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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttttgcttcctcactaatttcggtggaatggtaaggtctggatgccaattatacaaatttcaagtttctgcagGTGTGGGATGCAAACACTGGTTCTAAGCAGTATACTTTTGAGGGTCATGAGGCACCTGTATATTCTGTATGTCCACATCACAAGGAAAATATTCAG

Basic information

species Vitis vinifera
transcript Vv11s0016g05620.t01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g05620.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA17G12110.1 (Glycine max), 3'ss of exon 13
---gtttgtt--ttgcttcctcactaatttcggtggaatggtaaggtctggatgccaattatacaaatttcaagtttctgcagGTGTGGGATGCAAACACTGGTTCTAAGCAGTATACTTTTGAGGGTCATGAGGCACCTGTATATTCTGTATGTCCACATCACAAGGAAAATATTCAG
     ||||    |  ||  | |   || ||  |  |    |||       |   ||||| || ||  |||||| |  ||||||| |||||||||   |||||| | |||||||||||||||||||||||||| |||||||||||||||||||| || |||||||| |||| |||||||
gttagttgtcacatattttgttatagatatcaat--atcaataaaaa--aaaaaacaatttta-aatgttcaaggtcttgcagGTATGGGATGCAGTTACTGGTGCAAAGCAGTATACTTTTGAGGGTCATGAAGCACCTGTATATTCTGTATGCCCTCATCACAAAGAAAGTATTCAG

upper sequence: Vv11s0016g05620.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: GLYMA13G22720.1 (Glycine max), 3'ss of exon 13
---gtttgttt--tgcttcctcactaatttcggtggaatggtaaggtctggatgccaattatacaaatttcaagtttctgcagGTGTGGGATGCAAACACTGGTTCTAAGCAGTATACTTTTGAGGGTCATGAGGCACCTGTATATTCTGTATGTCCACATCACAAGGAAAATATTCAG
     ||||    |  ||  |||   || ||  |   |   |||  |    |  ||||||  | |   |||||| || ||||||| ||||||||    |||||| | |||||||||||||||||||||||||| |||||||||||||||||||| || |||||||| |||| |||||||
gttagttgtcacataatttgtcatagatatcaatatcaatataaa-taaaaaaaccaatttca-agtgttcaagattttgcagGTATGGGATGCCGTTACTGGTGCAAAGCAGTATACTTTTGAGGGTCATGAAGCACCTGTATATTCTGTATGCCCTCATCACAAAGAAAGTATTCAG

upper sequence: Vv11s0016g05620.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 3'ss of exon 12
------------------------------------------------------------------------gtttgttttgcttcctca---------------ctaatttcggtgga-atggtaaggtctggatgccaattat--acaaatttcaagtttctgcagGTGTGGGATGCAAACACTGGTTCTAAGCAGTATACTTTTGAGGGTCATGAGGCACCTGTATATTCTGTATGTCCACATCACAAGGAAAATATTCAG
                                                                         ||||  ||  |||  ||               | |||||   |  | ||  |    ||||||     | | |  || || ||  |  | || ||||| ||||||||    || ||    ||||||||||||||||| |||||||| ||||| || || ||||| |||||||| |||||||| |  ||||||
gtgcgcacttcattactacgtgcactacttcttaatttggaccatttccagtatgccaaaccatgcctgtgtatttgggttatttctacatatggtgagagagaccaaattttattctagataattgtatctggaatttgactttggacgaacttgtacatccttcagGTTTGGGATGCTGCAACAGGGCGGAAGCAGTATACTTTTGAAGGTCATGAAGCACCCGTGTACTCTGTTTGTCCACACCACAAGGAGAGCATTCAG

upper sequence: Vv11s0016g05620.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 12
gtttgttttgcttcctcactaatttcggtggaatggtaaggtctggatgccaattatacaaatttcaagtttctgcagGTGTGGGATGCAAACACTGGTTCTAAGCAGTATACTTTTGAGGGTCATGAGGCACCTGTATATTCTGTATGTCCACATCACAAGGAAAATATTCAG
            ||  ||  |  || |   |||   || || ||| | |   | |  | ||||            ||||||||||||||    | ||||   ||  | || |||||||||||||| || || || || || ||||| ||||| ||||||||||||||||| |||
-----------gtctgcataatctttg--agaaaaatatggactgaaagggcaatgaaaaaat------------cagGTGTGGGATGCGGTGAGTGGTCGCAACAAATACACTTTTGAGGGTCACGAAGCGCCAGTGTACTCTGTTTGTCCGCATCACAAGGAAAATATACAG

upper sequence: Vv11s0016g05620.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: EFJ17248 (Selaginella moellendorffii), 3'ss of exon 12
gtttgttttgcttcctcactaatttcggtggaatggtaaggtctggatgccaattatacaaatttcaagtttctgcagGTGTGGGATGCAAACACTGGTTCTAAGCAGTATACTTTTGAGGGTCATGAGGCACCTGTATATTCTGTATGTCCACATCACAAGGAAAATATTCAG
                   ||  |  | |       |  | || | || |   |||||    |||  |     || |||| ||||| || |  || | |   |||   |||   ||||| |||||||||||| | || |||||||||||||||||||| || ||||  || |||
-----------------gttacctctgctatcgatttttgttcggcattc---ttatatcggttttca---cgtgtagGTTTGGGAAGCCATGACCGCTCGCAAGATTTATGTATTTGAAGGTCATGAGGCAGCAGTGTATTCTGTATGTCCACATCATAAAGAAAGCATACAG

upper sequence: Vv11s0016g05620.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: EFJ30926 (Selaginella moellendorffii), 3'ss of exon 12
gtttgttttgcttcctcactaatttcggtggaatggtaaggtctggatgccaattatacaaatttcaagtttctgcagGTGTGGGATGCAAACACTGGTTCTAAGCAGTATACTTTTGAGGGTCATGAGGCACCTGTATATTCTGTATGTCCACATCACAAGGAAAATATTCAG
                   ||  |  | |       |  | | || || |   |||||    |||  |     || |||| ||||| || |  || | |   |||   |||   ||||| |||||||||||| | || |||||||||||||||||||| || ||||  || |||
-----------------gttacctctgctatcgatttttgttatgcattc---ttatatcggttttca---cgtgtagGTTTGGGAAGCCATGACCGCTCGCAAGATTTATGTATTTGAAGGTCATGAGGCAGCAGTGTATTCTGTATGTCCACATCATAAAGAAAGCATACAG

upper sequence: Vv11s0016g05620.t01 (Vitis vinifera), 3'ss of exon 13
lower sequence: EFJ37833 (Selaginella moellendorffii), 3'ss of exon 12
gtttgttttgcttcctcactaatttcggtggaatggtaaggtctggatgccaattatacaaatttcaagtttctgcagGTGTGGGATGCAAACACTGGTTCTAAGCAGTATACTTTTGAGGGTCATGAGGCACCTGTATATTCTGTATGTCCACATCACAAGGAAAATATTCAG
                              |  ||   |    | ||     | |  |  |      |     | ||||||||||||||    | ||||   ||  | || |||||||||||||| || || || || || ||||| ||||| ||||||||||||||||| |||
------------------------------gtctgcataatctttgagatggactgaaagagcaatgaaaaaat-cagGTGTGGGATGCGGTGAGTGGTCGCAACAAATACACTTTTGAGGGTCACGAAGCGCCAGTGTACTCTGTTTGTCCGCATCACAAGGAAAATATACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcggtggaatggtaaggtctggatgccaattatacaaatttcaagtttctgcagGTGTGGGATGCAAACACTGGTTCTAAGCAGTATACTTTTGAGGGTCATGAGGCACCTGTATATTCTGTATGTCCACATCACAAGGAAAATATTCAG
                                              tttctgc  CT-rich tract
                            aattatacaaatttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttttgcttcctcactaatttcggtggaatggtaaggtctggatgccaattatacaaatttcaagtttctgcagGTGTGGGATGCAAACACTGGTTCTAAGCAGTATACTTTTGAGGGTCATGAGGCACCTGTATATTCTGTATGTCCACATCACAAGGAAAATATTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA