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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGAACCCAACAAGGGTGTGAACCCGGATGAAGCCGTTGCTTATGGTGCTGCTGTACAAGGAAGCATCTTGAGTGGAGAGGGTGGTGATGAAACCAAAGgtattatttccatcctcaccatcttcgcagaaccttcaatggcatggttgaaagtttgctaactcttgttctgttgtttcatgtatcag

Basic information

species Vitis vinifera
transcript Vv16s0098g01580.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0098g01580.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os02g02410.1 (Oryza sativa), 5'ss of exon 5
AAAGAACCCAACAAGGGTGTGAACCCGGATGAAGCCGTTGCTTATGGTGCTGCTGTACAAGGAAGCATCTTGAGTGGAGAGGGTGGTGATGAAACCAAAGgtattatttccatc-ctcaccatcttcgcagaaccttcaatggc-atggttgaaagt-ttgctaactcttgttctg--ttgtttcatgtat-cag
|| || |||||||||||||| ||||| ||||| || ||||| ||||||||||| || || ||||||||  | || || ||||| ||||| ||||||||||||   |  |  ||| |  ||    | |   |       ||   |   | |     || ||||  |  ||| |  ||  ||| ||   |||  |||
AAGGAGCCCAACAAGGGTGTCAACCCTGATGAGGCTGTTGCCTATGGTGCTGCGGTTCAGGGAAGCATTCTCAGCGGCGAGGGCGGTGACGAAACCAAAGgttcgaccttgatcacatacatagtcctttgggttggtaacaactgcgatcatctgtcttgcatatacttatcgtgctttgattttggtacgcag

upper sequence: Vv16s0098g01580.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G114793_T01 (Zea mays), 5'ss of exon 5
AAAGAACCCAACAAGGGTGTGAACCCGGATGAAGCCGTTGCTTATGGTGCTGCTGTACAAGGAAGCATCTTGAGTGGAGAGGGTGGTGATGAAACCAAAGgt---------attatttccatcctcaccatcttcgcagaaccttcaatggcatggttgaaagtttgctaactcttgttctgttgtttcatgtat-cag
|| || |||||||||||||| ||||| ||||| || ||||| | |||||| ||||| || |||||||||||||| || ||||||||||| || |||||||||          || |||     ||        | | ||    ||   | |    ||    | | |||| ||    ||    || || | |  || |||
AAGGAGCCCAACAAGGGTGTCAACCCTGATGAGGCTGTTGCCTTTGGTGCCGCTGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACCAAAGgttcggctcatgttttttgtgctcttttgccactggtaggtgttttttttggtaagtgatcattctgcttacataagtgtgatttttgccttgatgcag

upper sequence: Vv16s0098g01580.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G415007_T01 (Zea mays), 5'ss of exon 5
AAAGAACCCAACAAGGGTGTGAACCCGGATGAAGCCGTTGCTTATGGTGCTGCTGTACAAGGAAGCATCTTGAGTGGAGAGGGTGGTGATGAAACCAAAGgtattat-ttccatcctcaccatcttcgcagaaccttcaatggcatggttgaaagtt----tgctaactcttgttctgttgtttcatgtatcag
|| || |||||||||||||||||||| ||||| || ||||| | |||||| || || || |||||||||||||| || ||||||||||| || || ||||||    |  ||  ||   |      | || |    ||   |    | ||     ||     |||| ||    ||    || |  | ||   |||
AAGGAGCCCAACAAGGGTGTGAACCCTGATGAGGCTGTTGCCTTTGGTGCCGCGGTGCAGGGAAGCATCTTGAGCGGCGAGGGTGGTGACGAGACAAAAGgttcggtgctctttcactagtgctatagctgggtgtttttttttcttgtaagtggtcatcctgcttacataagtgtgattttgccttgatgcag

upper sequence: Vv16s0098g01580.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA08G02960.1 (Glycine max), 5'ss of exon 5
AAAGAACCCAACAAGGGTGTGAACCCGGATGAAGCCGTTGCTTATGGTGCTGCTGTACAAGGAAGCATCTTGAGTGGAGAGGGTGGTGATGAAACCAAAGgtattatt--------tccatcctc---accatcttcgcagaa-ccttcaatggcatggttgaaagtttgctaactcttgttctgttgtttcatgtatcag-----------------
|| || || ||||||||||| ||||| |||||||| ||||| ||||||||||| || ||||||||||| |||||||||||||||||||| ||||||||||||| | |         || | | ||   |  |  |   |||||  | | |||   ||   || ||||    |    |   ||  | ||| ||||   |  |                 
AAGGAGCCAAACAAGGGTGTCAACCCTGATGAAGCAGTTGCCTATGGTGCTGCAGTGCAAGGAAGCATTTTGAGTGGAGAGGGTGGTGAGGAAACCAAAGgtactgtagtctgtaatctaacttctcaattacttgtccagaaatcataaatattatttatgcaagtagattgtgacacattacgctgtctcattgttgtgtggctctctggatccag

upper sequence: Vv16s0098g01580.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA05G36600.1 (Glycine max), 5'ss of exon 5
AAAGAACCCAACAAGGGTGTGAACCCGGATGAAGCCGTTGCTTATGGTGCTGCTGTACAAGGAAGCATCTTGAGTGGAGAGGGTGGTGATGAAACCAAAGgtatta----------tttccatcctcaccatcttcgcagaa-ccttcaatggcatggttgaaagtttgctaactcttgttctgttgtttcatgtatcag-----------------
|| || || ||||||||||| ||||| |||||||| ||||| ||||||||||| || ||||||||||| |||||||||||||||||||| ||||||||||||| ||          | |   | ||||  |  |   |||||  | | |||   ||   || ||||    |  | |   ||    | | ||||   |  |                 
AAGGAGCCAAACAAGGGTGTCAACCCTGATGAAGCAGTTGCCTATGGTGCTGCAGTGCAAGGAAGCATTTTGAGTGGAGAGGGTGGTGAAGAAACCAAAGgtactacagtctgtaatctaacttctcattacttgtccagaaatcctaaatattatttatgcaagtagattgccacgcattacactttctcattgttgtgtggctctctggatccag

upper sequence: Vv16s0098g01580.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA05G36620.1 (Glycine max), 5'ss of exon 5
AAAGAACCCAACAAGGGTGTGAACCCGGATGAAGCCGTTGCTTATGGTGCTGCTGTACAAGGAAGCATCTTGAGTGGAGAGGGTGGTGATGAAACCAAAGgtattat-----------ttccatcctcaccatct-tcgcagaaccttcaatggcatggttgaaagt---ttgctaactct--tgttctgttgtt-tcatgtatcag-----------
|| || || ||||||||||| ||||| |||||||| ||||| ||||||||||| || ||||||||||| |||||||||||||||||||| |||||||||||||   |           |  | |    |  |  | || |  |  | | |||   ||    | || |   |||||||   |     | | |  |  |  |||  ||            
AAGGAGCCAAACAAGGGTGTCAACCCTGATGAAGCAGTTGCCTATGGTGCTGCAGTGCAAGGAAGCATTTTGAGTGGAGAGGGTGGTGAAGAAACCAAAGgtaccgtagtctgtaatgtagcttttaaattacttgtcccgaagtcataaatattatttacgcaattagattgctaagcataacactttctaatcgttgtgtggcaatatctatccag

upper sequence: Vv16s0098g01580.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA08G02940.1 (Glycine max), 5'ss of exon 5
AAAGAACCCAACAAGGGTGTGAACCCGGATGAAGCCGTTGCTTATGGTGCTGCTGTACAAGGAAGCATCTTGAGTGGAGAGGGTGGTGATGAAACCAAAGgtattatt-tccatcctcaccatcttcgcagaaccttcaatggcatggttgaaagtttgctaactcttgttctgttgtttcatgtatcag
|| || || |||||||| || ||||| |||||||| ||||| ||||||||||| || ||||||||||| |||||||||||||||||||| |||||||||||||  ||  ||  |    |  || |  | |      |  || ||   |    |   || |||| | ||||   |   | || | |  |||
AAGGAGCCAAACAAGGGGGTCAACCCTGATGAAGCAGTTGCCTATGGTGCTGCAGTGCAAGGAAGCATTTTGAGTGGAGAGGGTGGTGAAGAAACCAAAGgtaccatagtctgtaaatattatttatggaag----tagattgctaagcattacactttctaattgttgtgtggcaatctc-tat-ccag

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|33402771|gb|CF208398.1|CF208398
EST:     TGCTGTACAAGGAAGCATCTTGAGTGGAGAGGGTGGTGATGAAACCAAAG                         ATATCCTTCTCTTGGATGTGGCTCCACTCACTCTTGGTATTGAAACGGTTG
genomic: TGCTGTACAAGGAAGCATCTTGAGTGGAGAGGGTGGTGATGAAACCAAAGgtattatttc ... catgtatcagATATCCTTCTCTTGGATGTGGCTCCACTCACTCTTGGTATTGAAACGGTTG
EST: gi|351029703|gb|FQ427543.1|FQ427543
EST:     TGCTGTACAAGGAAGCATCTTGAGTGGAGAGGGTGGTGATGAAACCAAAG                         ATATCCTTCTCTTGGATGTGGCTCCACTCACTCTTGGTATTGAAACGGTTG
genomic: TGCTGTACAAGGAAGCATCTTGAGTGGAGAGGGTGGTGATGAAACCAAAGgtattatttc ... catgtatcagATATCCTTCTCTTGGATGTGGCTCCACTCACTCTTGGTATTGAAACGGTTG
EST: gi|33402798|gb|CF208425.1|CF208425
EST:     TGCTGTACAAGGAAGCATCTTGAGTGGAGAGGGTGGTGATGAAACCAAAG                         ATATCCTTCTCTTGGATGTGGCTCCACTCACTCTTGGTATTGAAACGGTTG
genomic: TGCTGTACAAGGAAGCATCTTGAGTGGAGAGGGTGGTGATGAAACCAAAGgtattatttc ... catgtatcagATATCCTTCTCTTGGATGTGGCTCCACTCACTCTTGGTATTGAAACGGTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGAACCCAACAAGGGTGTGAACCCGGATGAAGCCGTTGCTTATGGTGCTGCTGTACAAGGAAGCATCTTGAGTGGAGAGGGTGGTGATGAAACCAAAGgtattatttccatcctcaccatcttcgcagaaccttcaatggcatggttgaaagtttgctaactcttgttctgttgtttcatgtatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG