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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctcaccatgaaaaattttgtattttgagttgagaaaaaatgaaaaaaaggaactttagtcacccacttcatttgggtttggtttgtttcagGTGGCTCAGGTTCTGCTGACTTTGCCATACTCATTTTCCCAGCTGGGGATGCTGTCTGGGATTCTATTCCAGCTGTTCTATGGCTTGATGGGAAGCTGGA

Basic information

species Vitis vinifera
transcript Vv03s0038g02140.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 1
-------------------------------------gtctcaccatgaaaaattttgtattttgagttgagaaaaaatgaaaaaaaggaactttagtcacccacttcatttgggtttggtttgtt------tcagGTGGCTCAGGTTCTGCTGACTTTGCCATACTCATTTTCCCAGCTGGGGATGCTGTCTGGGATTCTATTCCAGCTGTTCTATGGCTTGATGGGAAGCTGGA
                                      | |      ||||    | | | | | || |  |      ||     |  ||  | ||| |   |  || | |  |  ||| | |||       ||||||||| ||||| || |||||  |||| ||||| || |||||||||||||||||    || || || |||||||| ||||| ||  || |||| |||||||
gtgaccacattttctgatcgacgctatgcttgcttccattttcttgcgaaatgcat-gcaatctaaggtaggtttg--tgccgtgatcgatgtgtagccgttcggttaaatctgcattgctgtgtgcttcgatcagGTGGCCCAGGTGCTCCTGACGCTGCCCTACTCGTTCTCCCAGCTGGGGATGCTCAGCGGCATACTGTTCCAGCTCTTCTACGGGCTGTTGGGCAGCTGGA

upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA06G00690.1 (Glycine max), 3'ss of exon 1
------------------------------------gtctcac-catgaaaaattttgtattttgagttgagaaaaaatgaaaaaaaggaactttagt---cacccacttcatttgggtttggtttgtttcagGTGGCTCAGGTTCTGCTGACTTTGCCATACTCATTTTCCCAGCTGGGGATGCTGTCTGGGATTCTATTCCAGCTGTTCTATGGCTTGATGGGAAGCTGGA
                                     | |||   |   |   |  |  | ||        ||  | ||    | | |    | ||||        | ||  |||    |   |   | |||||||||||| |||||||| || |||||||||||||||||||||||||| ||||| ||||| | ||| || || || ||||| |||||| ||||  ||||||
gttggtttctgaagtgattagaatatcttatgctccatttcatgtagctagtgtcctccaattaatacattgattagatctttacatgcttttctagttgatgtttaattattttcatatatatacatgtcagGTGGCTCAAGTTCTGCTAACGTTGCCATACTCATTTTCCCAGCTGGGAATGCTTTCTGGCACTCTTTTTCAACTCTTCTACGGCTTGCTGGGTGGCTGGA

upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA04G00640.1 (Glycine max), 3'ss of exon 1
------gtctcaccatgaaaaattt----tgtattttgagttgagaaaaaatgaaaaaaaggaactttagtcacccacttc--atttgggtttggttt---------gtttcagGTGGCTCAGGTTCTGCTGACTTTGCCATACTCATTTTCCCAGCTGGGGATGCTGTCTGGGATTCTATTCCAGCTGTTCTATGGCTTGATGGGAAGCTGGA
       ||| |  |  |    |||    |  |||||  || | |   ||   |       || || |   ||  |  |||  |||   ||||  |||          | |||||||||||| |||||||| || ||||||||||| |||||||||||||| ||||| ||||| | ||| || || || ||||| |||||| ||||  ||||||
gttagtttctgattacaatggctttatgctccattttatgtagcgtccaatacattggttcgatctctttacatgcttttcaaattaatgtttattttcatacacacatgtcagGTGGCTCAAGTTCTGCTAACGTTGCCATACTCTTTTTCCCAGCTGGGAATGCTTTCTGGCACTCTTTTTCAACTCTTCTACGGCTTGCTGGGTGGCTGGA

upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA12G03490.1 (Glycine max), 3'ss of exon 1
-----------------------------------------------------gtctcaccatgaa--aaattttgta---ttttgagttgagaaaaaatgaaaaaaaggaactttagtc---acccacttcat-ttgggtttggtttgtttcagGTGGCTCAGGTTCTGCTGACTTTGCCATACTCATTTTCCCAGCTGGGGATGCTGTCTGGGATTCTATTCCAGCTGTTCTATGGCTTGATGGGAAGCTGGA
                                                      | |||    | |   ||| || ||   || |  |||   |    |||           |||| ||    | |   || || ||  ||        | ||||||||| || || ||||| || |||||||| ||||||||||||||||| ||||| ||||| || || ||||| || |||||||| ||  ||||||| ||||
gttggttttaagaacatattcccttccatattctattaatgttcttttgttccatttcatagagtatccaatattataggcttctctgtttttatgttatggttttcttatgcttttgttggaatcatgtttatgttatgtccttaacatgtcagGTGGCCCAAGTGCTGCTTACGTTGCCATATTCATTTTCCCAGCTGGGAATGCTTTCTGGCATACTTTTCCAACTCTTCTATGGTTTACTGGGAAGTTGGA

upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA11G11310.1 (Glycine max), 3'ss of exon 1
---------------------------------------------------------gtctcaccatgaaaaattttgtattttga------gttgagaaaaaatgaaaaaaaggaactttagtcacccacttcat-ttgggtttggtttgtttcagGTGGCTCAGGTTCTGCTGACTTTGCCATACTCATTTTCCCAGCTGGGGATGCTGTCTGGGATTCTATTCCAGCTGTTCTATGGCTTGATGGGAAGCTGGA
                                                          ||  ||  |  ||  || | || ||||       ||||  |        | | | ||   | | |  | |   || || ||  ||        | ||||||||| || || ||||| || |||||||||||||| ||||| ||||| ||||| ||||| || || |||||  | |||||||| ||  | ||||| ||||
gttggttttaagaacatatatagctgaatatcttttgttcaatttcatagatcgagtatccaacattataagcttctttaatttgtttatatgttgttactgttattatatatggttttgttggaatcatgtttatgttatgtccttaacatgtcagGTGGCCCAAGTGCTGCTTACGTTGCCATACTCATTCTCCCAACTGGGAATGCTTTCTGGCATACTTTTCCAAATCTTCTATGGTTTACTCGGAAGTTGGA

upper sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT2G21050.1 (Arabidopsis thaliana), 3'ss of exon 1
-------gtctcaccatgaaaaattttgtattttgagttgagaaaaaatgaaaaaa-aggaactttagtcacccacttcatt--tgggtttggtttgtttcagGTGGCTCAGGTTCTGCTGACTTTGCCATACTCATTTTCCCAGCTGGGGATGCTGTCTGGGATTCTATTCCAGCTGTTCTATGGCTTGATGGGAAGCTGGA
        | || |   ||  ||  |  |        ||  |   ||||  | |   ||   || |  | |      | |||  ||  | || | |  |  ||||||| || || ||| ||||  |||||||||| || || |||||||||||||| || |||||||| || ||||| || |||||| |  | || || ||||
gtaatagctttctctcagatgaaaatgatgaacaagttttggtttaaatatatatttagtctctctgcttatgattctgattcatgaatgtgctattatatagGTGGCACAAGTGCTGTTGACACTGCCATACTCGTTCTCACAGCTGGGGATGCTCTCAGGGATTCTGTTTCAGCTCTTTTATGGCATCTTAGGTAGTTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatgaaaaaaaggaactttagtcacccacttcatttgggtttggtttgtttcagGTGGCTCAGGTTCTGCTGACTTTGCCATACTCATTTTCCCAGCTGGGGATGCTGTCTGGGATTCTATTCCAGCTGTTCTATGGCTTGATGGGAAGCTGGA
                                             tttgtttc  CT-rich tract
     aaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctcaccatgaaaaattttgtattttgagttgagaaaaaatgaaaaaaaggaactttagtcacccacttcatttgggtttggtttgtttcagGTGGCTCAGGTTCTGCTGACTTTGCCATACTCATTTTCCCAGCTGGGGATGCTGTCTGGGATTCTATTCCAGCTGTTCTATGGCTTGATGGGAAGCTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA