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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttacattaaatgatgaaccataagtaatgaacaaacttattgattgcatctgttcctgttataaatctatctttgtatttgcattatctcttgctcttgttatctgagtgatctaaattacacaaatgtagAGTCACCCTTTGAATTCCGGGCCCTGGAGGTTGCTTTAGAAGCCATTTGTAGTTTTCTTGCTGCACGTACAACAGAATTGGAGATGGCTGCTTATCCTGC

Basic information

species Glycine max
transcript GLYMA20G35260.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G35260.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g53110.1 (Oryza sativa), 3'ss of exon 3
gtacgttacattaaatgatgaaccataagtaatgaacaaacttattgattgcatctgttcctgttataaatctatctttgtatttgcattatctcttgctc-ttgttatctgagtgatctaaattacacaaatgtagAGTCACCCTTTGAATTCCGGGCCCTGGAGGTTGCTTTAGAAGCCATTTGTAGTTTTCTTGCTGCACGTACAACAGAATTGGAGATGGCTGCTTATCCTGC
                                   ||||   |  || |||  |   ||    |  |  || | |  || | |   |   |||  | | |  ||  ||||   |  ||  || ||    || |  ||| || |||||||||||||| || ||||||||| |||| ||||||||||| |||||||||| |||||| || || || |||||||  |||||||| || ||
-----------------------------------acaactgttgtggttgttttgattgtaatattctatttgttgtt-tgtgaactccatcaatagtttgttaatatccc-gcaatacaattttatgaactccagAATCTCCCTTTGAATTCCGCGCACTGGAGGTTACTTTGGAAGCCATTTGCAGTTTTCTTGGTGCACGCACTACTGAGTTGGAGAGTGCTGCTTACCCAGC

upper sequence: GLYMA20G35260.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G09690.1 (Arabidopsis thaliana), 3'ss of exon 3
----------gtacgttacattaaatgatg--aaccataagtaatgaacaaacttattgattgcatctgttcctgttataaatctatctttgtatttgcattatctcttgctcttgttatctgagtgatctaaattacacaaatgtagAGTCACCCTTTGAATTCCGGGCCCTGGAGGTTGCTTTAGAAGCCATTTGTAGTTTTCTTGCTGCACGTACAACAGAATTGGAGATGGCTGCTTATCCTGC
             | | |  ||   | ||   ||  |||   | || | |||  | |||||    |   | |||     | | |||       |||  |  |   | |  || ||| |||   |||| |     ||      || |||| || || |||||||||||||| || ||||| || || ||||| |||||||||||||| |||||| | ||||||||| | |||| |  ||||||||||||
gtacccctcaaggcctcaacttttgttattttaaggatataaattggaaaaatct-ttgatc-ttttgatgcctacataagaactaatgaaccattcactct---tttcacttttggtattgaagtgttt--gtttgttactatatagAATCCCCGTTTGAATTCCGGGCGCTAGAGGTGGCCTTGGAAGCTATTTGTAGTTTTCTAGCTGCAAGGACAACAGAACTAGAGAAGTTTGCTTATCCTGC

upper sequence: GLYMA20G35260.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G09720.1 (Arabidopsis thaliana), 3'ss of exon 3
---gtacgttacatta---aatgatgaaccataagtaatgaacaaacttattgattgcatctgttcct--gttataaatctatctttgta----tttgcattatctcttgctcttgttatctgagtgatctaaattacacaaatgtagAGTCACCCTTTGAATTCCGGGCCCTGGAGGTTGCTTTAGAAGCCATTTGTAGTTTTCTTGCTGCACGTACAACAGAATTGGAGATGGCTGCTTATCCTGC
   |  | | || |||   | |  |  | |  || |  |||   |  || |||||    |   | |||  ||| || |  |||| |   |     |||       | || || ||| |||     |||| |   | | || | | |||| ||  | |||||||| ||||| || ||||||||||| ||||| |||||||| || || |||||| | |||| |||||| |||| | |||||||||||||
gtagcccttgaccttagtcatttttagaactcaattcttgattta--ttcttgatctttttgatacctatgttctataaatatcgtaagaaaaacttgtcactctttttacttttggtattaatatgat-tgcttgatacta-tatagAATCCGCGTTTGAATTTCGGGCACTAGAGGTTGCTTTGGAAGCTATTTGTAGCTTCCTAGCTGCAAGGACAATAGAATTAGAGAAGTCTGCTTATCCTGC

upper sequence: GLYMA20G35260.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv05s0020g04720.t01 (Vitis vinifera), 3'ss of exon 3
gtacgttacattaaatgatgaaccataagtaatgaacaaacttattgattgcatctgttcctgttataaatctatctttgtatttgcat-tatctcttgct--cttgttatctgagtgatctaaattacacaaatgtagAGTCACCCTTTGAATTCCGGGCCCTGGAGGTTGCTTTAGAAGCCATTTGTAGTTTTCTTGCTGCACGTACAACAGAATTGGAGATGGCTGCTTATCCTGC
                             |     || ||  || |||||      |    |  ||| |||  |  |    ||||   | | | |||||     | ||| ||||| ||||||   |  || |||||||||||| ||||||||||||||||| || ||||| ||||| ||||||||||||||||||||||||||||||||||||||| |||| |  ||||||||||| ||
--------------------------gtatgtctcactaatctagtgattttgaaggaaa-taatatgaatacaagtagagatttttctgtctttcttgaaaattagttttctgaatgatctgtgt--cataaatgtagAGTCTCCCTTTGAATTCCGGGCTCTTGAGGTGGCTTTGGAAGCCATTTGTAGTTTTCTTGCTGCACGTACAACAGAACTGGAAACTGCTGCTTATCCAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgcattatctcttgctcttgttatctgagtgatctaaattacacaaatgtagAGTCACCCTTTGAATTCCGGGCCCTGGAGGTTGCTTTAGAAGCCATTTGTAGTTTTCTTGCTGCACGTACAACAGAATTGGAGATGGCTGCTTATCCTGC
                                  atctaaa  putative branch site (score: 3)
                                     taaattacacaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgttacattaaatgatgaaccataagtaatgaacaaacttattgattgcatctgttcctgttataaatctatctttgtatttgcattatctcttgctcttgttatctgagtgatctaaattacacaaatgtagAGTCACCCTTTGAATTCCGGGCCCTGGAGGTTGCTTTAGAAGCCATTTGTAGTTTTCTTGCTGCACGTACAACAGAATTGGAGATGGCTGCTTATCCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT