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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCATGGAACAACAGAGTATTAGTATATCGAAGGCAGGAATAGTTACTTCTCTTCAAGCTCGTTGCTCTGTTATTGCTGCAGCTAATCCAGTTGGTGGAAGgtaagctagaaactaatgcccttcattgacctaaaatttgtaattttgatcttgctaatttgtttgtgacattgcaacttcag

Basic information

species Arabidopsis thaliana
transcript AT1G44900.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G44900.2 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: LOC_Os11g29380.1 (Oryza sativa), 5'ss of exon 12
CCATGGAACAACAGAGTATTAGTATATCGAAGGCAGGAATAGTTACTTCTCTTCAAGCTCGTTGCTCTGTTATTGCTGCAGCTAATCCAGTTGGTGGAAGgtaagctagaaactaatgcccttcattgacctaaaatttgtaattt---tgatcttgctaatttgtttgtgacattgcaacttcag
||||||| ||||| ||||| |||||||| ||||| ||||| || || || ||||||||||| |||  ||||||||||||||| || ||| | || ||||||| |  |   | ||| |  |      ||   | |||    |  |||     || |   ||||||  |  ||  ||||||       
CCATGGAGCAACAAAGTATCAGTATATCAAAGGCCGGAATTGTCACATCCCTTCAAGCTCGGTGCAGTGTTATTGCTGCAGCAAACCCAATAGGAGGAAGgtga--tgtgatctacttgctcaggatgttttcaaacaattgttttgagcaatatacttaattttatcatgttattgcag------

upper sequence: AT1G44900.2 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GRMZM2G139894_T02 (Zea mays), 5'ss of exon 12
CCATGGAACAACAGAGTATTAGTATATCGAAGGCAGGAATAGTTACTTCTCTTCAAGCTCGTTGCTCTGTTATTGCTGCAGCTAATCCAGTTGGTGGAAGgtaagctagaaactaatgcccttcattgacctaaaatttgtaattttgatcttgctaatt--tgtttgtgacattgcaacttcag
| ||||| ||||||||||| |||||||| || |||||||| || || |||||||||||| | |||  |||||||||||| || || ||||| || ||||||||| ||  |     ||||    |||  |     | |   |  | || |    | || |   ||     | | |||      |||
CTATGGAGCAACAGAGTATCAGTATATCAAAAGCAGGAATCGTCACATCTCTTCAAGCTAGATGCAGTGTTATTGCTGCGGCAAACCCAGTAGGGGGAAGgtaa-cttcagttccatgcatgccatgtagtaccagtgcatggtgttaagaaagatactgaatgcaatcgtccttgatctcacag

upper sequence: AT1G44900.2 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA07G36680.1 (Glycine max), 5'ss of exon 11
CCATGGAACAACAGAGTATTAGTATATCGAAGGCAGGAATAGTTACTTCTCTTCAAGCTCGTTGCTCTGTTATTGCTGCAGCTAATCCAGTTGGTGGAAGgtaagctagaaactaa---tgcccttcattgacctaaaatttgtaattttgatc-------ttgctaatttgtttgtgacattgcaacttcag--------------------------------------------------------------------------------------------------
||||||| || |||||||| || ||||| || || ||||| ||||| |||||||| || || || |||||||||||||| || ||||| ||||||||||||||||| |  |  |||   |||   |   || |   || || | | | || |||         |||||  | |         | ||  || |                                                                                                   
CCATGGAGCAGCAGAGTATAAGCATATCAAAAGCTGGAATTGTTACATCTCTTCAGGCACGCTGTTCTGTTATTGCTGCGGCAAATCCTGTTGGTGGAAGgtaagcaaatatgtaaggttgcatgtatctggctgcaagttggcactgtttatcagtgtcccagctaagatttcaacagtcatacacattgaaagatattggatgtactatgagtattgatttatggttttgatccatttttctagcatctaagctttactcttaaatttaactttttcttggacttgcag

upper sequence: AT1G44900.2 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA17G03920.1 (Glycine max), 5'ss of exon 11
CCATGGAACAACAGAGTATTAGTATATCGAAGGCAGGAATAGTTACTTCTCTTCAAGCTCGTTGCTCTGTTATTGCTGCAGCTAATCCAGTTGGTGGAAGgtaagctagaaactaatgcccttcattgacctaaaatttgta---attttgatcttgctaatttgtttgtgacattgcaacttcag-----------------------------------------------------------------------------------------------------------
||||||| || |||||||| || ||||| || || ||||| ||||| |||||||| || || ||||||||||||||||| || ||||| ||||| ||||||||||| |  |   || |   | |||  | ||  ||| ||     |  |||   ||| | ||  || |   |   |   | ||||                                                                                                            
CCATGGAGCAGCAGAGTATAAGCATATCAAAAGCTGGAATTGTTACATCTCTTCAGGCACGCTGCTCTGTTATTGCTGCTGCAAATCCTGTTGGAGGAAGgtaagcaaatatgcaaggt--tgcatgtatctggaatctggctgcaagttggcattgttcatcagtgtccca-gctaagatttcaactgtcatacacattgaaagatattaccatgagtattgatatatggttttgatccttttttcaagcatttaagctttactcttaaattaacttttctttgacttgcag

upper sequence: AT1G44900.2 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: Vv01s0150g00390.t01 (Vitis vinifera), 5'ss of exon 11
CCATGGAACAACAGAGTATTAGTATATCGAAGGCAGGAATAGTTACTTCTCTTCAAGCTCGTTGCTCTGTTATTGCTGCAGCTAATCCAGTTGGTGGAAGgtaagctagaaactaa---tgcccttcattgacctaaaatttgtaattttgatct--tgctaatttgtttgtgacattgcaacttcag------------------------------------------------------------------------------------------
| |||||||| ||||||||||| ||||| ||||| || || || |||||||| || ||||| |||||||| |||||||| || |||||| |||| |||||||| || || |  ||    |    |   | ||  |||  |   |    || |  |  |  || |    |  ||| |    | || ||                                                                                           
CAATGGAACAGCAGAGTATTAGCATATCAAAGGCTGGGATTGTCACTTCTCTCCAGGCTCGCTGCTCTGTCATTGCTGCTGCAAATCCAATTGGAGGAAGgtatgccagtagatagatttattttatgtagaaataagctaactggcattaacttgattttactgcactgatgaaaaatgatctacaaaccatgcattgtagcctcttgctgaatgatctgcaatttaatcatctgttgcttcaaaattgtgattctgaccaaaaatcctgtttccag

upper sequence: AT1G44900.2 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: PP1S28_266V6.1 (Physcomitrella patens), 5'ss of exon 11
CCATGGAACAACAGAGTATTAGTATATCGAAGGCAGGAATAGTTACTTCTCTTCAAGCTCGTTGCTCTGTTATTGCTGCAGCTAATCCAGTTGGTGGAAGgtaagctagaaactaatgcccttcattgacctaaaatttgtaattt--tgatcttgctaatttgtttgtgacattgcaacttcag-----------------
| |||||||| ||||| || |||||||| |||||||| || || |||||  | ||||| || ||| |||||||||||||||| |||||| |||| ||  ||||||||      |  ||   || |  |   |     |    | |    ||| ||       |  |  ||   |||    |||                   
CTATGGAACAGCAGAGCATCAGTATATCTAAGGCAGGCATTGTGACTTCGTTGCAAGCCCGGTGCGCTGTTATTGCTGCAGCAAATCCAATTGGAGGCCGgtaagctcttg--tgttggttttgaccgttgtgtgtatcacgactgaacgattttatggcaatagtaatggttttgttctttccttgggctatcaatatagt

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCATGGAACAACAGAGTATTAGTATATCGAAGGCAGGAATAGTTACTTCTCTTCAAGCTCGTTGCTCTGTTATTGCTGCAGCTAATCCAGTTGGTGGAAGgtaagctagaaactaatgcccttcattgacctaaaatttgtaattttgatcttgctaatttgtttgtgacattgcaacttcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG