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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattttttttccttaggactttccagtagccaaacataaccgaagcactagtggaataaatgaaattttgaattgactgtttgtgtgtttattatggcagGAGCAAAAGGTGGTTACTATATTTAGTGCACCAAATTATTGTTATCGCTGTGGGAACATGGCTTCCATCCTGGAAGTTGATGATTGCAAGGGCCACACAT

Basic information

species Vitis vinifera
transcript Vv06s0004g00830.t01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g00830.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: LOC_Os03g59060.1 (Oryza sativa), 3'ss of exon 9
aattttttttccttaggactttccagtagccaaacataaccgaagcactagtggaataaatgaaattttgaattgactgtttgtgtgtttattatggcagGAGCAAAAGGTGGTTACTATATTTAGTGCACCAAATTATTGTTATCGCTGTGGGAACATGGCTTCCATCCTGGAAGTTGATGATTGCAAGGGCCACACAT
                        | || |   || | | |  || | |  |||  |  ||     ||   | | ||  ||||       | |    ||||||||||| || ||||| |||||||||||||| |||||||| |||||||||||||||||||| || ||| |||||||||||||||||| ||  || ||||
---------------------gtaattatctctacttgaactcagtatttttggtttccataccggttc--actaacattttgcaaac--actg-aacagGAGCAAAAAGTTGTTACCATATTTAGTGCACCTAATTATTGCTATCGCTGTGGGAACATGGCATCAATCTTGGAAGTTGATGATTGCAGGGAGCATACAT

upper sequence: Vv06s0004g00830.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G062394_T01 (Zea mays), 3'ss of exon 9
aattttttttccttaggactttccagtagccaaacataaccgaagcactagtggaataaatgaaattttgaattgactgtttgtgtgtttattatggcagGAGCAAAAGGTGGTTACTATATTTAGTGCACCAAATTATTGTTATCGCTGTGGGAACATGGCTTCCATCCTGGAAGTTGATGATTGCAAGGGCCACACAT
             || |  ||||   | |  || |||   |       | | ||     |||     ||  ||  |    ||   | || ||||   |||||||||||||| || ||||||||||||||||| |||||||| || ||||||||||||||||| || ||||| ||||| |||||||||| ||  || || |
------------gtaagtgtttcttctgg--aagcatg--cagcttttttggggttcccatgcccagtttgatcaatacctt---tattcatta-aacagGAGCAAAAGGTCGTGACTATATTTAGTGCACCTAATTATTGCTACCGCTGTGGGAACATGGCATCAATCCTAGAAGTGGATGATTGCAGGGAACATACTT

upper sequence: Vv06s0004g00830.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GRMZM2G108355_T01 (Zea mays), 3'ss of exon 9
aattttttttccttaggactttccagtagccaaacataaccgaagcactagtggaataaatgaaattttgaattgactgtttgtgtgtttattatggcagGAGCAAAAGGTGGTTACTATATTTAGTGCACCAAATTATTGTTATCGCTGTGGGAACATGGCTTCCATCCTGGAAGTTGATGATTGCAAGGGCCACACAT
             || |  ||||   | |  || ||||  | |  |  |   ||      ||   | ||  ||  |    ||   |||| | ||   ||||||||||| || || ||||||||||||||||| |||||||| || ||||||||||||||||| || ||| | ||||| ||||||||||  |  || || |
------------gtaagtgtttcttctgg--aagcata--caactcttttcgggtccttgtgccctatttgatcaagacctt---tgttcacta-aacagGAGCAAAAAGTCGTGACTATATTTAGTGCACCTAATTATTGCTACCGCTGTGGGAACATGGCATCAATCTTAGAAGTGGATGATTGCAGAGAGCATACTT

upper sequence: Vv06s0004g00830.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA08G11940.2 (Glycine max), 3'ss of exon 8
aattttttttccttaggactttccagtagccaaacataaccgaagcactagtggaataaatgaaattttgaattgactgtttgtgtgtt--tattatggcagGAGCAAAAGGTGGTTACTATATTTAGTGCACCAAATTATTGTTATCGCTGTGGGAACATGGCTTCCATCCTGGAAGTTGATGATTGCAAGGGCCACACAT
                         |||   |      | |       | ||      | | |  | |||   | | || |||  |  |  |  | | |||||| ||||||||||||||||||||||||||||| || ||||||||||| |||||||| ||||| || || || || |||||||| ||||| || |||||||
-------------------------gtaaatacttgatatcattttgtttgttcttatattcatttgttgtggtaaatggttgatttatagtcctgttgcagGATCAAAAGGTGGTTACTATATTTAGTGCACCTAACTATTGTTATCGTTGTGGGAATATGGCATCAATTCTTGAGGTTGATGACTGCAAAGGACACACAT

upper sequence: Vv06s0004g00830.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA05G28790.2 (Glycine max), 3'ss of exon 8
aattttttttccttaggactttccagtagccaaacataaccgaagcactagtggaataaat-gaaattttgaattgactgtttgtgtgtttattatggcagGAGCAAAAGGTGGTTACTATATTTAGTGCACCAAATTATTGTTATCGCTGTGGGAACATGGCTTCCATCCTGGAAGTTGATGATTGCAAGGGCCACACAT
                        | ||    |    |          |  |  | | | | |   |  | ||| |    ||| |  ||   || | |||||| |||||||||||||||||||||||||| || || ||||||||||| |||||||||||||| || || || || ||||| || ||||| || |||||||
---------------------gtaaatacttgatatcattttgtttgttcttatattcattcgttgtggtaaatagttgatttata-gtcccttgttgcagGATCAAAAGGTGGTTACTATATTTAGTGCTCCTAACTATTGTTATCGTTGTGGGAACATGGCATCAATTCTTGAGGTTGACGACTGCAAAGGACACACAT

upper sequence: Vv06s0004g00830.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: PP1S88_179V6.1 (Physcomitrella patens), 3'ss of exon 9
------------------------------------------------aattttttttccttaggactttccagtagccaaacataaccgaagcactagtggaataaatgaaattttgaattgactgtttgtgtgtttattatggcagGAGCAAAAGGTGGTTACTATATTTAGTGCACCAAATTATTGTTATCGCTGTGGGAACATGGCTTCCATCCTGGAAGTTGATGATTGCAAGGGCCACACAT
                                                |    |||||| ||     |||  ||  |  |||  | || |      | |||  ||   |   || ||  ||| ||  ||  |||  |        ||||| ||||||||||| |||||||| || ||||| ||||| || ||||||||||                                                
gtatgtttctcacatatattcccactttctctttttatgttgctttggatgggtttttctttctattttttaagctggaaaatgtcactggctgtttggtg--atggctagcatcttatatt-acctttcatgtact--------cagGAACAAAAGGTGGTCACTATATTCAGCGCACCTAATTACTGCTATCGCTGTG------------------------------------------------

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|30131760|gb|CB917099.1|CB917099
EST:     TGATCGCTAGAGCTCACCAACTGGTTATGGAGGGATTCAACTGGGGCCAT                         GAGCAAAAGGTGGTTACTATATTTAGTGCACCANATTATTGTTATCGCTGT
genomic: TGATCGCTAGAGCTCACCAACTGGTTATGGAGGGATTCAACTGGGGCCATgtaactactt ... attatggcagGAGCAAAAGGTGGTTACTATATTTAGTGCACCAAATTATTGTTATCGCTGT
EST: gi|110379397|gb|EC944588.1|EC944588
EST:     TGATCGCTAGAGCTCACCAACTGGTTATGGAGGGATTCAACTGGGGCCAT                         GAGCAAAAGGTGGTTACTATATTTAGTGCACCAAATTATTGTTATCGCTGT
genomic: TGATCGCTAGAGCTCACCAACTGGTTATGGAGGGATTCAACTGGGGCCATgtaactactt ... attatggcagGAGCAAAAGGTGGTTACTATATTTAGTGCACCAAATTATTGTTATCGCTGT
EST: gi|110380939|gb|EC946242.1|EC946242
EST:     TGATCGCTAGAGCTCACCAACTGGTTATGGAGGGATTCAACTGGGGCCAT                         GAGCAAAAGGTGGTTACTATATTTAGTGCACCAAATTATTGTTATCGCTGT
genomic: TGATCGCTAGAGCTCACCAACTGGTTATGGAGGGATTCAACTGGGGCCATgtaactactt ... attatggcagGAGCAAAAGGTGGTTACTATATTTAGTGCACCAAATTATTGTTATCGCTGT
EST: gi|30134848|gb|CB920186.1|CB920186
EST:     TGATCGCTAGAGCTCACCAACTGGTTATGGAGGGATTCAACTGGGGCCAT                         GAGCAAAAGGTGGTTACTATATTTAGTGCACCAGATTATTGTTATCGCTGT
genomic: TGATCGCTAGAGCTCACCAACTGGTTATGGAGGGATTCAACTGGGGCCATgtaactactt ... attatggcagGAGCAAAAGGTGGTTACTATATTTAGTGCACCAAATTATTGTTATCGCTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactagtggaataaatgaaattttgaattgactgtttgtgtgtttattatggcagGAGCAAAAGGTGGTTACTATATTTAGTGCACCAAATTATTGTTATCGCTGTGGGAACATGGCTTCCATCCTGGAAGTTGATGATTGCAAGGGCCACACAT
                         aattgac  putative branch site (score: 3)
         aataaatgaaattttg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattttttttccttaggactttccagtagccaaacataaccgaagcactagtggaataaatgaaattttgaattgactgtttgtgtgtttattatggcagGAGCAAAAGGTGGTTACTATATTTAGTGCACCAAATTATTGTTATCGCTGTGGGAACATGGCTTCCATCCTGGAAGTTGATGATTGCAAGGGCCACACAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - ctttcca
- - - - - - - - - - - - - - -ccaaaca
- - - - - - - - - - - - - - - - - - -aaccgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - ggaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgactgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgtgt