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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAAGAGTGATGTCTTCCATTTATTATCAGGGATGTGGAAAACCCCAGCTGAGAGATGTTTCTTGTGGCTCGGCGGTTTCCGTTCATCAGAACTTCTCAAGgtaaaaaacacacgaccaggttcggtttatttggtctcttcactagcaagtttccaaactttttacttctctactacag

Basic information

species Arabidopsis thaliana
transcript AT5G06960.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G06960.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os01g17260.1 (Oryza sativa), 5'ss of exon 8
TAAGAGTGATGTCTTCCATTTATTATCAGGGATGTGGAAAACCCCAGCTGAGAGATGTTTCTTGTGGCTCGGCGGTTTCCGTTCATCAGAACTTCTCAAGgtaaaaaacacacgaccaggttcggtttatttggtctcttcactagcaagtttccaaactttttacttctctactacag---------------------
 ||    |||||||| ||| | |||||||| |||||||| || ||||||||||| |||||||||||||| || || |||||  |||| || ||| | |||||    ||      || | ||||   || |||  |     ||        || | || |   |    |  | |  ||                       
CAAAGCAGATGTCTTTCATGTGTTATCAGGCATGTGGAAGACACCAGCTGAGAGGTGTTTCTTGTGGCTAGGAGGATTCCGACCATCCGAGCTTTTAAAGgtctgtaaagtcttacgatgttcttgttgtttatttgagccatccttctattgcaaagcccctcctattaccaaaaccaatgtttctaccataatattat

upper sequence: AT5G06960.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os01g59350.1 (Oryza sativa), 5'ss of exon 9
TAAGAGTGATGTCTTCCATTTATTATCAGGGATGTGGAAAACCCCAGCTGAGAGATGTTTCTTGTGGCTCGGCGGTTTCCGTTCATCAGAACTTCTCAAGgtaaaaa-acac-acgaccaggttcggtttatttggtct----cttcact----agcaagtttccaaactttttacttctctactacag------------
 ||    || || || ||| |  | || || |||||||||||||| |||||||| || ||| ||||||| || || ||||| ||||| || ||||| ||||||| || | || |  |  |  ||  |  || ||  | |    | ||||      ||||  | |  | ||   ||  | | || |  |             
CAAAGCAGACGTTTTTCATGTGCTGTCGGGAATGTGGAAAACCCCTGCTGAGAGGTGCTTCATGTGGCTAGGTGGCTTCCGATCATCTGAGCTTCTTAAGgtaagaatatactattattatattgcgcctacttattttgaagcctcacccggaggcaaaatgctgacctgaatatatat-tattttaattgatccaatat

upper sequence: AT5G06960.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: LOC_Os03g20310.3 (Oryza sativa), 5'ss of exon 7
TAAGAGTGATGTCTTCCATTTATTATCAGGGATGTGGAAAACCCCAGCTGAGAGATGTTTCTTGTGGCTCGGCGGTTTCCGTTCATCAGAACTTCTCAAGgtaaaaaacacacgaccaggttcggtttatttggtctcttcactagcaagtttccaa-actttttacttctctactacag----------------------------------------------------------------------
 |||  |||||| || ||| || | ||||| ||||||||||| || ||||| || || ||||||||||| || ||||| ||||| || || ||||| |||||  | ||       ||  || | |  |||  |     |  |  ||||    ||    |   |||| | ||  |  | |                                                                       
AAAGGCTGATGTGTTTCATATACTTTCAGGCATGTGGAAAACACCTGCTGAAAGGTGCTTCTTGTGGCTTGGGGGTTTTCGTTCCTCTGAGCTTCTAAAGgtgcataa------gccgtgtgctgcatataagaaaattataaaagcacacctcagggatactttagtcctaaagaaaaaagtcatctaatatcttgttttaatgggtattgcatcgtaacactaatttcaatctcctgtaaaatttcag

upper sequence: AT5G06960.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G174284_T01 (Zea mays), 5'ss of exon 8
TAAGAGTGATGTCTTCCATTTATTATCAGGGATGTGGAAAACCCCAGCTGAGAGATGTTTCTTGTGGCTCGGCGGTTTCCGTTCATCAGAACTTCTCAAGgtaaaaaacacacgaccaggttcggtttatttggtctc---ttcactagcaagtttccaaactttttacttctctactacag-------------------
 |||  |||||| |||||| || | ||||| ||||||||||| || ||||| || || ||||||||||| || ||||||||||| || || ||||| |||||  |   || | ||    | ||   |||| |     |   ||   |  ||| |      | |   | | ||   |  || |                   
AAAGGCTGATGTGTTCCATATACTTTCAGGCATGTGGAAAACACCTGCTGAAAGGTGCTTCTTGTGGCTTGGGGGTTTCCGTTCGTCTGAGCTTCTAAAGgtgcatg-catatgatatagatcaaattatatcacaccgcctttgatttcaaatagttctagtacctgcctcaaaatgacggacacctgtacacaccacaa

upper sequence: AT5G06960.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G125243_T02 (Zea mays), 5'ss of exon 11
TAAGAGTGATGTCTTCCATTTATTATCAGGGATGTGGAAAACCCCAGCTGAGAGATGTTTCTTGTGGCTCGGCGGTTTCCGTTCATCAGAACTTCTCAAGgtaaaaaacacacgaccaggttcggtttatttggtctcttcactagcaagtttccaaactttttacttctctactacag-------------------------
|||    ||||| || ||| |  | || ||||||||||| ||||| ||||||||||||||| ||||| | || || ||||| ||||| || ||||| ||||||  || |  | |      || | |||   ||  |  || | |  |  |    |     | || |  ||  ||| ||                          
TAAAGCAGATGTTTTTCATGTGCTGTCTGGGATGTGGAAGACCCCTGCTGAGAGATGTTTCATGTGGTTAGGTGGCTTCCGATCATCTGAGCTTCTTAAGgtagtaatctaatggt----tttgttttgaatgcacaattaaatttcttgacctcttggctcttgcccctgaactccaaggtccccttatgggagttttcattc

upper sequence: AT5G06960.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G056099_T01 (Zea mays), 5'ss of exon 8
TAAGAGTGATGTCTTCCATTTATTATCAGGGATGTGGAAAACCCCAGCTGAGAGATGTTTCTTGTGGCTCGGCGGTTTCCGTTCATCAGAACTTCTCAAGgtaaaaaacacacgaccaggttcggtttatttgg---tctcttcactagcaagtttccaaactttttacttctctactacag-------------------
 |||  |||||| |||||| || | ||||| |||||||||||  | ||||| || || ||||||||||| || ||||||||||| || || ||||| |||||  |   || | ||    | ||   |||| ||       |||   |  ||| |   |    |   | | ||   |  || |                   
AAAGGCTGATGTGTTCCATATACTTTCAGGCATGTGGAAAACATCTGCTGAAAGGTGCTTCTTGTGGCTTGGGGGTTTCCGTTCGTCTGAGCTTCTAAAGgtgcatg-catatgatatagatcaagttatatgaaaccacctttgatttcaaatagtcttggtacctgcctcaaaatgactgacaccccacacaccataat

upper sequence: AT5G06960.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM2G019907_T01 (Zea mays), 5'ss of exon 5
TAAGAGTGATGTCTTCCATTTATTATCAGGGATGTGGAAAACCCCAGCTGAGAGATGTTTCTTGTGGCTCGGCGGTTTCCGTTCATCAGAACTTCTCAAGgtaaaaaacacacgaccaggttcggtttatttggtctcttcactagcaagtttccaaactttttacttctctactacag------------------------
||     ||||| || ||| |  | || ||||||||||| ||||| ||||||||||||||| ||||| | || || ||||| ||||| ||  |||| ||||||  || |  | |     |||  |  |      |   |  | | |      ||    || ||  | ||  |     ||                        
TAGATCAGATGTTTTTCATGTGCTGTCTGGGATGTGGAAGACCCCTGCTGAGAGATGTTTCATGTGGTTAGGTGGCTTCCGATCATCTGAGGTTCTTAAGgtagtaatctaatggttttgttttgaatgcacaat---taaatttgttgacctcttggctcttgccctcgatctccaaggtccccttatgggagttttcgttc

upper sequence: AT5G06960.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA13G26280.1 (Glycine max), 5'ss of exon 10
TAAGAGTGATGTCTTCCATTTATTATCAGGGATGTGGAAAACCCCAGCTGAGAGATGTTTCTTGTGGCTCGGCGGTTTCCGTTCATCAGAACTTCTCAAGgtaaaaaacacacgaccaggttcggttta-tttggtctcttcactagcaagtttccaaactttttacttctctactacag--------------------
||||  |||||| ||||||||  | || || ||||||||||| || |||||||| ||||| |||||||| || ||||| || ||||| |||||||||||||| |         || |   |||  | || |||  |   ||    | |  ||||   |  ||  || |   |   |                        
TAAGGCTGATGTTTTCCATTTGCTGTCTGGCATGTGGAAAACACCTGCTGAGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTTCTCAAGgtgaggttatgctgatccttttcattctagtttcatggtttagaaaacgggttttgtagattagtaatggacagttttgtttaaattttttaaaaagaag

upper sequence: AT5G06960.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA15G37220.1 (Glycine max), 5'ss of exon 6
TAAGAGTGATGTCTTCCATTTATTATCAGGGATGTGGAAAACCCCAGCTGAGAGATGTTTCTTGTGGCTCGGCGGTTTCCGTTCATCAGAACTTCTCAAGgtaaaaaacacacgaccaggttcggttta-tttggtctcttcactagcaagtttcc-aaactttttacttctctactacag-------------------
||||  |||||| |||||||| || || || ||||||||||| || |||||||| ||||| |||||||| || ||||| || ||||| ||||| |||||||| |         || |   |||  | |  |||  |   ||    |    |||| | | |    | | |   | | |                       
TAAGGCTGATGTTTTCCATTTGTTGTCTGGTATGTGGAAAACACCTGCTGAGAGGTGTTTTTTGTGGCTTGGTGGTTTTCGGTCATCTGAACTCCTCAAGgtcaggttttgctgatccttttcattctggtttcatggtttagaaaatgggttttctagagcagtaattgggccattttgtttaaatttttttaagaaaa

upper sequence: AT5G06960.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GLYMA20G39050.2 (Glycine max), 5'ss of exon 8
TAAGAGTGATGTCTTCCATTTATTATCAGGGATGTGGAAAACCCCAGCTGAGAGATGTTTCTTGTGGCTCGGCGGTTTCCGTTCATCAGAACTTCTCAAGgtaaaa-aacacacgacc---aggttcg--gtttatttggtctctt------cactagcaagtttccaaac----tttttacttctctac-tacag----
||||  ||||||||||||||| || || || |||||||| || ||||| ||||| |||||  | ||||| || ||||| || ||||| ||||| |||||||| |    |     ||||    | || |  |||    |||| | ||       | |   |  |||| |||      |||| |||    || |||||    
TAAGGCTGATGTCTTCCATTTGTTGTCTGGAATGTGGAAGACACCAGCAGAGAGGTGTTTTCTATGGCTTGGTGGTTTTCGGTCATCTGAACTCCTCAAGgtgagctgatttgtgacccttcgatttgctgttcgcatggtttgttgaaagatattgtgacttttctaaaaagtagtttttcttggtaacatacagagta

upper sequence: AT5G06960.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: Vv13s0084g00660.t01 (Vitis vinifera), 5'ss of exon 10
TAAGAGTGATGTCTTCCATTTATTATCAGGGATGTGGAAAACCCCAGCTGAGAGATGTTTCTTGTGGCTCGGCGGTTTCCGTTCATCAGAACTTCTCAAGgtaaaa-------aacac----acgaccaggttcggtt----tatttggtctctt-cactagcaagtt-tccaaactttttacttctctactacag-----
 |||  |||||| ||||||||||||||||| ||||||||||| || || ||||| ||||| |||||||| || |||||||||||||| ||||| || ||||||  |       | ||     | |      ||| |||    ||||  | | ||  | ||  ||| |  |   ||   || |  ||  || | ||      
CAAGGCTGATGTTTTCCATTTATTATCAGGCATGTGGAAAACACCTGCAGAGAGGTGTTTTTTGTGGCTTGGTGGTTTCCGTTCATCTGAACTCCTAAAGgtatgacccttttaccattttgatggtttccttctgttggggtattcagaccctcaccctgacaaataataggaagacttcatctccata-tccatttctt

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAAGAGTGATGTCTTCCATTTATTATCAGGGATGTGGAAAACCCCAGCTGAGAGATGTTTCTTGTGGCTCGGCGGTTTCCGTTCATCAGAACTTCTCAAGgtaaaaaacacacgaccaggttcggtttatttggtctcttcactagcaagtttccaaactttttacttctctactacag

- - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG