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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCATGCGTACAATAAAGGGAAGGCTCTTGTTGTTAGCAAAGTTCCTTTACCAGATTATCGAGCGGATCTTGATGAACGGCATGGATCCACTCAGAAAGAGgtaatagagatgttgctagtacgaaagttttgtactcagtggtggctgctgaaacgcttatactctttttcttgtag

Basic information

species Arabidopsis thaliana
transcript AT2G35920.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G35920.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os10g33275.2 (Oryza sativa), 5'ss of exon 3
TCATGCGTACAATAAAGGGAAGGCTCTTGTTGTTAGCAAAGTTCCTTTACCAGATTATCGAGCGGATCTTGATGAACGGCATGGATCCACTCAGAAAGAGgtaata---gagatgttgctagtacgaaagt----tttgtactcagtggtggctgctgaaacgcttatactctttttcttgtag----
  ||| |||||| ||||||||| |  ||||| | |||||||||||  |||| ||||||||||| || ||||||||  | |||||||| || ||  |||||||| ||         || | |||||  || |    |  || ||        |   || | ||  ||||  | |||    | | |    
CAATGTGTACAACAAAGGGAAGACAATTGTTTTCAGCAAAGTTCCACTACCTGATTATCGAGCAGACCTTGATGAGAGACATGGATCAACACAACAAGAGgtattatttagtgccttacaagtacacaaataacataggtgcttttcttatgtgacttatactgttattatatttaaactatggacag

upper sequence: AT2G35920.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G399212_T01 (Zea mays), 5'ss of exon 5
TCATGCGTACAATAAAGGGAAGGCTCTTGTTGTTAGCAAAGTTCCTTTACCAGATTATCGAGCGGATCTTGATGAACGGCATGGATCCACTCAGAAAGAGgtaatagagat---gttgctagtacgaaagttttgtactcagtggtggctgc---tga--aacgcttatactctttttcttgtag
| |||| ||||| ||||||||| | |||||| | ||||| || || ||||| ||||||||||| ||||| || ||  |||||||||| || || || |||||| |     |    ||| ||||  | ||       | |   |||   ||     |||  || ||||||| | ||  |   | ||
TAATGCATACAACAAAGGGAAGACACTTGTTTTCAGCAAGGTACCCTTACCTGATTATCGAGCAGATCTGGACGACAGGCATGGATCAACACAAAAGGAGgtactgtgtgtctgattgatagtttgtaataacatcattatatgggtcctcttcttgatcaatgcttatatttttactggggcag

upper sequence: AT2G35920.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA02G35240.1 (Glycine max), 5'ss of exon 5
TCATGCGTACAATAAAGGGAAGGCTCTTGTTGTTAGCAAAGTTCCTTTACCAGATTATCGAGCGGATCTTGATGAACGGCATGGATCCACTCAGAAAGAGgtaatagagatgttgctagtacgaaagttttgt-actcagtggtggctgct----gaaacgc-----ttatactctttttcttgtag
 ||||| || | ||| ||||||| |||  |||||||||||||||| || || |||||||| || ||||||||||| || |||||||| || |||||||||||     | |  |  |   |   || || |  | ||| | |  | |||||     |||| |       |||  |   ||| | | ||
CCATGCTTATAGTAAGGGGAAGGTTCTCATTGTTAGCAAAGTTCCATTGCCTGATTATCGTGCAGATCTTGATGAGCGTCATGGATCAACACAGAAAGAGgtggagtatacctatcctattttaatgtctgattacttatttcttgctgcatgtagaaatgtgctaactatgttaagtttttggcag

upper sequence: AT2G35920.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA10G10180.1 (Glycine max), 5'ss of exon 3
TCATGCGTACAATAAAGGGAAGGCTCTTGTTGTTAGCAAAGTTCCTTTACCAGATTATCGAGCGGATCTTGATGAACGGCATGGATCCACTCAGAAAGAGgtaatagagatgt-tgctagtacgaaagttttgtactcagtggtggctgct----gaaacgcttatactcttttt--cttgtag---
 ||||| || | ||| ||||||| ||| ||  ||||||| ||||| || || |||||||| || ||||||||||| || |||||||| || ||||| |||||     | || | | ||| | | |   ||   |||| | |  | || ||     |||| |     ||| ||||    ||   |   
CCATGCTTATAGTAAGGGGAAGGTTCTCGTCATTAGCAAGGTTCCATTGCCTGATTATCGTGCAGATCTTGATGAGCGTCATGGATCAACACAGAAGGAGgtggagtatatctatcctatttcaatgtttgattacttatttcttgccgcatgtagaaatgtggtaactattttaagttttcggcag

upper sequence: AT2G35920.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv08s0032g01230.t01 (Vitis vinifera), 5'ss of exon 3
TCATGCGTACAATAAAGGGAAGGCTCTTGTTGTTAGCAAAGTTCCTTTACCAGATTATCGAGCGGATCTTGATGAACGGCATGGATCCACTCAGAAAGAGgtaatagagatgttgctagtacgaaagttttgtactcagt-----ggtggctgctg--------aaacgcttatactctttttcttgtag----------------------------------
 ||||| || || || |||||| | |||||||| ||||||||||| || ||| |||| || || |||||||||||||| ||||||||||| || ||||||||      ||||||   | |        ||| |  |   |     ||||  || ||        |||   ||  |    ||||| | |                                    
CCATGCATATAACAAGGGGAAGACACTTGTTGTCAGCAAAGTTCCATTGCCAAATTACCGGGCTGATCTTGATGAACGCCATGGATCCACACAAAAAGAGgtgtatatgatgttttaaatttatcttctttttcttttatcagaaggtgcttgatgtacatggaaaatagtttaatctcttttcctatgtgtgtcttcgattttcattttcaaactttttgcag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCATGCGTACAATAAAGGGAAGGCTCTTGTTGTTAGCAAAGTTCCTTTACCAGATTATCGAGCGGATCTTGATGAACGGCATGGATCCACTCAGAAAGAGgtaatagagatgttgctagtacgaaagttttgtactcagtggtggctgctgaaacgcttatactctttttcttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA