||||||||||||||  | |||||||||||||| ||||| |||||| ||||||||||||| |||||| ||
gtttgcataaatgatttccatttttttgtttattattaaaatttatttacactggattaatttatgttgcatcaaacttttcaattggggttattaacaaatagttacttctgctccccccccctcctggttttatgacagAATTCAATTCCAGCTGCTGCTGGAGCTGTTGCAGCTGCTGCGATTGCTGATCAGATGCTAGGTCCCAAAGAGCATAGACATTTGGCGATTGTCATG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 6
gtttgtacaaagtgcaaaggcatacttgttctgtcagtgaagatcatga--agtcataattatttgccttgtttctaggtgttctt---ttgatacctgtgactctttctgttaattgttagAATGCAATGCCAGCAGCTGCTGGAGCTGTTGCAGCTGCTGCTGTAGCTGATCAGATGCTTGGTCCGAAAGAGGATAGACATTTGGCAATTGTCCTG
|| |||| | | || |    |||   |  | | |   | ||  | ||    ||||| | | | ||    |||||  |||| | |     |   |  ||||  || |  || || |||| |||||| |||||||||| ||||||||||| || || ||||| ||||| |||||||||||||| ||||| || || ||||||||||||| |||| |||||
gtctgtataca-tg-atttccatttcttgtttattgttcaaatttattgttagtca-actaacttattgtgttttgaggtttccacaaataattgtctgttcctttacctttttattgatagAATTCAATGCCAGCTGCTGCTGGAGCCGTCGCTGCTGCAGCTGTTGCTGATCAGATGCTGGGTCCCAAGGAAGATAGACATTTGGGAATTATCCTG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 13
gtttgtacaaagtgcaaaggcatacttgttctgtcagtgaagatcatgaagtcataatta-tttgccttgtttctaggtgttcttttga-----------------tacctgtgactctttctgttaattgtt-------agAATGCAATGCCAGCAGCTGCTGGAGCTGTTGCAGCTGCTGCTGTAGCTGATCAGATGCTTGGTCCGAAAGAGGATAGACATTTGGCAATTGTCCTG
||||||| ||| || |    |||  ||  | | | | | ||  | ||     |   |||| |||   |||  || |    |||  ||||                 | | | ||   |  ||   |  | |||       ||||| |||| ||||| ||||||||||||||||||||||||||  | || ||||||||||| ||||| || ||| ||||||||||||| |||||| ||
gtttgtataaaatg-atttccattttttgtttattattaaaatttatttccactggattaatttatgttgcatcaaacatttcacttgaggttattaacaaatagttgcttctgctcccctcccctcctggttttatggcagAATTCAATTCCAGCTGCTGCTGGAGCTGTTGCAGCTGCTGCGATTGCAGATCAGATGCTAGGTCCCAAGGAGCATAGACATTTGGCGATTGTCATG

upper sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 5
gtttgtacaaagtgcaaaggcatacttgttctgtcagtgaagatcatgaagtcataattatttgccttgtttctaggtgttcttttgatacctgtgactctttctgttaattgttagAATGCAATGCCAGCAGCTGCTGGAGCTGTTGCAGCTGCTGCTGTAGCTGATCAGATGCTTGGTCCGAAAGAGGATAGACATTTGGCAATTGTCCTG
|||||  |  ||         |   |   ||| |||||  || ||||     |  ||  |||||     ||| ||  | || || | |  | |||     ||  | |||||| ||||||| |||||||||| ||||| ||||||||||| || || || ||||||||||| |||||||| |||||||| ||||||||| | ||||||||||||
gtttggcctgagc-------tagtttctatctttcagtagag-tcat-----ctgaa--atttgagaatttttta--tatttttctcacccttgta----ttcgttttaatt-ttagAATTCAATGCCAGCCGCTGCAGGAGCTGTTGCCGCAGCAGCGGTAGCTGATCAAATGCTTGGACCGAAAGAAGATAGACATCTAGCAATTGTCCTG

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|122690284|gb|EC950420.1|EC950420
EST:     CTAGTGCTGCTACATTCACTGCTGATCTCAAACTAGACTCAGAAACCAAG                         AATGCAATGCCAGCAGCTGCTGGAGCTGTTGCAGCTGCTGCTGTAGCTGAT
genomic: CTAGTGCTGCTACATTCACTGCTGATCTCAAACTAGACTCAGAAACCAAGgtttgtacaa ... taattgttagAATGCAATGCCAGCAGCTGCTGGAGCTGTTGCAGCTGCTGCTGTAGCTGAT
EST: gi|352764398|gb|FQ472755.1|FQ472755
EST:     CTAGTGCTGCTACATTCACTGCTGATCTCAAACTAGACTCAGAAACCAAG                         AATGCAATGCCAGCAGCTGCTGGAGCTGTTGCAGCTGCTGCTTGTAGCTGA
genomic: CTAGTGCTGCTACATTCACTGCTGATCTCAAACTAGACTCAGAAACCAAGgtttgtacaa ... taattgttagAATGCAATGCCAGCAGCTGCTGGAGCTGTTGCAGCTGCTGCT-GTAGCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgccttgtttctaggtgttcttttgatacctgtgactctttctgttaattgttagAATGCAATGCCAGCAGCTGCTGGAGCTGTTGCAGCTGCTGCTGTAGCTGATCAGATGCTTGGTCCGAAAGAGGATAGACATTTGGCAATTGTCCTG
                                          tgttaat  putative branch site (score: 3)
                                   ctctttctgtt  CT-rich tract
                                            ttaattgtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtacaaagtgcaaaggcatacttgttctgtcagtgaagatcatgaagtcataattatttgccttgtttctaggtgttcttttgatacctgtgactctttctgttaattgttagAATGCAATGCCAGCAGCTGCTGGAGCTGTTGCAGCTGCTGCTGTAGCTGATCAGATGCTTGGTCCGAAAGAGGATAGACATTTGGCAATTGTCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT