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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgaagaagcttataagttattaaggaacttcttttatagatacttatcaaaaaaaaaaaaaaggaacttcttttatagatcctctttattttcttgatgttccttgtatttctagttgttttttgtttccgtgtctgaataacaatatttcagGTTCAAACCATCCGACAAGGTTACCTCTCAAAACGCTCCTCAAACCTGAGAGGTGACTGGAAAAGAAGGTTTTTTGTTCTTGATAGCCGAGGAATGCTAT

Basic information

species Vitis vinifera
transcript Vv01s0150g00030.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0150g00030.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os09g33600.1 (Oryza sativa), 3'ss of exon 11
gtctgaagaagcttataagttattaaggaacttcttttatagatacttatcaaaaaaaaaaaaaaggaacttcttttatagatcctctttattttcttgatgttccttgtatttctagttgttttttgtttccgtgtctgaataacaatatttcagGTTCAAACCATCCGACAAGGTTACCTCTCAAAACGCTCCTCAAACCTGAGAGGTGACTGGAAAAGAAGGTTTTTTGTTCTTGATAGCCGAGGAATGCTAT
                                    |   | || ||  |        ||   ||    |||  || ||   | | ||     |     |  || |  | ||    | |  | |  | |||    ||  || ||    |||||||||| || ||||| |||||||| || |||||||| || || |||||| ||||||||||||||||||||||||| |||||||||||||||||||||||| |||
-----------------------------------gtagcacattctggttgtcctggaagttaatactcttgctt-atgtctacgctcaggctc----acatttca-gcatggaaattcatgtcatattttaaagt--gagtact--tatttcagGTACAGACCATTCGACAAGGCTATCTCTCAAAGCGATCTTCAAACTTGAGAGGTGACTGGAAAAGAAGGTTCTTTGTTCTTGATAGCCGAGGAATGTTAT

upper sequence: Vv01s0150g00030.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os08g42530.1 (Oryza sativa), 3'ss of exon 11
gtctgaagaagcttataagttattaaggaacttcttttatagatacttatcaaaaaaaaaaaaaaggaacttcttttatagatcctctttattttcttgatgttccttgtatttctagttgttttt-tgtttccgtgtctgaataacaatat---ttcagGTTCAAACCATCCGACAAGGTTACCTCTCAAAACGCTCCTCAAACCTGAGAGGTGACTGGAAAAGAAGGTTTTTTGTTCTTGATAGCCGAGGAATGCTAT
                                                                              ||   | || |  ||  || |   ||     |   |  ||   || |  |  |  | |  |||||  | | |||   ||||||| || ||||| || |||||||||||||| ||| | || |||||| |||||| ||| |||||||||||||||||||| |||||||| ||||||||||| |
-----------------------------------------------------------------------------gtaccacttcctggttcactaggaattaaagcttcatgcagacattctagtactgtcattcctgaaacaaagtatatgttcagGTCCAGACCATTCGTCAAGGTTACCTCTCGAAAAGATCTTCAAACTTGAGAGCTGATTGGAAAAGAAGGTTTTTTGTCCTTGATAGTCGAGGAATGCTGT

upper sequence: Vv01s0150g00030.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM5G872204_T01 (Zea mays), 3'ss of exon 8
gtctgaagaagcttataagttattaaggaacttcttttatagatacttatcaaaaaaaaaaaaaaggaacttcttttatagatcctctttattttcttgatgttccttgtatttctagttgttttttgtttccgtgtctgaataacaatatttcagGTTCAAACCATCCGACAAGGTTACCTCTCAAAACGCTCCTCAAACCTGAGAGGTGACTGGAAAAGAAGGTTTTTTGTTCTTGATAGCCGAGGAATGCTAT
                                                               |||  ||   |  |  | || | ||  |  | |          |    |||  |         |      |||  || |  ||    || |||||  | |||||||| |||||||| || || ||| | || |||||| ||||||  ||||||||||||||||| || || |||||||| ||||||||||| |
-------------------------------------------------------------gtaagacaccgatagtcca-atacactggagatccaaagcaggtttacagtttgaaaaaaaaaagttaaatggtga-tgtactac----ttccagGTAGAGACCATCCGTCAAGGTTATCTTTCGAAAAGATCTTCAAACTTGAGAGCCGACTGGAAAAGAAGGTTCTTCGTACTTGATAGTCGAGGAATGCTGT

upper sequence: Vv01s0150g00030.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G059225_T02 (Zea mays), 3'ss of exon 11
gtctgaagaagcttataagttattaaggaacttcttttatagatacttatcaaaaaaaaaaaaaaggaacttcttttatagatcctctt-tattttcttgatgttccttgtatttctagttgttttttgtttccgtgtctgaataacaatatttcagGTTCAAACCATCCGACAAGGTTACCTCTCAAAACGCTCCTCAAACCTGAGAGGTGACTGGAAAAGAAGGTTTTTTGTTCTTGATAGCCGAGGAATGCTAT
                                     |   |  |||   |||| | || |         ||| |  ||  ||  |    || |||| | |       || ||        ||||| |  |     ||   |  ||| || ||||||||||| ||||| || ||||| || || || ||  | || |||||| |||||||||| |||||||| ||||| ||||| || || || ||||||||| | |
-------------------------------------tgctggaactctccaaagacaata---------ttcatgcatgcatgattaagtaatttcataaaagaagatgcat--------gttttatactgaaacgt--aaggaactat-tttcagGTTCAGACCATTCGCCAAGGCTATCTATCTAAGAGATCTTCAAACTTGAGAGGTGATTGGAAAAGGAGGTTCTTTGTCCTCGACAGTCGAGGAATGTTGT

upper sequence: Vv01s0150g00030.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA18G51810.1 (Glycine max), 3'ss of exon 11
gtctgaagaagcttataagttattaaggaacttcttttatagatacttatcaaaaaaaaaaaaaaggaacttcttttatagatcctctttattttcttgatgttccttgtatttctagttgttttttgtttccgtgtctgaataacaatatttcagGTTCAAACCATCCGACAAGGTTACCTCTCAAAACGCTCCTCAAACCTGAGAGGTGACTGGAAAAGAAGGTTTTTTGTTCTTGATAGCCGAGGAATGCTAT
                                                           ||   |||        || | |||     |||||  | |    || ||  || |  | |   ||| |  | | | |||||   |  ||  |||| |||||||||| || ||||||||||| |||||||| || ||||||||| | || || ||||||||||| || ||||||||||||||||| || |||||||| |
-------------------------------------------------------gttgaattgaggcctggaaattgttgattgaagttattaacatttactttctcctagtggttgacttttataatattcttgtct---tttcatcattttagGTTCAAACTATTCGACAAGGTTATCTCTCAAAGCGTTCCTCAAACTTAAGGGGGGACTGGAAAAGGAGATTTTTTGTTCTTGATAGTCGGGGAATGCTGT

upper sequence: Vv01s0150g00030.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA08G28890.2 (Glycine max), 3'ss of exon 11
gtctgaagaagcttataagttattaaggaacttcttttatagatacttatcaaaaaaaaaaaaaaggaacttcttttatagatcctctttattttcttgatgttccttgtatttctagttgttttttgtttccgtgtctgaataacaatatttcagGTTCAAACCATCCGACAAGGTTACCTCTCAAAACGCTCCTCAAACCTGAGAGGTGACTGGAAAAGAAGGTTTTTTGTTCTTGATAGCCGAGGAATGCTAT
                                                           ||   |||        || | |||     |||||  |      || ||   | |  | |   ||| |   || | |||||   || ||  |||| |||||||||| || ||||||||||| |||||||| || ||||| ||| | || || ||||||||||| || ||||||||||||||||| || |||||||| |
-------------------------------------------------------gttgaattgaggcctggaaattgttgattgaagttattaacaattactttctcccagtggttgacttttataactttcttgtct---tatcatcattttagGTTCAAACTATTCGACAAGGTTATCTCTCAAAGCGTTCCTCTAACTTAAGGGGGGACTGGAAAAGGAGATTTTTTGTTCTTGATAGTCGGGGAATGCTGT

upper sequence: Vv01s0150g00030.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT5G13300.1 (Arabidopsis thaliana), 3'ss of exon 11
gtctgaagaagcttataagttattaaggaacttcttttatagatacttatcaaaaaaaaaaaaaaggaacttcttttatagatcctctttattttcttgatgttccttgtatttctagttgttttttgtttccgtgtctgaataacaatatttcagGTTCAAACCATCCGACAAGGTTACCTCTCAAAACGCTCCTCAAACCTGAGAGGTGACTGGAAAAGAAGGTTTTTTGTTCTTGATAGCCGAGGAATGCTAT
                                                                              | ||||  | |  ||  | | ||| |   |  || |      |  |  | ||  | | |||   |       |||||||| ||||| ||  | |||||||| ||||| ||||| || |||||||||||||| ||||||||||||||||||||||||||||| ||||| |||||||| |
-----------------------------------------------------------------------------gttgatcaacgtctttaacat-atgattgatacatcttccagagagtactattaacatttcttggtgc-----tttcagGTGCAAACAATAAGGCAAGGTTATCTCTCTAAACGATCTTCAAACCTGAGAGGAGACTGGAAAAGAAGGTTTTTTGTTCTTGACAGCCGGGGAATGCTCT

upper sequence: Vv01s0150g00030.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: PP1S249_58V6.1 (Physcomitrella patens), 3'ss of exon 6
gtctgaagaagcttataagttattaaggaacttcttttatagatacttatcaaaaaaaaaaaaaaggaacttcttttatagatcctctttattttcttgatgttccttgtatttctagttgttttttgtttccgtgtctgaataacaatatttcagGTTCAAACCATCCGACAAGGTTACCTCTCAAAACGCTCCTCAAACCTGAGAGGTGACTGGAAAAGAAGGTTTTTTGTTCTTGATAGCCGAGGAATGCTAT
    | || |  ||         | ||||| |   |  |||  || ||    |  | |         | ||        ||| ||| |||||  |  |        ||  || |||  || ||||||  ||   |   |               || | |||||||||   ||||| ||| | |  || || ||||||||  ||||||||||||||||  ||||||||||||| || |||||  | |||||| | |
----gtaggaatttgag-----ctgaggaatt--ctaaatatgtagttgcttacgatacgggcttaaagctgaaaacgcaga-cctttttatccttat--------ttacatatctgtttatttttttcttttttactta-------------tagATACAAACCATCAAGCAAGGATACATTTTGAAGCGTTCCTCAAATTTGAGAGGTGACTGGAAGCGAAGGTTTTTTGTGCTGGATAGTAGGGGAATGTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttccttgtatttctagttgttttttgtttccgtgtctgaataacaatatttcagGTTCAAACCATCCGACAAGGTTACCTCTCAAAACGCTCCTCAAACCTGAGAGGTGACTGGAAAAGAAGGTTTTTTGTTCTTGATAGCCGAGGAATGCTAT
                                      gaataac  putative branch site (score: 2)
                                     tgaataacaatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgaagaagcttataagttattaaggaacttcttttatagatacttatcaaaaaaaaaaaaaaggaacttcttttatagatcctctttattttcttgatgttccttgtatttctagttgttttttgtttccgtgtctgaataacaatatttcagGTTCAAACCATCCGACAAGGTTACCTCTCAAAACGCTCCTCAAACCTGAGAGGTGACTGGAAAAGAAGGTTTTTTGTTCTTGATAGCCGAGGAATGCTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG