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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacatgatatgattactcacttccatttccagcttggtctaatatatgattcttataggtgtgtgattgatcttaacagAAAAAAATCAGCACCATGACTGCAAATGAATACTTTGAGAAGCATCCTGAGCTGAAGAAGAAGTTTGATGATGAAATCCGCAATGACTATTGGGGCTATT

Basic information

species Vitis vinifera
transcript Vv13s0019g03860.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0019g03860.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os08g37320.1 (Oryza sativa), 3'ss of exon 4
-----------------------------------------gtaacatgatatgattactca--cttccatt-tccagcttggtctaatatatgattcttataggtgtgtgattgatcttaacagAAAAAAATCAGCACCATGACTGCAAATGAATACTTTGAGAAGCATCCTGAGCTGAAGAAGAAGTTTGATGATGAAATCCGCAATGACTATTGGGGCTATT
                                          |  ||     || ||   ||  | |||||| |  ||     | |   || || || | | |  |   || || |  |  ||||||||| |||||||| ||||| ||| ||||||||||||  |||||||||||| | ||| ||||||| |||||||||||||| || ||| | |||||||| |
gtgaggatgatctctggcgaaacttgtatattgcagtccatttgtcagagattggttgtgcatgcatccattattaagagcatttttccatttgctt-taacatatacttg-ttcacgtatacagAAAAATATCAGCACAATGACAGCAGATGAATACTTTGCAAAGCATCCTGAGGTCAAGCAGAAGTTCGATGATGAAATCCGTAACGACAACTGGGGCTACT

upper sequence: Vv13s0019g03860.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G157018_T01 (Zea mays), 3'ss of exon 4
-------------------------gtaacatgatatgattactcacttccattt-ccagcttggtctaatatatgat------tcttataggtgtgtgattgatcttaacagAAAAAAATCAGCACCATGACTGCAAATGAATACTTTGAGAAGCATCCTGAGCTGAAGAAGAAGTTTGATGATGAAATCCGCAATGACTATTGGGGCTATT
                          |||    || |    | ||| |  |||||  |  | |  |  || | |  ||      ||   |   | | |  || || |  ||||||||| ||||| || ||||| ||| |||| |||||||||||| | ||||| || | |||||||||||| ||||||||||| || ||  | ||||| ||||
gtaggggatattcttcagtgttcatataattccatttccagaatcattagcatttatcgtcatttttaaagacaccataccctttcgctttaatatcttgtttatgtgtacagAAAAAGATCAGTACAATGACAGCAGATGATTACTTTGAGAAGTACCCTGAACTCAGGAAGAAGTTTGACGATGAAATCCGTAACGATAACTGGGGATATT

upper sequence: Vv13s0019g03860.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: AT3G52300.2 (Arabidopsis thaliana), 3'ss of exon 4
-------------------------------gtaacatgatatgattactcacttccatttccagcttggtctaatat-atgattcttataggtgtgtgattgatcttaacagAAAAAAATCAGCACCATGACTGCAAATGAATACTTTGAGAAGCATCCTGAGCTGAAGAAGAAGTTTGATGATGAAATCCGCAATGACTATTGGGGCTATT
                                | |  |  | ||  || |   || ||  || || ||    ||| || || ||  || |   | |||| ||| | | | ||||||||  ||||||||||||||||| |||| |||||||||||||| || || || || |||||||||||||| |||||||| |||||| | ||||| || |
gtaagtagccagaaaaaacaaatcctcttctatgaagtt-tgtgtgtattttttttcaactcaagattctgataaaatgatcatggttgtttctatgtg-ttggtgtaatcagAAAAAGCTCAGCACCATGACTGCAGATGAGTACTTTGAGAAGCACCCGGAACTCAAAAAGAAGTTTGATGACGAAATCCGTAATGACAACTGGGGATACT

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|71873778|gb|DT022833.1|DT022833
EST:     AGGAATCTGAGCGCCTGGAGAAAGAGATTGCTGAAGTCCAAGAGCTGAAG                         NNNNNNNTCAGCACCATGACTGCAAATGAATACTTTGAGAAGCATCCTGAG
genomic: AGGAATCTGAGCGCCTGGAGAAGGAGATTGCTGAAGTCCAAGAGCTGAAGgtaacatgat ... atcttaacagAAAAAAATCAGCACCATGACTGCAAATGAATACTTTGAGAAGCATCCTGAG
EST: gi|110389923|gb|EC954797.1|EC954797
EST:     AGGAATCTGAGCGCCTGGAGAAAGAGATTGCTGAAGTCCAAGAGCTGAAG                         AAAAAA-TCAGCACCATGACTGCAAATGAATACTTTGAGAAGCATCCTGAG
genomic: AGGAATCTGAGCGCCTGGAGAAGGAGATTGCTGAAGTCCAAGAGCTGAAGgtaacatgat ... atcttaacagAAAAAAATCAGCACCATGACTGCAAATGAATACTTTGAGAAGCATCCTGAG
EST: gi|30325219|gb|CD008481.1|CD008481
EST:     AGGAATCTGAGCGCCTGGAGAAAGAGATTGCTGAAGTCCAAGAGCTGAAG                         NNNNNNNTCAGCACCATGACTGCAAATGAATACTTTGAGAAGCATCCTGAG
genomic: AGGAATCTGAGCGCCTGGAGAAGGAGATTGCTGAAGTCCAAGAGCTGAAGgtaacatgat ... atcttaacagAAAAAAATCAGCACCATGACTGCAAATGAATACTTTGAGAAGCATCCTGAG
EST: gi|77577878|gb|DV217689.1|DV217689
EST:     AGGAATCTGAGCGCCTGGAGAAAGAGATTGCTGAAGTCCAAGAGCTGAAG                         NNNNNNNTCAGCACCATGACTGCAAATGAATACTTTGAGAAGCATCCTGAG
genomic: AGGAATCTGAGCGCCTGGAGAAGGAGATTGCTGAAGTCCAAGAGCTGAAGgtaacatgat ... atcttaacagAAAAAAATCAGCACCATGACTGCAAATGAATACTTTGAGAAGCATCCTGAG
EST: gi|110430091|gb|EC996620.1|EC996620
EST:     AGGAATCTGAGCGCCTGGAGAAGGAGATTGCTGAAGTCCAAGAGCTGAAG                         NNNNNNNTCAGCACCATGACTGCAAATGAATACTTTGAGAAGCATCCTGAG
genomic: AGGAATCTGAGCGCCTGGAGAAGGAGATTGCTGAAGTCCAAGAGCTGAAGgtaacatgat ... atcttaacagAAAAAAATCAGCACCATGACTGCAAATGAATACTTTGAGAAGCATCCTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttccagcttggtctaatatatgattcttataggtgtgtgattgatcttaacagAAAAAAATCAGCACCATGACTGCAAATGAATACTTTGAGAAGCATCCTGAGCTGAAGAAGAAGTTTGATGATGAAATCCGCAATGACTATTGGGGCTATT
               taatatatgattctta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacatgatatgattactcacttccatttccagcttggtctaatatatgattcttataggtgtgtgattgatcttaacagAAAAAAATCAGCACCATGACTGCAAATGAATACTTTGAGAAGCATCCTGAGCTGAAGAAGAAGTTTGATGATGAAATCCGCAATGACTATTGGGGCTATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT