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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGTgtaagtattttttttttgtttggaaaaataaaatggcttaattaatggcttaactaattatgtattggaaatttgaaaaaatataatag

Basic information

species Arabidopsis thaliana
transcript AT1G77690.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G77690.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os10g05690.1 (Oryza sativa), 5'ss of exon 3
GCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGTgtaagt--attttttttttgtttggaaaaata-aaatggcttaattaatggcttaactaattatgtattggaaatttgaaaaaatataatag--------
|  |||| ||||   |||||||| || || |  || ||||| |||||||| || ||||||||||| ||||||||||| || |||||||| ||||| |||||||   |   |  | |   |||   |  ||    | | ||||  | | | ||    | |  ||  |    ||||| |  || | || |          
GTGGAGGGTGTGGCGCACTCTGGGCCCACAAGCATCGTGCTCTACTTCACGGGGGCCACCAACATCCTCTACACCTTCGGGGGCCACGCTGTCACCGTgtaagccgaccatcctctctcttgattagctatggctcgattaaccatttgattggtcattagtgcctacttaattttactaagtttagtttagtttaat

upper sequence: AT1G77690.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: LOC_Os03g14080.1 (Oryza sativa), 5'ss of exon 5
GCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGTgtaagta---------ttttttttttgtttggaaaaataaaatggcttaattaatggcttaactaattatgtattggaaatttgaaaaaatataatag--
|  || |  ||||| ||||| || || || |  ||||| || ||||||||||| ||||| ||||||||||||||||| ||||| ||||| || || |||||||           | | | || | |         | ||| ||  || |  | |   |            ||   | |    | | | ||   |||  
GTCGATGGAGTGAAGCACTCGGGCCCTACAAAGATGGTCCTCTACTTCACCGGGGCCACAAACATTCTCTACACCTTCGGTGGGCACGCTGTTACTGTgtaagccgacaaacgctctctattctatgcccctgtgtcaaaaggaatactgcacgaaatggtctcagtcacatgccacaccgtagagagtaccgtaggc

upper sequence: AT1G77690.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G045057_T02 (Zea mays), 5'ss of exon 5
GCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGTgtaagtat---tttttttttgtttggaaaaata-----aaatggcttaattaatggcttaactaattatgtatt-ggaaatttgaaaaaatataatag--------------------------------------
|  || | |||||  ||||| || |||| ||  |||||||| ||||||||||| ||||||||||| |||||||||||||| ||||| || ||||| |||||||  |    |       || |  |   |||     | |  ||  || | | |  |     | ||  |  ||  ||  |  | |   |  | ||                                        
GTGGAAGGTGTGACGCACTCGGGCCCAAGCAAGATGGTGCTCTACTTCACCGGTGCCACCAACATCCTCTACACCTTTGGAGGCCATGCTGTCACTGTgtaagcctcagctgccagcagtctatatctatacccacacacagcagaagtgaagtttaggtcacttcagagttcagagctacgtacgtacgtgatgagtgtcacagtgtgtgtacaaatgggccggttggtgcag

upper sequence: AT1G77690.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G149481_T04 (Zea mays), 5'ss of exon 4
--GCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGTgtaagta-----------ttttttttttgtttggaaaaataaaatggcttaattaatggcttaactaattatgtattggaaatttgaaaaaatataatag-
  | ||| |  ||||| ||||| || || ||||  |||||||| ||||||||||| ||||| |||||||||||||| || || || ||||| || || ||||||| |           ||| ||| || |||  | |   |   |  |   |  || |    ||  ||| | | ||   || |  ||  ||  | |  |  
AGGTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGTgtaaggagacaaaacacctttctttcttttttatatatgcatggtccccggaacaaagaag-aagaaataacgcatcacaactgggaccaacgaaagcatt

upper sequence: AT1G77690.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G149481_T02 (Zea mays), 5'ss of exon 5
GCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGTgtaagta-----------ttttttttttgtttggaaaaataaaatggcttaattaatggcttaactaattatgtattggaaatttgaaaaaatataatag-
| ||| |  ||||| ||||| || || ||||  |||||||| ||||||||||| ||||| |||||||||||||| || || || ||||| || || ||||||| |           ||| ||| || |||  | |   |   |  |   |  || |    ||  ||| | | ||   || |  ||  ||  | |  |  
GTTGATGGCGTGAAGCACTCCGGGCCGACCAAGATGGTGCTCTACTTCACCGGGGCCACAAACATTCTCTACACTTTCGGAGGGCACGCTGTTACCGTgtaaggagacaaaacacctttctttcttttttatatatgcatggtccccggaacaaagaag-aagaaataacgcatcacaactgggaccaacgaaagcatt

upper sequence: AT1G77690.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GRMZM2G129413_T01 (Zea mays), 5'ss of exon 1
--GCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGTgtaagtattttttttttgtttggaaaaataaaatggcttaattaatggcttaactaattatgtattggaaatttgaaaaaatataatag--------------
  |  ||||  ||  | || || || || || |  || || || ||||||||||| || |||||||| |||||||| || || || ||||| |||||||||| ||||| | | |   ||   |  |    || |      || | | | ||| |    | |   |||   | |   ||     || |||              
AGGTCGAGGGCGTCCAGCATTCGGGGCCCACAAGGATCGTACTCTACTTCACCGGGGCGACCAACATACTCTACACGTTCGGGGGACACGCGGTCACAGTgtgagtatatctct---gtcctgttagcctaattaatcgcatcattagtttatcagtctgtcccttgattactcctaatcggctagtagtagtagtagttaat

upper sequence: AT1G77690.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv18s0001g03540.t01 (Vitis vinifera), 5'ss of exon 5
GCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGTgtaagtatttttttt--ttgtttggaaaaataaaatggcttaattaatggcttaactaattatgtat---tggaaatttgaaaaaatataatag------
| |||||  ||||| |||||||| ||||||| |||||| || |||||||| || || |||||||||||||||||||||||||| || || |||||||||| || | ||  ||   |  |    |||| |  | |     |   | | |  |    | |   | ||   |  |  |   |     | | |  |      
GTTGAGGGGGTGAAGCACTCTGGCCCAACCAAAATGGTTCTCTACTTCACTGGGGCTACCAACATTCTCTACACCTTTGGTGGTCATGCTGTCACAGTgtgagaacttaattaaatactcatcaaaactgcatttatacatgcatttgtatgtacattctcgcatgtctaaaggtacaaccctttttgaaggaaagga

upper sequence: AT1G77690.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S90_46V6.1 (Physcomitrella patens), 5'ss of exon 5
GCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGTgtaagtatttttttt--ttgtttggaaaaata--aaatggcttaattaatg--gcttaactaattatgtattggaaatttgaaaaaatataatag----------------------------------------------------------
| ||   ||||    || |||| |||||| || | |||  | |||||||| ||||| ||||| ||||| |||||||||||||| ||||| || || |||| |||| ||  | |  ||  |    || |     |  | | |   | |||  |  |   | ||| |    |  || ||        |  |   |                                                          
GTTGCCAATGTTGTTCATTCTGCTCCAACGACCAAGGTCTTGTACTTCACAGGAGCAACCAATATTCTGTACACCTTTGGTGGTCACGCTGTTACTGTgtgagtacttgctataattactcaccaagactccgatcgacgtccatgatgttgagtttttcattctagtatataacttattttctctgcacctgtccggctggaacttctgaatttgtgaggctgacttggattcaaaatcaccatctgcag

upper sequence: AT1G77690.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S211_67V6.1 (Physcomitrella patens), 5'ss of exon 5
GCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGTgtaagtattttttttttgt-ttggaaaaataaaatggcttaattaatggcttaactaattatgtattggaaatttgaaaaaatataatag---------------------------------------------------------------------------------------------
| ||   ||||    ||  | |  || || || | |||  | |||||||| ||||| ||||||||||| || || || ||||||||||| || || ||||||||| ||       |   | | |   |   || | |     | |           || | || |    ||  ||  |  | | || |                                                                                             
GTTGCCAATGTCGTCCATACGGCGCCGACAACGAAGGTCTTGTACTTCACAGGAGCAACCAACATTCTGTATACTTTCGGTGGCCACGCTGTTACTGTgtaagtaattgacccagggactaggattctcctattgatgttcaagttttcagttctcttgtttaatcatgataggaccagtttttatcggtgcacttttcgaatattttttttgtgtacctgcatatttagaccatctaattctgtgaaaggaactttcttggatgtgtatgtcattcgcag

upper sequence: AT1G77690.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: PP1S213_89V6.1 (Physcomitrella patens), 5'ss of exon 5
GCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGTgtaagta-----------ttttttttttgtttggaaaaataaaatggcttaattaatggcttaactaattatgtattggaaatttgaaaaaatataatag---------------------------------------------------
 |    |  || |  |||  ||| ||     | | |||  | |||||||| ||||| |||||||||||||||||||||||  ||||||| || ||||||||||||           |  |  |  || |         |   |         ||| | |   | | || |||    | |||||   |   |     |                                                    
ACCTCTGGCGTAACGCACAATGGCCCCGTGTCGAGGGTTTTATACTTCACGGGAGCAACCAACATTCTCTACACCTTTGGAAGCCACGCTGTGACAGTgtaagtaaaaaagggagctcctcctcctgctcctctctcaacggttttcatcccaatcgttcctcgatttttgttccagcaattttgtattgtcactcactgaggctcagagagaaaaaaggccctcaaacttcctaattactattgccag

upper sequence: AT1G77690.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: EFJ36050 (Selaginella moellendorffii), 5'ss of exon 5
GCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGTgtaagt-----attttttt-----------tttgtttggaaaaataaaatggcttaattaatggcttaactaattatgtattggaaatttgaaaaaatataatag-----------------------------------------------------------------------------------
|     | ||| || || || |  ||||  |   | || |  || ||||| ||||||||||||||  | |||||||||||||| || |||||||| ||||||||     ||  || |           |||| |||     |  | ||   |  ||  ||  | |   |  |  |   |        ||   | ||  |||                                                                                     
GACCCAGGTGTAAAGCATTCGGCCCCAAATAATCTCGTCCAATATTTCACTGGAGCCACCAACATCTTGTACACCTTTGGTGGTCATGCCGTCACTGTgtaagtcgatcatgattctcacggcaccactttgcttgatcctacgatatcattccatcgattccctcctttttctttcctgttcttcctgctcagatcaaatcattcccttccggatcaaatcaagttttttcttacttctttttgcaagaccagatgatatagctaagtttgtggttttcttgcag

upper sequence: AT1G77690.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: EFJ18760 (Selaginella moellendorffii), 5'ss of exon 5
GCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGTgtaagt-----attttttt-----------tttgtttggaaaaataaaatggcttaattaatggcttaactaattatgtattggaaatttgaaaaaatataatag--------------------------------------------------------------------------------------
|     | ||| || || || |  ||||  |   | || |  || ||||| ||||||||||||||  | ||||||||||||||||| |||||||| ||||||||     ||  || |           |||| |||     |  | ||   |  ||  ||  | |   |  |  |   |        ||   | ||  |||                                                                                        
GACCCAGGTGTAAAGCATTCGGCCCCAAATAATCTCGTCCAATATTTCACTGGAGCCACCAACATCTTGTACACCTTTGGTGGCCATGCCGTCACTGTgtaagtcgatcatgattctcacggcaccactttgcttgatcctacgatatcattccatcgattccctcctttttctttcctgttcttcctgctcagatcaaatcatacccctccggatcaaatcaagttttttcttacttctttttgcaagaccagatgatataactaagttgtttgtggttttcttgcag

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGAGGATGTGAAACACTCTGGTCCAACCACAATGGTGCTTTACTTCACCGGAGCCACCAACATTCTCTACACCTTTGGTGGCCACGCCGTCACAGTgtaagtattttttttttgtttggaaaaataaaatggcttaattaatggcttaactaattatgtattggaaatttgaaaaaatataatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG