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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttattacacattcggctcttctttgttgcactttaaaagcaaataggtatttattacttgggatgctggtcccactagtactttcattgagataacgcctaatattttgctctgtgcatgcacttaaaacaattctcttgactgatgtttcacagCTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAA

Basic information

species Vitis vinifera
transcript Vv18s0076g00260.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0076g00260.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os05g35530.1 (Oryza sativa), 3'ss of exon 10
gtatttattacacattcggctcttctttgttgcactttaaaagcaaataggtatttattacttgggatgctggtcccactagtactttcattgagataacgcctaatattttgctctgtgcatgcacttaaaacaattctcttgactgatgtttcacagCTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAA
                                                                | ||||| | |    ||  |||| ||    | ||          | |   | | ||  || || | | |  ||  |  ||    |||  |  ||||||||   | | ||||||||||||||||||||||| |||||||  |||||||| ||||||||    || ||||| ||
----------------------------------------------------------------gtatgctaggcaggttaacacttgcagattgctattattatgagtgtacatatatgtctg-acatgataacatggttgtgctaaatggat-gcagCTTACAGCTTCTCAAATCAAAGCTGAAATGGAGAAGACTTTGCGATGGCTTGTCCCTATTGCAAATAATACAACGAA

upper sequence: Vv18s0076g00260.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os01g65330.2 (Oryza sativa), 3'ss of exon 9
gtatttattacacattcggctcttctttgttgcactttaaaagcaaataggtatttattacttgggatgctggtcccactagtactttcattgagataacgcctaatattttgctctgtgcatgca-cttaaaacaattc--tcttg-actgatgtttcacagCTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAA-----------------------
                                                              ||  |    |  | ||  |     |  ||| || | |  | | ||  | ||     | |||  | || |||   |||   ||||| ||| |       ||| ||||   | | |||||||| |||||||||||||| |||||||  |||||||| || |||||    ||||| |||||                       
-----------------------------------------------------------gtatgcaaaatagcacacaacatatgctctattaaggtca-acatcatgctatgactattacatataactgaaattgatttaatcttgtactaaatcgatgcagGTTACTGCTGCTCAAATCAAGGCTGAAATGGAGAAGACTTTGCGGTGGCTTGTCCCAATTGCAAATAACACCACCAAGTATTATAAGCTATCTTAATAGA

upper sequence: Vv18s0076g00260.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os01g65330.1 (Oryza sativa), 3'ss of exon 9
gtatttattacacattcggctcttctttgttgcactttaaaagcaaataggtatttattacttgggatgctggtcccactagtactttcattgagataacgcctaatattttgctctgtgcatgca-cttaaaacaattc--tcttg-actgatgtttcacagCTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAA
                                                              ||  |    |  | ||  |     |  ||| || | |  | | ||  | ||     | |||  | || |||   |||   ||||| ||| |       ||| ||||   | | |||||||| |||||||||||||| |||||||  |||||||| || |||||    ||||| |||||
-----------------------------------------------------------gtatgcaaaatagcacacaacatatgctctattaaggtca-acatcatgctatgactattacatataactgaaattgatttaatcttgtactaaatcgatgcagGTTACTGCTGCTCAAATCAAGGCTGAAATGGAGAAGACTTTGCGGTGGCTTGTCCCAATTGCAAATAACACCACCAA

upper sequence: Vv18s0076g00260.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA10G36210.1 (Glycine max), 3'ss of exon 12
gtatttattacacattcggctcttctttgttgcactttaaaagcaaataggtatttattacttgggatgctggtcccactagtactttcattgagataacgcctaatattttgctctgtgcatgcacttaaaacaattctcttgactgatgtttcacagCTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAA
                                         ||| ||  |   | || || |    | |||  | | || | | |    |||||  |   | | || |||||          |  |  | |||  | |     ||   || |||  ||||||||| | ||||||||||||||||||||||||||||  ||||| |||||||| |||||||||||||| ||||| ||
-----------------------------------------agccaaaggagttctactaat----aagcttatactac-atttccaatattgattt--tgaccaaaattttaaatc-----taaatctgaaatgaat-----gaaacat-ttttgcagCTTACCGTGCCACAAATCAAAGCTGAAATGGAGAAAATATTGCAATGGCTTGTTCCTATTGCCGCCAATACAACAAA

upper sequence: Vv18s0076g00260.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA20G31400.1 (Glycine max), 3'ss of exon 12
gtatttattacacattcggctcttctttgttgcactttaaaagcaaataggtatttattacttgggatgctggtcccactagtactttcattgagataacgcctaatattttgctctgtgcatgcacttaaaacaattctcttgactgatgtttcacagCTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAA
                                               ||   |  | ||   ||  |     ||   |||| ||  || |||| ||     || ||| |||   ||      || | | ||   ||   | |||            ||||||||| | ||||||||||||||||||||||||||||  ||||| |||||||| |||||||| ||||||||||| ||
----------------------------------------tgatttttattgaacttttttctgccaaaggagttatactaata--ttgattgtga-----ccaaatttttaaatccaaatctgaaatgaaggaaacattgttg------------cagCTTACCGTCCCACAAATCAAAGCTGAAATGGAGAAAATATTGCAGTGGCTTGTTCCTATTGCAGCCAACACAACGAA

upper sequence: Vv18s0076g00260.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT1G34320.1 (Arabidopsis thaliana), 3'ss of exon 10
gtatttattacacattcggctcttctttgttgcactttaaaagcaaataggtatttattacttgggatgctggtcccactagtactttcattgagataacgcctaatattttgctctgtgcatgcacttaaaacaattctcttgactgatgtttcacagCTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAA
                       | ||  |     || | |          |  || |    ||  | | ||     || |     | || ||  |     | | | || ||  | |||       || |   || |     ||| |  | ||   ||||| ||  |||| ||||| |||||||||||||| ||||| ||||| |||||||| ||| ||||  | ||||| |||||
----------------------gtattaatactgtttcacacttcccataatgcttttgtgctgacaagatgaatttacca---tgtccagtgtta-----cttgaaatgttatt-tgtatccctgctcacctcactatatctgatttgttttcaccagCTCACTGTTCCTCAAATAAAAGCTGAAATGGAAAAAACATTGCAGTGGCTTGTTCCTGTTGCTACAAACACCACCAA

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|110719053|gb|EE096590.1|EE096590
EST:     TAAAGTCAGCTTTACGCAACAGACTACAATCCTTTCAGCTTAAGGAAGAG                         CTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTT
genomic: TAAAGTCAGCATTACGCAACAGACTACAATCCTTTCAGCTTAAGGAAGAGgtatttatta ... tgtttcacagCTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTT
EST: gi|110720867|gb|EE097166.1|EE097166
EST:     TAAAGTCAGCTTTACGCAACAGACTACAATCCTTTCAGCTTAAGGAAGAG                         CTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTT
genomic: TAAAGTCAGCATTACGCAACAGACTACAATCCTTTCAGCTTAAGGAAGAGgtatttatta ... tgtttcacagCTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTT
EST: gi|110720638|gb|EE096734.1|EE096734
EST:     TAAAGTCAGCATTACGCAACAGACTACAATCCTTTCAGCTTAAGGAAGAG                         CTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTT
genomic: TAAAGTCAGCATTACGCAACAGACTACAATCCTTTCAGCTTAAGGAAGAGgtatttatta ... tgtttcacagCTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTT
EST: gi|110718519|gb|EE095448.1|EE095448
EST:     TAAAGTCAGCATTACGCAACAGACTACAATCCTTTCAGCTTAAGGAAGAG                         CTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTT
genomic: TAAAGTCAGCATTACGCAACAGACTACAATCCTTTCAGCTTAAGGAAGAGgtatttatta ... tgtttcacagCTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTT
EST: gi|110696366|gb|EE072430.1|EE072430
EST:     CTTTCAGCTTAAGGAAGAG                         CTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTT
genomic: CTTTCAGCTTAAGGAAGAGgtatttatta ... tgtttcacagCTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTT
EST: gi|110720216|gb|EE095942.1|EE095942
EST:     TAAAGTCAGCTTTACGCAACAGACTACAATCCTTTCAGCTTAAGGAAGAG                         CTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTT
genomic: TAAAGTCAGCATTACGCAACAGACTACAATCCTTTCAGCTTAAGGAAGAGgtatttatta ... tgtttcacagCTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTT
EST: gi|110720676|gb|EE096807.1|EE096807
EST:     TAAAGTCAGCATTACGCAACAGACTACAATCCTTTCAGCTTAAGGAAGAG                         CTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTT
genomic: TAAAGTCAGCATTACGCAACAGACTACAATCCTTTCAGCTTAAGGAAGAGgtatttatta ... tgtttcacagCTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTT
EST: gi|110720592|gb|EE096647.1|EE096647
EST:     TAAAGTCAGCTTTACGCAACAGACTACAATCCTTTCAGCTTAAGGAAGAG                         CTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTT
genomic: TAAAGTCAGCATTACGCAACAGACTACAATCCTTTCAGCTTAAGGAAGAGgtatttatta ... tgtttcacagCTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTT
EST: gi|110719214|gb|EE096935.1|EE096935
EST:     TAAAGTCAGCATTACGCAACAGACTACAATCCTTTCAGCTTAAGGAAGAG                         CTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTT
genomic: TAAAGTCAGCATTACGCAACAGACTACAATCCTTTCAGCTTAAGGAAGAGgtatttatta ... tgtttcacagCTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTT
EST: gi|110713860|gb|EE090149.1|EE090149
EST:     TAAAGTCAGTTTTACGCAACAGACTACAATCCTTTCAGCTTAAGGAAGAG                         CTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTT
genomic: TAAAGTCAGCATTACGCAACAGACTACAATCCTTTCAGCTTAAGGAAGAGgtatttatta ... tgtttcacagCTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTT
EST: gi|110718805|gb|EE096054.1|EE096054
EST:     TAAAGTCAGCATTACGCAACAGACTACAATCCTTTCAGCTTAAGGAAGAG                         CTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTT
genomic: TAAAGTCAGCATTACGCAACAGACTACAATCCTTTCAGCTTAAGGAAGAGgtatttatta ... tgtttcacagCTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTT
EST: gi|110719766|gb|EE095191.1|EE095191
EST:     TAAAGTCAGCATTACGCAACAGACTACAATCCTTTCAGCTTAAGGAAGAG                         CTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTT
genomic: TAAAGTCAGCATTACGCAACAGACTACAATCCTTTCAGCTTAAGGAAGAGgtatttatta ... tgtttcacagCTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTT
EST: gi|110720643|gb|EE096746.1|EE096746
EST:     TAAAGTCAGCATTACGCAACAGACTACAATCCTTTCAGCTTAAGGAAGAG                         CTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTT
genomic: TAAAGTCAGCATTACGCAACAGACTACAATCCTTTCAGCTTAAGGAAGAGgtatttatta ... tgtttcacagCTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatattttgctctgtgcatgcacttaaaacaattctcttgactgatgtttcacagCTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAA
                                       gactgat  putative branch site (score: 3)
                       ttaaaacaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttattacacattcggctcttctttgttgcactttaaaagcaaataggtatttattacttgggatgctggtcccactagtactttcattgagataacgcctaatattttgctctgtgcatgcacttaaaacaattctcttgactgatgtttcacagCTTACCATTCCACAAATCAAAGCTGAAATGGAGAAAACTTTGCATTGGCTTGTGCCTATTGCCGCCAACACAACCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA