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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttctattcaaaactgaaaagttaatgtatataatctgttggcatgctattaaaagcgagcaagggatggcttcaattgctaagacttacctttgattttttttgttagCCTGAGTGGATGGCACCAGAAGTTCTCCGTGATGAGCCATCAAATGAAAAGTCAGATGTTTACAGCTTTGGTGTAATCTTGTGGGAACTTGTGACCTTGC

Basic information

species Vitis vinifera
transcript Vv13s0074g00430.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0074g00430.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os02g32610.3 (Oryza sativa), 3'ss of exon 13
gtaagttctattcaaaactgaaaagttaatgtatataatctgttggcatgctattaaaagcgagcaagggatggcttcaat--tgctaagacttacctttgattt--tttttgttagCCTGAGTGGATGGCACCAGAAGTTCTCCGTGATGAGCCATCAAATGAAAAGTCAGATGTTTACAGCTTTGGTGTAATCTTGTGGGAACTTGTGACCTTGC
                        || | |  |||| | | |||      || |||   |           |    | |||  |||||  |  | | || ||| |  | ||   ||||||||||||||||||||||||||| | || ||||||||||||||||| ||||| ||||| |||||||||||||| ||| | ||||| ||  |||| ||||
------------------------gtaagttcatattacc-gtta-----cttttatttgttgattttttttcagctaaatcgtgctagtaagtgctttcgatgtaatattctctagCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAGTCTGATGTCTACAGCTTTGGTGTTATCCTATGGGAGCTCATGACATTGC

upper sequence: Vv13s0074g00430.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os09g39320.1 (Oryza sativa), 3'ss of exon 13
gtaagttctatt--caaaactgaaaagttaatgtatataatctgttggcatgctattaaaagcg--agcaagggatggcttcaattgctaagacttacctttgattttttttgttagCCTGAGTGGATGGCACCAGAAGTTCTCCGTGATGAGCCATCAAATGAAAAGTCAGATGTTTACAGCTTTGGTGTAATCTTGTGGGAACTTGTGACCTTGC
|||||| | |||  ||    | | ||||| |    |  ||||  ||    |   ||| |||     |   |    ||||||   |||       ||   |||   |||   | |||||| || ||||||||||| ||||| ||||| ||||| ||||| ||||| || || ||||| ||||| |||||||||||| | ||||||||| ||||  |||
gtaagtaccatttccattcttcagaagttcaccctt-caatccctt----tttcattgaaaatattattcatctttggcttatcttg-------ttctttttccatttaaatattagCCCGAATGGATGGCACCTGAAGTGCTCCGAGATGAACCATCCAATGAGAAATCTGATGTCTACAGTTTTGGTGTAATCCTATGGGAACTTATGACAATGC

upper sequence: Vv13s0074g00430.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G059671_T04 (Zea mays), 3'ss of exon 12
gtaagttctattcaaaactgaaaagttaatgtatataatctgttggcatgctattaaaagcgagcaagggatggcttcaattgctaagacttacctttgattttttttgttagCCTGAGTGGATGGCACCAGAAGTTCTCCGTGATGAGCCATCAAATGAAAAGTCAGATGTTTACAGCTTTGGTGTAATCTTGTGGGAACTTGTGACCTTGC
                          |||  |||||  |    |    || ||||          | |  ||    |   | ||||||  |||   |      |  |   ||||||||||||||||||||||||||||| || || ||||| |||||||| ||||| |||||||||||||| ||||||||||| ||||| ||| |||| ||||
-------------------------gtaagttatattgttccgtttagtg-tattttgttttgttacgcaat--tctatgtggctaagtgttattctgtgccatgctatctagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGC

upper sequence: Vv13s0074g00430.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G036902_T01 (Zea mays), 3'ss of exon 1
gtaagttctattcaaaactgaaaagttaatgtatataatctgttggcatgctattaaaagcgagcaagggatggcttcaattgctaagacttacctttgattttttttgttagCCTGAGTGGATGGCACCAGAAGTTCTCCGTGATGAGCCATCAAATGAAAAGTCAGATGTTTACAGCTTTGGTGTAATCTTGTGGGAACTTGTGACCTTGC
                                 ||  | |   |   |   | || ||      |      ||   |   ||||   |  | | | |   ||||   | | ||||||| ||||||||||| ||||| || || ||||| ||||| ||||| || || ||||| || ||||| ||||| ||| | ||||||||  ||||  |||
--------------------------------gtaagagcctcttcaactttttttaagttcccctttcactgaaat---ttgccttgtataatcctgtcttttaaatatcagCCTGAATGGATGGCACCTGAAGTGCTTCGAGATGAACCATCCAATGAGAAATCTGATGTCTATAGCTTCGGTGTTATCCTATGGGAACTAATGACACTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agcgagcaagggatggcttcaattgctaagacttacctttgattttttttgttagCCTGAGTGGATGGCACCAGAAGTTCTCCGTGATGAGCCATCAAATGAAAAGTCAGATGTTTACAGCTTTGGTGTAATCTTGTGGGAACTTGTGACCTTGC
                                   cctttgatttttttt  CT-rich tract
                                     tttgattttttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttctattcaaaactgaaaagttaatgtatataatctgttggcatgctattaaaagcgagcaagggatggcttcaattgctaagacttacctttgattttttttgttagCCTGAGTGGATGGCACCAGAAGTTCTCCGTGATGAGCCATCAAATGAAAAGTCAGATGTTTACAGCTTTGGTGTAATCTTGTGGGAACTTGTGACCTTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG