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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgtgtgtgtgtgtgtgtgtgtgtgaaagagagagagagaggtaatatatttgaataatatggcctaaactttggaaccctacatggtttttttaccagACGGCAAGATTCTTCAATTGGTTTTGGAGCACCTGTTCGTGCTAACATGAGAACTGGTGGGTTAACCAATGCTGTGGTGACATCATCCTTACTAGAATCG

Basic information

species Vitis vinifera
transcript Vv18s0089g01240.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0089g01240.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os02g35630.1 (Oryza sativa), 3'ss of exon 9
----tgtgtgtgtgtgtgtgtgtgtgtgtgaaagagagagagagaggtaatatatttgaataatatggcctaaactttggaaccctacatggttttttta---ccagACGGCAAGATTCTTCAATTGGTTTTGGAGCACCTGTTCGTGCTAACATGAGAACTGGTGGGTTAACCAATGCTGTGGTGACATCATCCTTACTAGAATCG
    ||  | |   | | || |  |     |  |  | |         ||| | ||   | |   |   ||||  | |     ||| | |   ||||| |    ||| |||||||||||||| ||||| ||||| |||||||| ||||||||||||||  | |||||  |  | | ||||   ||||||||||||||  | ||||| 
gtattgcatattgatctttgagacttacctattggaacaattgtctccaatgttttctcaaatcgtcatctaatgtatttgcacctgctttaatttttaaaaatcagGCGGCAAGATTCTTCTATTGGCTTTGGGGCACCTGTCCGTGCTAACATGAGGGCAGGTGGCATCTCAAGTGCTCAAGTGACATCATCCTTGTTGGAATCA

upper sequence: Vv18s0089g01240.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA10G32040.1 (Glycine max), 3'ss of exon 7
--------tgtgtgtgtgtgtgtgtgtgtgtgtgaaagagagagagagaggtaatatatttgaataatatggcctaaactttggaaccctacatggtttttttaccagACGGCAAGATTCTTCAATTGGTTTTGGAGCACCTGTTCGTGCTAACATGAGAACTGGTGGGTTAACCAATGCTGTGGTGACATCATCCTTACTAGAATCG
        | | ||| | |||  |  ||| | |  |  |  |      |  |  |   ||||    || |  | | || ||| ||    ||  ||     |  |||||||| |||||||||||||||||||||||||||||||| ||| | || |||||| |||||||  | || |||||||  || |||||||| ||||| || |||
gtattttttttttgtct-tgtaagaatgttttttcacaaatgttctgcat-tcttggttttgctagatttttcatcaaattttga---ttatttgtgaaataaaccagACGACAAGATTCTTCAATTGGTTTTGGAGCACCTGTCCGTTCCAATATGAGAGCTGGTGGAATTACAAATGCTGCAGTCACATCATCTTTACTTGAGTCG

upper sequence: Vv18s0089g01240.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA16G33080.1 (Glycine max), 3'ss of exon 10
----tgtgtgtgtgtgtgt-gtgtgtgtgtgaaagagagagagagaggtaatatatttgaataatatggcctaaactttggaaccctacatggttttttta-----ccagACGGCAAGATTCTTCAATTGGTTTTGGAGCACCTGTTCGTGCTAACATGAGAACTGGTGGGTTAACCAATGCTGTGGTGACATCATCCTTACTAGAATCG
    |||  |  | ||| | |      | |         |   | || |  | ||  |  || |  |||  |   || |   | | || | | ||| |  |     ||||||| ||||||||||| ||||||||||||||||| |||||||| || |||||| |||||||  ||||  || |||  || |||||||| ||||| || || 
gtaatgttggcctttgtcttgcaaaaatatttgctcataaatcacagttggtttacat--atgacttggtttctgctgtactaacttatacgatttatcaaataaaccagACGACAAGATTCTTCTATTGGTTTTGGAGCACCAGTTCGTGCCAATATGAGAGCTGGTGGAATAACAGATTCTGCAGTAACATCATCTTTACTTGAGTCA

upper sequence: Vv18s0089g01240.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA20G35600.1 (Glycine max), 3'ss of exon 9
tgtgtgtgtgtgtgtgtgtgtgtgtgaaagagagagagagaggtaatatatttgaataatatggcctaaactttggaaccctacatggttttttt---------accagACGGCAAGATTCTTCAATTGGTTTTGGAGCACCTGTTCGTGCTAACATGAGAACTGGTGGGTTAACCAATGCTGTGGTGACATCATCCTTACTAGAATCG
                                          ||| | | |||   |  |   | ||    |||   | | ||  | | || |||         |||||||| |||||||||||||||||||||||| |||| || ||| | || ||||||||||||||  | || |||||||  || |||||||| ||||| || |||
------------------------------------------gtattttgtttttctttttatgtctttgttttttcatcatattttgattatttgtgaaataaaccagACGACAAGATTCTTCAATTGGTTTTGGATCACCAGTCCGTTCCAATATGAGAACTGGTGGAGTTACAAATGCTGCAGTCACATCATCTTTACTTGAGTCG

upper sequence: Vv18s0089g01240.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA09G28260.1 (Glycine max), 3'ss of exon 10
-------------tgtgtgtgtgtgtgtgtgtgtgtgtgaaagagagagagagaggtaatatatttgaataatatggcctaaactttggaaccctacatggttttttta-----ccagACGGCAAGATTCTTCAATTGGTTTTGGAGCACCTGTTCGTGCTAACATGAGAACTGGTGGGTTAACCAATGCTGTGGTGACATCATCCTTACTAGAATCG
               |  |  ||      | | ||     ||   | ||   |     |||| | |   |  | || |  |   ||    | | |  |   ||| |  |     ||||||| ||||||||||| |||||||||||||| || |||||||| || |||||| ||| |||  ||||  || |||  || |||||||| ||||| || || 
gtaaaatgttggccttcggcttgcaaaaatatttgctcataaatcacagttggtttacatatgtcttggtt-tctgtcggagtattcactaacttgtactatttatcaaataaaccagACGACAAGATTCTTCTATTGGTTTTGGAGCCCCAGTTCGTGCAAATATGAGAGCTGTTGGAATAACAGATTCTGCAGTAACATCATCTTTACTTGAGTCA

upper sequence: Vv18s0089g01240.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: AT1G33360.1 (Arabidopsis thaliana), 3'ss of exon 9
-----tgtgtgtgtgtgtgtgtgtgtgtgtgaaagagagagagagaggtaatatatttgaataatatggcctaaactttggaaccctacatggtttttttaccagACGGCAAGATTCTTCAATTGGTTTTGGAGCACCTGTTCGTGCTAACATGAGAACTGGTGGGTTAACCAATGCTGTGGTGACATCATCCTTACTAGAATCG
     |   | |  ||   | | | | | || || |||     || |||  | | |||   | | || |   |      | | | ||| |||     | | ||||||| ||||| || ||||||||||||||||| ||||||||||| ||||||   ||  ||||  | |||| || ||   | || ||||| || |||||||||
gtaattcattattcgtccttttttttttttgcaatagatt---aggggt--tctgttt---tgacattgatca------gcatctcta-atg----ctctgccagACGACAAGACTCATCAATTGGTTTTGGAGCTCCTGTTCGTGCCAACATGGCTACCAGTGGAGTGACCAGTGGTGCAATAACTTCATCTTTGCTAGAATCG

upper sequence: Vv18s0089g01240.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S98_222V6.1 (Physcomitrella patens), 3'ss of exon 10
tgtgtgtgtgtgtgtgtgtgtgtgtgaaagagagagagagaggt-----aatatatttg----------aataa-----tatggcct----aaactttggaaccctaca-----tggtttttttaccagACGGCAAGATTCTTCAATTGGTTTTGGAGCACCTGTTCGTGCTAACATGAGAACTGGTGGGTTAACCAATGCTGTGGTGACATCATCCTTACTAGAATCG
 ||  |  | |   | |    |||| || |  |  ||      |      || ||||||           ||||     | | |  |    ||||  |    || | ||      | || || |  |||   ||||||||| ||||||||||||||||||||||||||||| || ||| ||          | | | | || |   | || ||||| || || ||  ||
-gtaggcttcttcatcttcaagtgttaaggtcaacgaatagcatttcatgatttatttgtcttctttttgataactttttgttgtgttatcaaaccctcatgcctttcaaccttcgtttcttgtttcagGAAGCAAGATTCATCAATTGGTTTTGGAGCACCTGTTCGTGCCAATATGCGAGGAAACAAACTGATCGACGCCGCCATTACTTCATCTTTGCTTGAGACG

upper sequence: Vv18s0089g01240.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S171_84V6.1 (Physcomitrella patens), 3'ss of exon 9
tgtgtgtgtgtgtgtgtgtgtgtgtgaaagagagagagagaggtaatat-atttgaataatatggcctaaactttggaaccctacatggtttttt-taccagACGGCAAGATTCTTCAATTGGTTTTGGAGCACCTGTTCGTGCTAACATGAGAACTGGTGGGTTAACCAATGCTGTGGTGACATCATCCTTACTAGAATCG
  |    | | |  |   ||    || ||      |      | || ||  | ||  |   ||  |  |  | || | |      ||   ||||| |  |||    |||||||| |||||||| |||||| ||||||||||||| |  |||||         | ||||| |  |||   | || || || || ||||||  |
--ttcaagagcgattccatgaagctggaactccatgctgtcagcaaaatcgtatggctgtgatatctaattcatttgtaattcgtatacctttttgtttcagGAAACAAGATTCGTCAATTGGATTTGGATCACCTGTTCGTGCCAGTATGAGGGGGAACAAGCTAACCGACTCTGCCATTACTTCTTCTTTGCTAGAAATG

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|26257016|gb|CA808079.1|CA808079
EST:     TTTATATGTGGTGGAGCATTTGTTGATTTAGAAAAAACCATTTCAGATAG                         ACGGCAAGATTCTTCAATTGGTTTTGGAGCACCTGTTCGTGCTAACATGAG
genomic: TTTATATGTGGTGGAGCATTTGTTGATTTAGAAAAAACCATTTCAGATAGgtatgcactt ... tttttaccagACGGCAAGATTCTTCAATTGGTTTTGGAGCACCTGTTCGTGCTAACATGAG
EST: gi|71862340|gb|DT011395.1|DT011395
EST:     TTTATATGTGGTGGAGCATTTGTTGATTTAGAAAAAACCATTTCAGATAG                         ACGGCAAGATTCTTCAATTGGTTTTGGAGCACCTGTTCGTGCTAACATGAG
genomic: TTTATATGTGGTGGAGCATTTGTTGATTTAGAAAAAACCATTTCAGATAGgtatgcactt ... tttttaccagACGGCAAGATTCTTCAATTGGTTTTGGAGCACCTGTTCGTGCTAACATGAG
EST: gi|110698280|gb|EE075629.1|EE075629
EST:     TTTATATGTGGTGGAGCATTTGTTGATTTAGAAAAAACCATTTCAGATAG                         ACGGCAAGATTCTTCAATTGGTTTTGGAGCACCTGTTCGTGCTAACATGAG
genomic: TTTATATGTGGTGGAGCATTTGTTGATTTAGAAAAAACCATTTCAGATAGgtatgcactt ... tttttaccagACGGCAAGATTCTTCAATTGGTTTTGGAGCACCTGTTCGTGCTAACATGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatatttgaataatatggcctaaactttggaaccctacatggtttttttaccagACGGCAAGATTCTTCAATTGGTTTTGGAGCACCTGTTCGTGCTAACATGAGAACTGGTGGGTTAACCAATGCTGTGGTGACATCATCCTTACTAGAATCG
                  gcctaaa  putative branch site (score: 3)
                                           tttttttacc  putative PPT
     tttgaataatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgtgtgtgtgtgtgtgtgtgtgtgaaagagagagagagaggtaatatatttgaataatatggcctaaactttggaaccctacatggtttttttaccagACGGCAAGATTCTTCAATTGGTTTTGGAGCACCTGTTCGTGCTAACATGAGAACTGGTGGGTTAACCAATGCTGTGGTGACATCATCCTTACTAGAATCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
-gtgtgtg
- - - - - - - - - - - - - aaagaga
- - - - - - - - - - - - - - agagaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatggcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctaca