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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatggttgagatgaccacctttcctttctagtgactctaggaatctaaatttcttcctttctagcatccctcattcttttttaagcagtattaatttaaatatatgtagctaagacagcactagtgcagGTTCAAACCATTCGACAAGGATATCTTTCAAAACGTTCCTCAAATTTGAGGGGTGACTGGAAGAGAAGGTTCTTTGTTCTTGATAGCCGAGGCATGTTGT

Basic information

species Vitis vinifera
transcript Vv17s0000g00310.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g00310.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 11
gtaatggttgagatgaccacctttcctttctagtgactctaggaatctaaatttcttcctttctagcatccctcattcttttttaagcagtattaatttaaatatatgtagctaagacagcact-agtgcagGTTCAAACCATTCGACAAGGATATCTTTCAAAACGTTCCTCAAATTTGAGGGGTGACTGGAAGAGAAGGTTCTTTGTTCTTGATAGCCGAGGCATGTTGT
                         | |||| ||    || | | |  | | |  | | | | |     | |    ||   ||| |||| |   |||| |  |  || |    |||  || ||| | | ||||| || |||||||||||||| ||||| ||||| || || ||||| ||||| ||||||||||| ||||||||||||||||||||||||||||| ||||| |
-------------------gtagcacattctggttgtcctggaagttaatactcttgcttatgtctacgctcaggctcacatttcagca-tggaaattcatgt-catattttaaagtgagtacttatttcagGTACAGACCATTCGACAAGGCTATCTCTCAAAGCGATCTTCAAACTTGAGAGGTGACTGGAAAAGAAGGTTCTTTGTTCTTGATAGCCGAGGAATGTTAT

upper sequence: Vv17s0000g00310.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G059225_T02 (Zea mays), 3'ss of exon 11
gtaatggttgagatgaccacctttcctttctagtgactctaggaatctaaatttcttcctttctagcatccctcattcttttttaagcagtattaatttaaatatatgtagctaagacagcactagtgcagGTTCAAACCATTCGACAAGGATATCTTTCAAAACGTTCCTCAAATTTGAGGGGTGACTGGAAGAGAAGGTTCTTTGTTCTTGATAGCCGAGGCATGTTGT
                           | || |  |||||   ||   ||  ||| | | | |  | ||     | | |  |  ||| ||    |  ||  |||     |  ||||  |  | |  | |||||||| |||||||| ||||| ||||| || ||  | || ||||| ||||| ||||| ||||| || ||||||||||| || || || ||||| |||||||
---------------------------tgctgg-aactctccaaagacaatattcatgcatgcatg-attaagtaatttcataaaagaagatgcatgttttatactgaaacgtaaggaactatt--ttcagGTTCAGACCATTCGCCAAGGCTATCTATCTAAGAGATCTTCAAACTTGAGAGGTGATTGGAAAAGGAGGTTCTTTGTCCTCGACAGTCGAGGAATGTTGT

upper sequence: Vv17s0000g00310.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM5G872204_T01 (Zea mays), 3'ss of exon 8
gtaatggttgagatgaccacctttcctttctagtgactctaggaatctaaatttcttcctttctagcatccctcattcttttttaagcagtattaatttaaatatatgta-gctaagacagcactagtgcagGTTCAAACCATTCGACAAGGATATCTTTCAAAACGTTCCTCAAATTTGAGGGGTGACTGGAAGAGAAGGTTCTTTGTTCTTGATAGCCGAGGCATGTTGT
                                       || ||  |  |   ||       || |    ||  |     |||    |||| | ||   ||| |  |  | | | |   |  |||  | |||||  | ||||| || ||||| |||||||| ||| | || ||||| ||||| |  |||||||| ||||||||||| || |||||||| ||||| ||| |||
--------------------------------------gtaagacaccgatagtccaatacactggagatccaaagcaggttt---acagtttgaaaaaaaaaagttaaatggtgatgtactact--tccagGTAGAGACCATCCGTCAAGGTTATCTTTCGAAAAGATCTTCAAACTTGAGAGCCGACTGGAAAAGAAGGTTCTTCGTACTTGATAGTCGAGGAATGCTGT

upper sequence: Vv17s0000g00310.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA04G37780.1 (Glycine max), 3'ss of exon 11
gtaatggttgagatgaccacctttcctttctagtgactctaggaatctaaatttcttc-ctttctagcatccctcattcttttttaagcagtattaatttaaatatatgtagctaagacagcacta-gtgcagGTTCAAACCATTCGACAAGGATATCTTTCAAAACGTTCCTCAAATTTGAGGGGTGACTGGAAGAGAAGGTTCTTTGTTCTTGATAGCCGAGGCATGTTGT
                          | | ||  |||   | ||  ||  |    ||| |||  |   ||      ||| ||| | ||   |||| | |   || | |  | ||      ||||||  |  ||||||||| ||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||  |||||||||||||| || || ||| | |
-------------------------gtatttaaggacataatgatgcttcacactttcacttcattctatatagttttcatttatgagtcctatttact--gatctctccatct------gcactacatttagGTTCAAATCATTCGACAAGGATATCTTTCAAAACGGTCCTCAAATTTGAGGGGTGACTGGAAGAGAAGGTATTTTGTTCTTGATAGTCGCGGAATGCTTT

upper sequence: Vv17s0000g00310.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA06G17300.1 (Glycine max), 3'ss of exon 12
gtaatggttgagatgaccacctttcctttctagtgactctaggaatctaaatttcttcctttctagcatccctcattcttttttaagcagtattaatttaaatatatg-tagctaagacagcactagt-gcagGTTCAAACCATTCGACAAGGATATCTTTCAAAACGTTCCTCAAATTTGAGGGGTGACTGGAAGAGAAGGTTCTTTGTTCTTGATAGCCGAGGCATGTTGT
                                  |  | || | |  |||   | || |  |||    | |   ||    |        |||| | |   | | | || |  |     | |||||| | | ||||||||| |||||||||||||| |||||||||||| ||| ||||| ||||||||||||||||||||||||  |||||||||||||               
----------------------------------gtatttaaggacataatgatgtttcactct----ttctctatgtactcacgtcatgtatgagtcctattctctgatctcgccatctgcactacttgtagGTTCAAATCATTCGACAAGGATTTCTTTCAAAACGGTCCACAAATCTGAGGGGTGACTGGAAGAGAAGGTATTTTGTTCTTGATA---------------

upper sequence: Vv17s0000g00310.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA05G38550.1 (Glycine max), 3'ss of exon 11
gtaatggttgagatgaccacctttcctttctagtgactctaggaatctaaatttcttcctttctagcatccctcattcttttttaagcagtattaatttaaatatatgtagctaagacagcactagtgcagGTTCAAACCATTCGACAAGGATATCTTTCAAAACGTTCCTCAAATTTGAGGGGTGACTGGAAGAGAAGGTTCTTTGTTCTTGATAGCCGAGGCATGTTGT
    |  || |||     || |||||||  |  |||   |     | |  ||| |||| |||  |   |     |||||   || ||   | |  |||    | | |  | |   |   |||  | |  ||||||||| ||||||||||||||||||||| ||||| ||||| |||||||| ||||||||||| |||||||  |||||| |||| || ||||| |||||||
---gtattttagaatttgacgtttccttctttctgagatt-----tatgtattacttcattttaaaacttttcaattctgagttgagtcctgtccattgccgtttcttcatc---gcttgcaaaattttagGTTCAAATCATTCGACAAGGATATCTTTCTAAACGATCCTCCAATTTGAGAGGTGACTGGAAAAGAAGGTATTTTGTTGTTGACAGTCGAGGAATGTTGT

upper sequence: Vv17s0000g00310.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT5G61980.1 (Arabidopsis thaliana), 3'ss of exon 11
gtaatggttgagatgaccacctttcctttctagtgactctaggaatctaaatttcttcctttctagcatccctcattcttttttaagcagtattaatttaaatatatgtagctaagacagcactagtgcagGTTCAAACCATTCGACAAGGATATCTTTCAAAACGTTCCTCAAATTTGAGGGGTGACTGGAAGAGAAGGTTCTTTGTTCTTGATAGCCGAGGCATGTTGT
                          |    |   |   |  | ||  |   ||  || |  | | |  |  |||  | | ||||  |  | ||  |||| || ||| | | | | | | |  |  | |||||||| || ||  ||||||| ||||| || |||||||||||||| ||||| ||||||||||| ||||| |||||| | ||||||||||| || ||| | |
-------------------------gtaaggaaatatcttttgtattgaggcttactcgt--caaactgctgtca--catctttatactctcttgttttatatttatct-gttgatataactgttcttcagGTTCAGACTATCAGACAAGGGTATCTGTCTAAACGTTCCTCAAACTTGAGAGGTGACTGGAAAAGAAGATTCTTTATCCTTGATAGCCGTGGGATGCTAT

upper sequence: Vv17s0000g00310.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: PP1S249_58V6.1 (Physcomitrella patens), 3'ss of exon 6
gtaatggtt-gagatgaccacctttcctt-tctagtgactctaggaatctaaatttcttcctttctagcatccctcattcttttttaagcagtattaatttaaatatatgtagctaagacagcactagtgcagGTTCAAACCATTCGACAAGGATATCTTTCAAAACGTTCCTCAAATTTGAGGGGTGACTGGAAGAGAAGGTTCTTTGTTCTTGATAGCCGAGGCATGTTGT
|||    || ||| |||  |  | |   | | ||||  || || ||  |    ||    |       |||  |||  || |  ||       |||   ||||  | | | |   |        |||  |  || | ||||||||    ||||||||  |||  || ||||||||||||||||| |||||||||||| ||||||| ||||| || |||||  | || |||||||
gtaggaatttgagctgaggaattctaaatatgtagttgct-tacgatacgggcttaaagctgaaaacgcagacctttttatccttatttacatatctgtttatttttttcttttt-------tact--tatagATACAAACCATCAAGCAAGGATACATTTTGAAGCGTTCCTCAAATTTGAGAGGTGACTGGAAGCGAAGGTTTTTTGTGCTGGATAGTAGGGGAATGTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttttttaagcagtattaatttaaatatatgtagctaagacagcactagtgcagGTTCAAACCATTCGACAAGGATATCTTTCAAAACGTTCCTCAAATTTGAGGGGTGACTGGAAGAGAAGGTTCTTTGTTCTTGATAGCCGAGGCATGTTGT
              tattaat  putative branch site (score: 2)
     tttaagcagtattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatggttgagatgaccacctttcctttctagtgactctaggaatctaaatttcttcctttctagcatccctcattcttttttaagcagtattaatttaaatatatgtagctaagacagcactagtgcagGTTCAAACCATTCGACAAGGATATCTTTCAAAACGTTCCTCAAATTTGAGGGGTGACTGGAAGAGAAGGTTCTTTGTTCTTGATAGCCGAGGCATGTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA