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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agactggcttgtgaattgtgatacagtgtgtaccatctacactcattttgcctgtcttcatggcttacactgtaaatctcttttgcattgtcttttacagAGAGAGTATGAGGAATTTAAAGTTCGGATTAATGCCTTGGTTGCCAAAGCTCAAAAGGTCCCAGAAGAAGGGTGGACAATGCAGGATGGGACGCCTTGGC

Basic information

species Vitis vinifera
transcript Vv03s0038g04250.t01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os07g14850.1 (Oryza sativa), 3'ss of exon 6
agactggcttgtgaattgtgatacagtgtgtaccatctacactcattttgcctgtcttcatggcttacactgtaaatctcttttgcattgtcttttacagAGAGAGTATGAGGAATTTAAAGTTCGGATTAATGCCTTGGTTGCCAAAGCTCAAAAGGTCCCAGAAGAAGGGTGGACAATGCAGGATGGGACGCCTTGGC
 |      |  | | ||||      |||  |  |  || |  | ||| |   | | || || |||        || | |  ||| |||         |||||||| ||||||||||| || ||  |||| || ||||||||||||||||| |||||||| ||||| ||||| |||||||||||||| || |  |||||||
-gtagatgtcctcatttgt----tcgtgcttttctact-cgattattctttttatatt-atagctagttacacaagtttaattttcatc--------cagAGAGATTATGAGGAATTCAAGGTGAGGATCAACGCCTTGGTTGCCAAAGCCCAAAAGGTTCCAGAGGAAGGATGGACAATGCAGGACGGAAGCCCTTGGC

upper sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: LOC_Os07g24190.1 (Oryza sativa), 3'ss of exon 7
agactggcttgtgaattgtgatacagtgtgtaccatctacact--cattttgcctgtcttcatggcttacactgtaaatctcttttgcattgtcttttacagAGAGAGTATGAGGAATTTAAAGTTCGGATTAATGCCTTGGTTGCCAAAGCTCAAAAGGTCCCAGAAGAAGGGTGGACAATGCAGGATGGGACGCCTTGGC
                 ||||   | || ||   |   | | |   ||||    ||  || || | | ||| |   |||          ||||||||| |||||||||||||||||||| || ||  | || ||||| |||||||| |||||||| || || || || ||||| ||||||||||| ||||| || || ||||
-----------------gtgaataattgggtcttaaaaaaattgctatttgttttgattttatag-taacatt---aattaggccaagcttgtctttt-cagAGAGAGTATGAGGAATTCAAGGTGAGAATCAATGCATTGGTTGCTAAAGCTCAGAAAGTTCCCGAGGAAGGTTGGACAATGCAAGATGGAACTCCCTGGC

upper sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G113137_T01 (Zea mays), 3'ss of exon 7
agactggcttgtgaattgtgatacagtgtgtaccatctacactcattttgcctgtcttcatggcttacactgtaaatctcttttgcattgtcttttacagAGAGAGTATGAGGAATTTAAAGTTCGGATTAATGCCTTGGTTGCCAAAGCTCAAAAGGTCCCAGAAGAAGGGTGGACAATGCAGGATGGGACGCCTTGGC
      |      | ||||       | | ||||   |      ||  |   |||  | |   ||       |  |   |  |   ||| | ||   |||||||||||||||||||| || ||  | || |||||||||||||| ||||| |||||||| || || ||||| ||||||||||||||||| || || ||||
------gtgcactatttgtacctttttat-tacctcttgatacaatcctttatgttgtaagcactgtgctaatttagggcagtcttattattttcc-cagAGAGAGTATGAGGAATTCAAGGTCAGAATCAATGCCTTGGTTGCTAAAGCCCAAAAGGTTCCTGAGGAAGGATGGACAATGCAGGATGGAACTCCATGGC

upper sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G082580_T01 (Zea mays), 3'ss of exon 5
agactggcttgtgaattgtgatacagtgtgtaccatctacactcattttgcctgtcttcatggcttacactgtaaatctcttttgcattgtcttttacagAGAGAGTATGAGGAATTTAAAGTTCGGATTAATGCCTTGGTTGCCAAAGCTCAAAAGGTCCCAGAAGAAGGGTGGACAATGCAGGATGGGACGCCTTGGC
          ||    ||| || | ||||    | | |     || ||| |     |  |||      |  || |     ||||| ||| || ||  |||||||| ||||||||||| || ||  |||| |||||||||||||| ||||| |||||||| || || ||||| ||||||||||| ||||| |  |  ||||
----------gtacgatgttatcctgtgttatgcttttctgtgcaatttcctaacttgtatgaacaggatagttacatggttttg-attttcatt--cagAGAGAATATGAGGAATTCAAGGTAAGGATCAATGCCTTGGTTGCAAAAGCCCAAAAGGTACCCGAGGAAGGATGGACAATGCAAGATGGAAGCCTCTGGC

upper sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G177631_T01 (Zea mays), 3'ss of exon 5
agactggcttgtgaattgtgatacagtgtgtaccatctacactcattttgcctgtcttcatggcttacactgtaaatctcttttgcattgtctttta--cagAGAGAGTATGAGGAATTTAAAGTTCGGATTAATGCCTTGGTTGCCAAAGCTCAAAAGGTCCCAGAAGAAGGGTGGACAATGCAGGATGGGACGCCTTGGC
            | |   || |  |   ||||  ||          |     |  ||   | |  |  || |   |  |   | || ||||  || |  |||||||| || |||||||| || ||  |||| |||||||||||||| ||||| |||||||| || || ||||| ||||||||||| ||||| |  || ||||
------------gtaccatgtt-tatcctgtattatgcttttctggtgcaatttcctatcttgtatgaacaggctagttacatggctttgttcttcattcagAGAGAATACGAGGAATTCAAGGTAAGGATCAATGCCTTGGTTGCAAAAGCCCAAAAGGTTCCTGAGGAAGGATGGACAATGCAAGATGGAAGCCCCTGGC

upper sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G025231_T02 (Zea mays), 3'ss of exon 7
agactggcttgtgaattgtgatacagtgtgtaccatctacactcattttgcctgtcttcatggcttacactgtaaatctcttttgcattgtcttttacagAGAGAGTATGAGGAATTTAAAGTTCGGATTAATGCCTTGGTTGCCAAAGCTCAAAAGGTCCCAGAAGAAGGGTGGACAATGCAGGATGGGACGCCTTGGC
    ||  || |   |  |  |      |||    |||    |  ||  |  | | || ||           |||| |   |||| ||  | ||   |||||||||||||||||||| || ||  | || |||||||| ||||||||||| || || || || |||||||| ||||||||||| ||||| || || ||||
---gtgctttatttgtccttttctttaatgtgttgtctggtattgttaagagtatgttaat-----------taaaccaagtttggataatttt---cagAGAGAGTATGAGGAATTCAAGGTGAGAATCAATGCCTTAGTTGCCAAAGCCCAGAAAGTTCCTGAAGAAGGATGGACAATGCAAGATGGAACCCCCTGGC

upper sequence: Vv03s0038g04250.t01 (Vitis vinifera), 3'ss of exon 7
lower sequence: GRMZM2G028353_T02 (Zea mays), 3'ss of exon 7
agactggcttgtgaattgtgatacagtgtgtaccatctacactcattttgcctgtcttcatggcttacactgtaaatctcttttgcattgtcttttacagAGAGAGTATGAGGAATTTAAAGTTCGGATTAATGCCTTGGTTGCCAAAGCTCAAAAGGTCCCAGAAGAAGGGTGGACAATGCAGGATGGGACGCCTTGGC
    ||  || |   |  |  |      |||    ||    |  ||  |   |||  | |  |  |      |||| |   |||| ||| | |||   |||||||||| |||||||| || ||  | || |||||||||||||| ||||| || || || || |||||||| ||||||||||| ||||| || || ||||
---gtgctttatttgtccttttctttaatgtgttgtcc---cctatcctatttgt--taagagtatgttaattaaaccaagtttggattattttt---agAGAGAGTACGAGGAATTCAAGGTCAGAATCAATGCCTTGGTTGCTAAAGCCCAGAAAGTTCCTGAAGAAGGATGGACAATGCAAGATGGAACCCCCTGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgcctgtcttcatggcttacactgtaaatctcttttgcattgtcttttacagAGAGAGTATGAGGAATTTAAAGTTCGGATTAATGCCTTGGTTGCCAAAGCTCAAAAGGTCCCAGAAGAAGGGTGGACAATGCAGGATGGGACGCCTTGGC
                ggcttac  putative branch site (score: 3)
                                          ttgtctttt  putative PPT
                         tgtaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agactggcttgtgaattgtgatacagtgtgtaccatctacactcattttgcctgtcttcatggcttacactgtaaatctcttttgcattgtcttttacagAGAGAGTATGAGGAATTTAAAGTTCGGATTAATGCCTTGGTTGCCAAAGCTCAAAAGGTCCCAGAAGAAGGGTGGACAATGCAGGATGGGACGCCTTGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - gcttgtg
- - - - - - - - - - - - - - - - - - - acactca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggctta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cactgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcattg