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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTTTAGGTACACCAACAAGGGAAGAAATCAAGTGCATGAATCCAAACTATACAGAATTTAAGTTTCCGCAGATAAAACCTCATCCATGGCACAAGgtatgccttctaatgttattgattatcacctaccagaataatctttaatcagtggttttgttggtgaatgcattttttcaaagaggagttctggtatttg...

Basic information

species Arabidopsis thaliana
transcript AT1G09840.2
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G09840.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: LOC_Os03g62500.1 (Oryza sativa), 5'ss of exon 10
GTTTTAGGTACACCAACAAGGGAAGAAATCAAGTGCATGAATCCAAACTATACAGAATTTAAGTTTCCGCAGATAAAACCTCATCCATGGCACAAGgtatgccttctaatgttattga---ttatcacctaccagaataatctttaatcagtggttttgttggtgaatgcattttttcaaagaggagttctggtatttg
||||| ||||| |||||||||||||| ||||||||||||||||| ||||| || || || || || || || || ||  ||||||||||||||||||||| |   | |   ||    |   | ||    || |    |    |||  |   |  |||||  ||  |  |   | ||| || |   | | ||    | | 
GTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAATTCCCTCAAATTAAGGCTCATCCATGGCACAAGgtattctgcccatccttgacaaaactaatgcaatatcgatgtccgatttggtacatacttttg--ggacagggagatcttttaacgcaaattactatgctgt-

upper sequence: AT1G09840.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GRMZM2G138676_T01 (Zea mays), 5'ss of exon 10
GTTTTAGGTACACCAACAAGGGAAGAAATCAAGTGCATGAATCCAAACTATACAGAATTTAAGTTTCCGCAGATAAAACCTCATCCATGGCACAAGgtatgccttctaatgttattgattatcacctaccagaataatctttaatcagtggttttgttggtgaatgcattttttcaaagaggagttctggtatttg------
||||| ||||| |||||||||||||| |||||||||||||| ||||||||||| || || ||||| || || || ||| ||||||| ||||||||||||       |||| |        || |  || |    ||   |   |    || | | | |||      |     | ||||  |||    || |||         
GTTTTGGGTACTCCAACAAGGGAAGAGATCAAGTGCATGAACCCAAACTATACGGAGTTCAAGTTCCCACAAATTAAAGCTCATCCGTGGCACAAGgtaa-----ttaatatacaaatagataatttagctctgtatcatcacagtgatg-tctagctggaattaactggcatacaaaatggatgcgtgatatgcacaaacg

upper sequence: AT1G09840.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA16G00400.1 (Glycine max), 5'ss of exon 9
GTTTTAGGTACACCAACAAGGGAAGAAATCAAGTGCATGAATCCAAACTATACAGAATTTAAGTTTCCGCAGATAAAACCTCATCCATGGCACAAGgtatgccttctaatgttattgattatcacctaccagaataatctttaatcagtggttttgttggtgaatgcattttttcaaagaggagttctggtatttg------
||||| || || ||||| ||||| || || ||||||||||| ||||| ||||| |||||||||||||| |||||||||||||||||||||||||||||      |||  | |  ||  |||    ||       |||  |    | | || || |  |  |  | |  ||   | |||   |  |      |||        
GTTTTGGGAACTCCAACCAGGGAGGAGATAAAGTGCATGAACCCAAATTATACTGAATTTAAGTTTCCACAGATAAAACCTCATCCATGGCACAAGgttcattgtctcttatgcttacttacattctg------taacttactgtgaatgtttgtagtaattcagggtttaggttaaatttgcatatgctaattcattgcct

upper sequence: AT1G09840.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: GLYMA12G28730.1 (Glycine max), 5'ss of exon 10
GTTTTAGGTACACCAACAAGGGAAGAAATCAAGTGCATGAATCCAAACTATACAGAATTTAAGTTTCCGCAGATAAAACCTCATCCATGGCACAAGgtatgccttctaatgttattgattatcacctaccagaataatctttaatcagtggttttgttggtgaatgcattttttcaaagaggagttctggtatttg-------
||||| || || ||||| ||||| || || ||||||||||| ||||| ||||| |||||||||||||| ||||||||||||||||| |||||||||||      |||  | |  ||  |||     |       |||  |    | | || || |  |  |  | |  ||   | |||   |  || || || ||        
GTTTTGGGAACTCCAACCAGGGAGGAGATAAAGTGCATGAACCCAAATTATACTGAATTTAAGTTTCCACAGATAAAACCTCATCCGTGGCACAAGgttcattctcttttctgcttacttacattttg------taacttactgtgaatgtttgtagtaattcaggatttaggttaaatttgc-ttatgctaattcattgcct

upper sequence: AT1G09840.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: Vv12s0035g01060.t01 (Vitis vinifera), 5'ss of exon 9
GTTTTAGGTACACCAACAAGGGAAGAAATCAAGTGCATGAATCCAAACTATACAGAATTTAAGTTTCCGCAGATAAAACCTCATCCATGGCACAAGgtatgc-cttctaatgttattgattatcacctaccagaataatctttaatcagtggttttgttggtgaatgcattttttcaaagaggagttctggtatttg--
|| || || ||||| || ||||| || || || || |||||||||||||| || |||||||| || || || ||||| |||||||||||||||||||||||| |||    | |  ||    | ||        |||     |   ||| || || || |  |   |     | | |         | |    |      
GTCTTGGGAACACCTACCAGGGAGGAGATAAAATGTATGAATCCAAACTACACCGAATTTAAATTCCCACAAATAAAGCCTCATCCATGGCACAAGgtatgctctttccctttcctttgaaaccataagttcaaatg--tatctgtcaatgtttgtgctc-tctttctccctctccctctccctctccctccacccacc

upper sequence: AT1G09840.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: PP1S60_100V6.1 (Physcomitrella patens), 5'ss of exon 9
GTTTTAGGTACACCAACAAGGGAAGAAATCAAGTGCATGAATCCAAACTATACAGAATTTAAGTTTCCGCAGATAAAACCTCATCCATGGCACAAGgtatgccttctaatgttattg-attatcacctaccagaataatctttaatcagt--ggttttgttggtgaatg--cattttttcaaagaggagttctggtatttg
|| || || ||||| ||  | || || ||||||||||||||||| ||||| || || || ||||||||||| || ||  |||| ||||||||||| |||||   |||  ||| | || | | |   |  |  |     |  |     |||   |   ||  | || | |  | | |||||      |||   |||      
GTGTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCGCAAATCAAGGCTCACCCATGGCACAAAgtatgtggtctg-tgtgaatgcactgttttcatcttgggctttggtagtgtagtccagaagtggagatgtacgaccgtgttttcgtgtgtgagcggtgggt----

upper sequence: AT1G09840.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 5'ss of exon 8
GTTTTAGGTACACCAACAAGGGAAGAAATCAAGTGCATGAATCCAAACTATACAGAATTTAAGTTTCCGCAGATAAAACCTCATCCATGGCACAAGgtatgccttctaatgttattgattatcacctaccagaataatctttaatc--agtggttttgttggt--gaatgcattttttcaaagaggagttctggtatttg
|| || || ||||| ||| | || || || |||||||||||||| ||||| || || || |||||||| || || ||  ||||||| |||||||||||| | ||     | |   || |  |   ||   |   |  | |  |     | ||     |||| |  ||| || ||   |  |     | |   |||  || 
GTGTTGGGGACACCCACACGCGAGGAGATAAAGTGCATGAATCCGAACTACACGGAGTTCAAGTTTCCTCAAATTAAGGCTCATCCTTGGCACAAGgtacggct---ggtctgtgtgttagtggtctggtatggtgctttggagatgtactgtaacagttgattggaaagcgttacctgtattcataataacggtgatt-

upper sequence: AT1G09840.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: PP1S306_62V6.1 (Physcomitrella patens), 5'ss of exon 8
GTTTTAGGTACACCAACAAGGGAAGAAATCAAGTGCATGAATCCAAACTATACAGAATTTAAGTTTCCGCAGATAAAACCTCATCCATGGCACAAGgtatgccttctaatgttattgat-tatcacctaccagaataatctttaatcagtggttttgttggtgaatgca---ttttttcaaagaggagttctggtatttg-----------------------------------------------------------------------------
||||| || ||||| ||  | || || ||||||||||||||||| ||||| ||||| || |||||||| || || ||  | || || |||||||| |||||  || |  ||  | || | |     |  || |  |  |        ||||   | || | ||   |      ||| ||    ||  |   || || |||                                                                             
GTTTTGGGGACACCGACTCGTGAGGAGATCAAGTGCATGAATCCGAACTACACAGAGTTCAAGTTTCCACAAATCAAGGCGCACCCGTGGCACAAAgtatgttttttg-tgcgaatgctatgatgtcatcctgggtgttgcggttgtagtgcggtagtggatgtgggtcagcctttctcgtgtagcggcattgttagttgcgtgcgtcgtggtttgttggatgttgggttttgacgacggtaaccggcgtttggtatggccgatgtgggaattgcag

upper sequence: AT1G09840.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: EFJ07923 (Selaginella moellendorffii), 5'ss of exon 10
GTTTTAGGTACACCAACAAGGGAAGAAATCAAGTGCATGAATCCAAACTATACAGAATTTAAGTTTCCGCAGATAAAACCTCATCCATGGCACAAGgtatgccttctaatgttattgattatcacctaccagaataatctttaatcagtggttttgttggtgaatgcattttttcaaagaggagttctggtatttg
|| |||||||| || ||  |||| |||||||| ||||||||||||||||| || || |||||||| || ||||| ||| | ||||| |||||||||||| |      |||  |   |  ||||  ||  |    |     || ||  |||| |  ||||                                     
GTCTTAGGTACTCCTACTCGGGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAGgtaagagc---aatcatccggtatatc-tctctctctgtctctcttgat--gtggctc-gttgacag---------------------------------

upper sequence: AT1G09840.2 (Arabidopsis thaliana), 5'ss of exon 11
lower sequence: EFJ07216 (Selaginella moellendorffii), 5'ss of exon 10
GTTTTAGGTACACCAACAAGGGAAGAAATCAAGTGCATGAATCCAAACTATACAGAATTTAAGTTTCCGCAGATAAAACCTCATCCATGGCACAAGgtatgccttctaatgttattgattatcacctaccagaataatctttaatcagtggttttgttggtgaatgcattttttcaaagaggagttctggtatttg
|| |||||||| || ||  | || |||||||| ||||||||||||||||| || || |||||||| || ||||| ||| | ||||| |||||||||||| |      |||  |   |  ||||  ||  |    |     || ||  |||| |  ||||                                     
GTCTTAGGTACTCCTACTCGCGAGGAAATCAAATGCATGAATCCAAACTACACGGAGTTTAAGTTCCCTCAGATTAAAGCGCATCCCTGGCACAAGgtaagagc---aatcatccggtatatc-tctctctctgtctctcttgat--gtggctc-gttgacag---------------------------------

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTTTAGGTACACCAACAAGGGAAGAAATCAAGTGCATGAATCCAAACTATACAGAATTTAAGTTTCCGCAGATAAAACCTCATCCATGGCACAAGgtatgccttctaatgttattgattatcacctaccagaataatctttaatcagtggttttgttggtgaatgcattttttcaaagaggagttctggtatttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT