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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaagcccttctgtactaatttgtcgtgattaacatggaaaactgtcttgcttaaaatggaaaggtttatatccattgacatacttctctcctaacaaactatgtccttaacaatgactattcttggtttcagGTCCCCACTGGATGGAAATTTTTTGGGAACCTTATGGATGCTGGAAAGTTGTCTATTTGTGGGGAAGAAAGTTTTGGAACAGGTTCTGATCACATTCGTG

Basic information

species Vitis vinifera
transcript Vv16s0022g02320.t01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv16s0022g02320.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: LOC_Os10g11140.1 (Oryza sativa), 3'ss of exon 15
gtgaagcccttctgtactaatttgtc-gtgattaacatggaaaactgtcttgcttaaaatggaaaggtttatatccattgacatacttctctcctaacaaactatgtccttaacaatgactattcttggtttcagGTCCCCACTGGATGGAAATTTTTTGGGAACCTTATGGATGCTGGAAAGTTGTCTATTTGTGGGGAAGAAAGTTTTGGAACAGGTTCTGATCACATTCGTG
             |||||  |||||| |||| |  ||||   |  ||  ||| ||  ||   ||  ||  |||  |  || |    ||||     ||||  ||| | |  ||    ||   | |     || ||||| || || ||||||||||||||||| ||||| |||||||| || || |||||||| ||||| || ||||||||||| ||||| |||||||||||  | |
-------------gtact--tttgtcagtgaattgcatgtgca--tgatttgtttgcaa---aatagtcaataggccatggc----ttctagaagaacag-ctaagacaata----tggtcact-----ttgcagGTACCAACAGGATGGAAATTTTTTGGAAACCTAATGGATGCAGGTAAATTGTCTATATGTGGAGAGGAAAGTTTTGGGACAGGATCTGATCACATCAGGG

upper sequence: Vv16s0022g02320.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GRMZM2G025854_T02 (Zea mays), 3'ss of exon 15
gtgaagcccttctgtactaatttgtcgt-gattaacatggaaaactgtcttgctta-aaatggaaaggtttatatccattgacatacttctctcctaacaaactatgtccttaacaatgactattcttggtttcagGTCCCCACTGGATGGAAATTTTTTGGGAACCTTATGGATGCTGGAAAGTTGTCTATTTGTGGGGAAGAAAGTTTTGGAACAGGTTCTGATCACATTCGTG
             |||| |  ||| | | ||    ||  |   | |||| |   || |||  || |   |  | |  |      || ||    | | |  | ||| | |    |  ||| |  |||||      |||| || || || |||||||||||||| ||||| |||||||| ||||| |||||||||||||| || ||||||||||| || || |||||||||||  | |
-------------gtacca--ttgccatagagcttcactgttcattgtcatatatacaaactgacaaagtgttgtaaacc--tgtaatttctacttgatcatctaagact---aagatgccacttctt------agGTTCCAACAGGCTGGAAATTTTTTGGCAACCTAATGGATGCAGGAAAATTGTCTATTTGTGGAGAGGAAAGTTTTGGGACTGGATCTGATCACATCAGAG

upper sequence: Vv16s0022g02320.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA10G38590.1 (Glycine max), 3'ss of exon 15
gtgaagcccttctgtactaatttgtcgtgattaacatggaaaactgtcttgcttaaaatggaaaggtttatatccattgacatacttctctcctaacaaactatgtccttaacaat-gactattcttggtttcagGTCCCCACTGGATGGAAATTTTTTGGGAACCTTATGGATGCTGGAAAGTTGTCTATTTGTGGGGAAGAAAGTTTTGGAACAGGTTCTGATCACATTCGTG
                      ||   |  ||    |  ||  || |||| ||||||||   ||  |  ||       |    || | | |    ||| | |       ||||||  ||     | ||| |||||||||||||||| ||||||||||||||||| |||||||||||||| || |||||  |||| |||||||| |||||||||||||||||||||||||||||||
-------------------gcatgctttattttttttacaattctttctt-cttaaaatattaatataaatgaaataggcttcacatatttttagacatagttctcaaataacaagagatgggccctggattcagGTCCCCACTGGTTGGAAATTTTTTGGGAATCTTATGGATGCTGGGAATTTGTCCGTTTGCGGGGAAGAGAGTTTTGGAACAGGTTCTGATCACATTCGTG

upper sequence: Vv16s0022g02320.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA20G29230.1 (Glycine max), 3'ss of exon 15
gtgaagcccttctgtactaatttgtcgtgattaacatggaaaactgtcttgcttaaaatggaaaggtttatatccattgacatacttctctcctaacaaactatgtccttaacaatgactattcttggtttcagGTCCCCACTGGATGGAAATTTTTTGGGAACCTTATGGATGCTGGAAAGTTGTCTATTTGTGGGGAAGAAAGTTTTGGAACAGGTTCTGATCACATTCGTG
                      ||   |  ||  | |  ||     |  | |||||| |   ||  |  ||    || | | |       |  ||   |  | ||   | |  || ||     |  || |||||||||||||||| ||||||||||||||||| |||||||||||||| || |||||  |||| ||||||||||||||||||||||||||||| ||||||||||
-------------------gcatgctttatttttcttacaatttctttcttcttaaattattaatataaatgaa-ataggcttcacatatttttagacagttctgaaataacaaaagatggacccgggattcagGTCCCCACTGGTTGGAAATTTTTTGGGAATCTTATGGATGCTGGGAATTTGTCGGTTTGCGGGGAAGAAAGTTTTGGAACAGGTTCTGACCACATTCGTG

upper sequence: Vv16s0022g02320.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: AT5G51820.1 (Arabidopsis thaliana), 3'ss of exon 15
gtgaagcccttctgtactaatttgtcgtgattaacatggaaaactgtcttgcttaaaatggaaaggtttatatccattgacatacttctctcctaacaaactatgtccttaacaatgactattcttggtttcagGTCCCCACTGGATGGAAATTTTTTGGGAACCTTATGGATGCTGGAAAGTTGTCTATTTGTGGGGAAGAAAGTTTTGGAACAGGTTCTGATCACATTCGTG
                    ||   | |  |||   |  | |  ||| ||   ||         |||||  | |||  || | | ||            |  |  |  || |||| |    || |  |||| |||| ||||||||||||||||||||||| || ||||||||||||||||| ||||| || ||||| ||||| || ||||| ||||||||||||||||| ||||
-------------------gttcaccctttttag--tcaacagatgtattttcta---------ggtttgcaacca--gataaaatta------ggaggataaactttttgacaaagcaacttgtatgttttagGTTCCCACTGGATGGAAATTTTTTGGAAATCTTATGGATGCTGGAAAATTGTCAATCTGTGGAGAAGAGAGCTTTGGCACAGGTTCTGATCACATCCGTG

upper sequence: Vv16s0022g02320.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: EFJ34621 (Selaginella moellendorffii), 3'ss of exon 14
gtgaagcccttctgtactaatttgtcgtgattaacatggaaaactgtcttgcttaaaatggaaaggtttatatccattgacatacttctctcctaacaaactatgtccttaacaatgactattcttggtttcagGTCCCCACTGGATGGAAATTTTTTGGGAACCTTATGGATGCTGGAAAGTTGTCTATTTGTGGGGAAGAAAGTTTTGGAACAGGTTCTGATCACATTCGTG
                                                                              |  |  || |   | | |  | | |||      |||   |  ||| |||     |||| || ||||| ||||| |||||||| || || ||||| || |||||  |||| ||||| || || |||||||||||||| || |||||||| |||||||
--------------------------------------------------------------------------gtacgggacgctaccgactttatgagcaatggttcacacagcaaa-attgttga----agGTTCCAACTGGCTGGAAGTTTTTTGGCAATCTCATGGACGCGGGAAAACTGTCGATTTGCGGAGAGGAAAGTTTTGGAACGGGATCTGATCATATTCGTG

upper sequence: Vv16s0022g02320.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: EFJ32824 (Selaginella moellendorffii), 3'ss of exon 14
gtgaagcccttctgtactaatttgtcgtgattaacatggaaaactgtcttgcttaaaatggaaaggtttatatccattgacatacttctctcctaacaaactatgtccttaacaatgactattcttggtttcagGTCCCCACTGGATGGAAATTTTTTGGGAACCTTATGGATGCTGGAAAGTTGTCTATTTGTGGGGAAGAAAGTTTTGGAACAGGTTCTGATCACATTCGTG
                                                                              |  |  || |   | | |  | | ||| |    |||   |  ||| |||     |||| || ||||| ||||| |||||||| || || ||||| || |||||  |||| ||||| || || |||||||||||||| || |||||||| |||||||
--------------------------------------------------------------------------gtacgggacgctaccgactttatgagcgatggctcacacagcaaa-attgttga----agGTTCCAACTGGCTGGAAGTTTTTTGGCAATCTCATGGACGCGGGAAAACTGTCGATTTGCGGAGAGGAAAGTTTTGGAACGGGATCTGATCATATTCGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatacttctctcctaacaaactatgtccttaacaatgactattcttggtttcagGTCCCCACTGGATGGAAATTTTTTGGGAACCTTATGGATGCTGGAAAGTTGTCTATTTGTGGGGAAGAAAGTTTTGGAACAGGTTCTGATCACATTCGTG
                                       ctattctt  CT-rich tract
                             ttaacaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaagcccttctgtactaatttgtcgtgattaacatggaaaactgtcttgcttaaaatggaaaggtttatatccattgacatacttctctcctaacaaactatgtccttaacaatgactattcttggtttcagGTCCCCACTGGATGGAAATTTTTTGGGAACCTTATGGATGCTGGAAAGTTGTCTATTTGTGGGGAAGAAAGTTTTGGAACAGGTTCTGATCACATTCGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA