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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATGGAAATACCCAAAGTTATGGGTAGGATTCTTGAAGTGTGCACTCTTAACAAAGCCTCAGTCTTTCAGTGTGTTGCTGCAGgtgaaattctgtttgctatcataatttatgatttcttcttctctttggaaaactttcatttatgaaattttggaacagacaccaaccattacttatttttctctgattttttggctatcctttacactgaagaattatctgtttttgaacttgtattgatttttcag

Basic information

species Vitis vinifera
transcript Vv08s0105g00330.t01
intron # 25
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0105g00330.t01 (Vitis vinifera), 5'ss of exon 25
lower sequence: LOC_Os07g49320.1 (Oryza sativa), 5'ss of exon 25
ATATGGAAATACCCAAAGTTATGGGTAGGATTCTTGAAGTGTGCACTCTTAACAAAGCCTCAGTCTTTCAGTGTGTTGCTGCAGgtgaaattctgtttgctatcataatttatg-atttcttcttctctttggaaaacttt----catttatgaaattttggaacaga--caccaaccattacttatttttctctgattttttggctatcctttacactgaagaattatctgtttttg-aacttgta--ttgatttttcag
|||||||| || || |||||||||||||||||| ||||||||||  |||| || || |||||||| |   ||||| ||||||||||    |    ||||||   |      ||  | || ||||| | |    ||| || |    ||| |     ||     | | |    ||   | ||    || |      ||| ||  |   |||| |     |  ||     |    ||||   ||| |  |  ||| ||| ||||
ATATGGAAGTATCCCAAGTTATGGGTAGGATTCCTGAAGTGTGCTATCTTGACGAAACCTCAGTCATATGGTGTGCTGCTGCAGgttggctcacttttgcttctacgtagaatctacttgttcttgtatgcaaaaatctctgtagcatgtgcaccatccgctagctgttttacatgctatctgctagtggctcttgagttcatttttatcata-gtgccaaactgccaataattttcataacatcaaacttggtttatcag

upper sequence: Vv08s0105g00330.t01 (Vitis vinifera), 5'ss of exon 25
lower sequence: GRMZM2G086937_T03 (Zea mays), 5'ss of exon 2
ATATGGAAATACCCAAAGTTATGGGTAGGATTCTTGAAGTGTGCACTCTTAACAAAGCCTCAGTCTTTCAGTGTGTTGCTGCAGgtgaaattctgtttgctatcataatttatgatttcttcttctctttggaaaactttcatttatgaaattttggaacagacaccaaccattacttatttttctctgattttttggctatcctttacactgaagaattatctgtttttgaacttgtat-tgatttttcag
|| |||||||| || |||||||||||||||||  ||||||||||  |||| ||||| |||||||| |   ||||||||||||||||     | | | ||| ||| |  | | |||| | ||  |   | |     |   ||  |||| |     |  |    ||||   | ||  || ||||   | |   |||||   ||    | |   ||||  ||| ||      |||  | | || || ||||||||
ATTTGGAAATATCCCAAGTTATGGGTAGGATTTCTGAAGTGTGCTATCTTGACAAAACCTCAGTCATATGGTGTGTTGCTGCAGgttggcatgtttctgc-atc-tcttatgtgatctatttgttcttgttagttatgctcgattatcatcgagtt-attttacactgtctat-gctaatttacatatatgttttt--ttaataatcatcttgaaagattttcc---cgtgacatggcatatgttttttcag

upper sequence: Vv08s0105g00330.t01 (Vitis vinifera), 5'ss of exon 25
lower sequence: GRMZM2G086937_T02 (Zea mays), 5'ss of exon 1
----------------ATATGGAAATACCCAAAGTTATGGGTAGGATTCTTGAAGTGTGCACTCTTAACAAAGCCTCAGTCTTTCAGTGTGTTGCTGCAGgtgaaattctgtttgctatcataatttatgatttcttcttctctttggaaaactttcatttatgaaattttggaacagacaccaaccattacttatttttctctgattttttggctatcctttacactgaagaattatctgtttttgaacttgtat-tgatttttcag
                || |||||||| || |||||||||||||||||  ||||||||||  |||| ||||| |||||||| |   ||||||||||||||||     | | | ||| ||| |  | | |||| | ||  |   | |     |   ||  |||| |     |  |    ||||   | ||  || ||||   | |   |||||   ||    | |   ||||  ||| ||      |||  | | || || ||||||||
TCACTTGCCATGGTAGATTTGGAAATATCCCAAGTTATGGGTAGGATTTCTGAAGTGTGCTATCTTGACAAAACCTCAGTCATATGGTGTGTTGCTGCAGgttggcatgtttctgc-atc-tcttatgtgatctatttgttcttgttagttatgctcgattatcatcgagtt-attttacactgtctat-gctaatttacatatatgttttt--ttaataatcatcttgaaagattttcc---cgtgacatggcatatgttttttcag

upper sequence: Vv08s0105g00330.t01 (Vitis vinifera), 5'ss of exon 25
lower sequence: GLYMA01G30320.1 (Glycine max), 5'ss of exon 28
ATATGGAAATACCCAAAGTTATGGGTAGGATTCTTGAAGTGTGCACTCTTAACAAAGCCTCAGTCTTTCAGTGTGTTGCTGCAGgtgaaat-tctgtttgctatcataatttatgatttcttcttctctttggaaaactttcatttatgaaattttggaacagacaccaaccattacttatttttctctgattttttggctatcctttacactgaagaattatctgtttttgaacttgtattgatttttcag
|||||||||||||||||||||||||| ||||||||||||||||  |  || ||||| || ||||| ||  |  | ||||| |||||   || ||| ||  ||    | ||     | || || || |  ||     | | | |||| | || || ||| ||||     | | || | |     || | |                                                               
ATATGGAAATACCCAAAGTTATGGGTGGGATTCTTGAAGTGTGTGCAGTTGACAAAACCACAGTCATTTGGCATTTTGCTTCAGgtattatctctcttcactccttttatcaggaacttattattattatt-----attattattttttaacttatggcacagttgtaatctat-attctgcattatgta--------------------------------------------------------------

upper sequence: Vv08s0105g00330.t01 (Vitis vinifera), 5'ss of exon 25
lower sequence: GLYMA03G07790.1 (Glycine max), 5'ss of exon 25
ATATGGAAATACCCAAAGTTATGGGTAGGATTCTTGAAGTGTGCACTCTTAACAAAGCCTCAGTCTTTCAGTGTGTTGCTGCAGgtgaaattctgtttgctatcataatttatgattt-cttcttctctttggaaaactttcatttatgaaattttggaacagacaccaaccattacttatttttctctgattttttggctatcctttacactgaagaattatctgtttttgaacttgtattgatttttcag
|||||||||||||| ||||| ||||| ||||||||||||||||  |  || ||||| || ||||| ||  |  | ||||| |||||   ||  | | || |  |    ||||| ||   |||  |  ||||       |||  ||| | || || ||| ||||     || |  || |     |  ||                                                                
ATATGGAAATACCCTAAGTTGTGGGTGGGATTCTTGAAGTGTGTGCAGTTGACAAAACCACAGTCATTTGGCATTTTGCTTCAGgtattatcatctctgtttactccttttatcatgaacttaataactttttt---tttttttttttaaacttatggcacagttgt-aatctctattctgcatcatc----------------------------------------------------------------

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|56408967|gb|CX017219.1|CX017219
EST:     TGAAGTGTGCACTCTTAACAAAGCCTCAGTCTTTCAGTGTGTTGCTGCAG                         CTACCTCCAGCGCAGCTAGAGAATGCCCTCAATAGAACAGCAACACTTAAG
genomic: TGAAGTGTGCACTCTTAACAAAGCCTCAGTCTTTCAGTGTGTTGCTGCAGgtgaaattct ... gatttttcagCTACCTCCAGCGCAGCTAGAAAATGCCCTCAATAGAACAGCAGCACTTAAG
EST: gi|56409300|gb|CX017552.1|CX017552
EST:     TGAAGTGTGCACTCTTAACAAAGCCTCAGTCTTTCAGTGTGTTGCTGCAG                         CTACCTCCAGCGCAGCTAGAGAATGCCCTCAATAGAACAGCAGCACTTAAG
genomic: TGAAGTGTGCACTCTTAACAAAGCCTCAGTCTTTCAGTGTGTTGCTGCAGgtgaaattct ... gatttttcagCTACCTCCAGCGCAGCTAGAAAATGCCCTCAATAGAACAGCAGCACTTAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATGGAAATACCCAAAGTTATGGGTAGGATTCTTGAAGTGTGCACTCTTAACAAAGCCTCAGTCTTTCAGTGTGTTGCTGCAGgtgaaattctgtttgctatcataatttatgatttcttcttctctttggaaaactttcatttatgaaattttggaacagacaccaaccattacttatttttctctgattttttggctatcctttacactgaagaattatctgtttttgaacttgtattgatttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG