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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactattcaaatttttttaaccatatcaaagttttccaatgattagtcacttcagatatgctatttaaagggattcgcataacagGTAGCATTGAAGTTTGAGCACCGGAATAGCAAAGGATGCAATTATGGCCCTCCTTATGAGTGGCAAGTCTACAA

Basic information

species Vitis vinifera
transcript Vv08s0007g07420.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 3
-----gtactattcaaatttttttaaccatatcaaagttttccaatgattagtcacttcagatatgctatttaaagggattcgcata--acagGTAGCATTGAAGTTTGAGCACCGGAATAGCAAAGGATGCAATTATGGCCCTCCTTATGAGTGGCAAGTCTACAA
        | || |   ||  |||     ||  ||  || | | || ||   |||| |  |   || || | | | |||||| ||||   |||||||| ||||| || |||||||| || || || || ||||||||||||||||| |||||||||||||| || | 
gtctaaccccatcctttttccttttcttttaaaaagtttctgctataat--atcacat-ggtggtgataat-agatggattctcatattgcagGTAGCTTTGAAATTCGAGCACCGCAACAGTAAGGGTTGCAATTATGGCCCTCCATATGAGTGGCAAGTTTATAG

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os07g07560.1 (Oryza sativa), 3'ss of exon 3
gtactattcaaatttttttaaccatatcaaagttttccaatgat-tagtcacttcagat--atgctatttaaagggattcgcataacagGTAGCATTGAAGTTTGAGCACCGGAATAGCAAAGGATGCAATTATGGCCCTCCTTATGAGTGGCAAGTCTACAA
      ||      | | |||  | |  | | ||| |     || ||  |  |||| ||  || | || ||||      |  ||   |||| ||||||||| ||||||| || || || ||||| |||||||||||  | || |||||||||||||| ||| |
-----gtttg---ctctctaaatagaatatattttgctgtaaatatatccttttcacattaatacaatctaaaaatgaccctatg-tagGTTGCATTGAAGCTTGAGCATCGAAACAGTAAAGGGTGCAATTATGGTGCCCCCTATGAGTGGCAAGTTTACCA

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G116086_T01 (Zea mays), 3'ss of exon 3
gtactattcaaatttttttaaccatatcaaagttttccaatgattagtcacttcagatatgctatttaaagggattcgc-ataacagGTAGCATTGAAGTTTGAGCACCGGAATAGCAAAGGATGCAATTATGGCCCTCCTTATGAGTGGCAAGTCTACAA
      || | || |  || ||  |   ||  |  |  ||    ||  | ||||   ||||  | ||| |   || |   |  |||||| || ||||| ||||||||||| || ||||| || ||||||||||||||||| |||||||||||||| || | 
-----gtttatatatagttcactctgg-aagttacttaaaaagataccctcttc---tatggaagttacactaatacatgaccacagGTTGCTTTGAAATTTGAGCACCGAAACAGCAAGGGCTGCAATTATGGCCCTCCATATGAGTGGCAAGTTTATAG

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G164265_T03 (Zea mays), 3'ss of exon 3
gtactattcaaatttttttaaccatatcaaagttttccaatgattagtcacttcagatatg-ctatttaaagggattcgcataacagGTAGCATTGAAGTTTGAGCACCGGAATAGCAAAGGATGCAATTATGGCCCTCCTTATGAGTGGCAAGTCTACAA
      ||     |   |||  ||| | |    |||   |||  |  |  | | | |||   | ||| || || |      |   |||| |||||||| || ||||| || || || ||||||||||||||||||||||| ||||||||||| || || ||
-----gtttg---tcacttacacattttatgaattt--gatggattttttccttacataaatccattaaatggtaaaatttttgtagGTCGCATTGAAATTAGAGCATCGAAACAGTAAAGGATGCAATTATGGCCCTCCATATGAGTGGCAGGTTTATAA

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G037923_T02 (Zea mays), 3'ss of exon 3
gtactattcaaatttttttaaccatatcaaagttttccaatgattagtcactt-cagatatgctatttaaagggattcgcataacagGTAGCATTGAAGTTTGAGCACCGGAATAGCAAAGGATGCAATTATGGCCCTCCTTATGAGTGGCAAGTCTACAA
      ||     |   |||||| | |   | |||   | | |||  || ||| || | || | ||  |  |  |||    |   |||| |||||||| || ||||| || || || |||||||||||||||||||| || |||||||||||||| || ||
-----gtttg---tcacttaaccttttatgaatttg--attcatttttcccttacataaatccaatcaattgtaatttt--ttgtagGTTGCATTGAAATTCGAGCATCGTAACAGTAAAGGATGCAATTATGGCCCCCCATATGAGTGGCAAGTTTATAA

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA16G04580.1 (Glycine max), 3'ss of exon 3
gtactattcaaatttttttaaccatatcaaagtt--------ttccaatgattagtcacttca-gatatgctattt------aaagggattcgcataacagGTAGCATTGAAGTTTGAGCACCGGAATAGCAAAGGATGCAATTATGGCCCTCCTTATGAGTGGCAAGTCTACAA
||| |||| |   ||       |  || || |||        |   |||||      |||  | ||||   | |||      |     | |    | |||||| ||| | |||||||||||| | || |||||||| ||||| ||||| |||||||||||||||||||| |||| 
gtattattaaggattccagtttctcattaaggttgaatgaagtattaatgaacctatactgtatgatacattgttttttcttattttaactttgtttacagGTTGCACTTAAGTTTGAGCACAGAAACAGCAAAGGTTGCAACTATGGGCCTCCTTATGAGTGGCAAGTATACAG

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G18190.1 (Arabidopsis thaliana), 3'ss of exon 3
----gtactattcaaatttttttaaccatatcaaagttttccaatgattagtcacttcagatatgctatttaaagggattcgcataacagGTAGCATTGAAGTTTGAGCACCGGAATAGCAAAGGATGCAATTATGGCCCTCCTTATGAGTGGCAAGTCTACAA
     |  ||   ||   |  || |   | |  | |  | |  | ||  ||     | |    |   |  | ||    ||  | || ||||| ||  |||| |||||||| || ||||||||||||||||||| ||| || ||||| ||||||||||| |||||
gtatattgtaaagaagcatacttgagatttttgagggatacagacgaa-agaagtctaatcgttaacaaattaattatttttcttaccagGTGGCCCTGAAATTTGAGCATCGAAATAGCAAAGGATGCAATTTTGGTCCACCTTACGAGTGGCAAGTGTACAA

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 2
---------------------------------------------gtactattcaaatttttttaaccatatcaaagttttccaatgattagtcacttcagatatgctatttaaagggattcgcata---acagGTAGCATTGAAGTTTGAGCACCGGAATAGCAAAGGATGCAATTATGGCCCTCCTTATGAGTGGCAAGTCTACAA
                                             |||   | |  |   || | |  || | |  |  |  |  || || ||  ||  |  ||    | | |      ||  | |     |||||||| || |||||||| || ||||  ||||| || ||||||||||| |||||||| ||||||||||| |||||
gtactctttactctaattcgttgaggtccggtcgtgtcgtattccgtatagtgccgagggttgtgattat-ttagcgagtatctttgctttgtgtctggaagtacaa-actgagtcttgttttcgtgctcgcagGTAGCTTTAAAGTTTGAACATCGGAGCAGCAAGGGTTGCAATTATGGTCCTCCTTACGAGTGGCAAGTTTACAA

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S131_16V6.1 (Physcomitrella patens), 3'ss of exon 2
--------------------------------------------------gtactattcaaatttttttaaccatatcaaagttttccaatgattagtcacttcagatatgctatttaaagggattcgcata-acagGTAGCATTGAAGTTTGAGCACCGGAATAGCAAAGGATGCAATTATGGCCCTCCTTATGAGTGGCAAGTCTACAA
                                                  ||       | | | |    |    ||| | || ||   ||  ||| |    | || | ||   |   |  | | |||  |   ||||| || |||||||| ||||| |||| ||| || || ||||||||||| ||||||||||||||||| || |||| 
gtattcaatttcttacaatttgttctgctctacttctttcgcagcagcatgtttggaagatactctgcatattgcatcgaggtcttgtgatttttaatgtaataagttttgtattcatattgaactcgtttgtgcagGTTGCGTTGAAGTTCGAGCATCGGAGTAGTAAGGGCTGCAATTATGGTCCTCCTTATGAGTGGCAGGTTTACAC

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 2
gtactattcaaatttttttaaccatatcaaagttttc-caat--gattag-tcacttcagatatgctatttaaagggattcgcataacagGTAGCATTGAAGTTTGAGCACCGGAATAGCAAAGGATGCAATTATGGCCCTCCTTATGAGTGGCAAGTCTACAA
                 |  ||  |   ||  ||| | || |  |||| | ||  |||  |   |||  | ||||   |     |  ||||| || ||||||||||| ||| | |  || ||||||||||| ||||| ||||| |||||||||||||| |||| 
----------------gtagactgttcgaagatttgctcagttggattggctcttttctcagcggctgatcaaagatgt-----tgtcagGTTGCTTTGAAGTTTGAACACAGAAGCAGTAAAGGATGCAACTATGGGCCTCCGTATGAGTGGCAAGTTTACAC

upper sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 2
gtactattcaaatttttttaaccatatcaaagttttc-caat--gattagtcacttcagatatgctatttaaagggattcgcataacagGTAGCATTGAAGTTTGAGCACCGGAATAGCAAAGGATGCAATTATGGCCCTCCTTATGAGTGGCAAGTCTACAA
                 |  ||  |   ||  ||||| || |  ||||  ||  |||  |   |||  | ||||   |     |  ||||| || ||||||||||| ||| | |  || ||||||||||| ||||| ||||| |||||||||||||| |||| 
----------------gtagactgttcgaagattttctcagttggattgctcttttctcagcggctgatcaaagatgt-----tgtcagGTTGCTTTGAAGTTTGAACACAGAAGCAGTAAAGGATGCAACTATGGGCCTCCGTATGAGTGGCAAGTTTACAC

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|110385816|gb|EC950372.1|EC950372
EST:     GCAGAAGGGTAAGTGGTGGCACTGAAAGAACGGGACCTGATGCGCTTGAG                         GTAGCATTGAAGTTTGAGCACCGGAATAGCAAAGGATGCAATTATGGCCCT
genomic: GCAGAAGGGTAAGTGGTGGCACTGAAAGAACGGGACCTGATGCGCTTGAGgtactattca ... cgcataacagGTAGCATTGAAGTTTGAGCACCGGAATAGCAAAGGATGCAATTATGGCCCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttttccaatgattagtcacttcagatatgctatttaaagggattcgcataacagGTAGCATTGAAGTTTGAGCACCGGAATAGCAAAGGATGCAATTATGGCCCTCCTTATGAGTGGCAAGTCTACAA
                         atatgctatttaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactattcaaatttttttaaccatatcaaagttttccaatgattagtcacttcagatatgctatttaaagggattcgcataacagGTAGCATTGAAGTTTGAGCACCGGAATAGCAAAGGATGCAATTATGGCCCTCCTTATGAGTGGCAAGTCTACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG