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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGTTCTTAAGACAACCTCATTTCATTGTTTGGGACAATAGTGATCTTGTGACACATGAAGTAATGGGAGGTCTCAAGAATGTCTACGCCATTGGAGCTGgtaagtttctgtatgtagacacggatttgagtgataattatcaagttttcacactttgatccttcttgttgtgttcag

Basic information

species Arabidopsis thaliana
transcript AT2G41540.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G41540.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os01g71280.1 (Oryza sativa), 5'ss of exon 3
AAGTTCTTAAGACAACCTCATTTCATTGTTTGGGACAATAGTGATCTTGTGACACATGAAGTAATGGGAGGTCTCAAGAATGTCTACGCCATTGGAGCTGgtaagt-ttctgtatgtagacacggatttgagtgataattatcaa--gttttcaca-ctttgatccttcttgttgtgttcag------------------
|||||  | |||||||| ||||||||||| ||||| || ||||||||||| |||||||| || ||||| ||| | ||||||||||||||||| || |||||||||  |  | ||  ||    | | ||    |   || ||| ||   | || | | |  | |   |  ||      | |                    
AAGTTTCTGAGACAACCACATTTCATTGTCTGGGATAACAGTGATCTTGTTACACATGAGGTGATGGGTGGTTTGAAGAATGTCTACGCCATCGGTGCTGgtaagaatattttaaatacgttctgtttgttttccaaaatattaactatctttataacagtaaaaataattaactaatcctactaacaaacgaatggagt

upper sequence: AT2G41540.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os01g58740.1 (Oryza sativa), 5'ss of exon 3
AAGTTCTTAAGACAACCTCATTTCATTGTTTGGGACAATAGTGATCTTGTGACACATGAAGTAATGGGAGGTCTCAAGAATGTCTACGCCATTGGAGCTGgtaagtttctgtatgtagacacggatttgagtgataattatcaagttttcacactttgatccttcttgttgtg---ttcag----------------------
|| || || || || |||||||| ||||| ||||| |||||||||||  | ||||||||||| ||||||||| | || ||||| || |||||||| || ||||| ||||| | |     |  |  | |   || ||  |     ||  ||||  |        |  |||||||   || ||                      
AAATTTTTGAGGCAGCCTCATTTTATTGTATGGGATAATAGTGATCTCATTACACATGAAGTCATGGGAGGTTTGAAAAATGTGTATGCCATTGGTGCCGgtaa-tttctatttcctctcttgattgtttttgctatcttct--gtaatcacggtagagcatatactgttgtgatatttagcatggggtatgttggaatgcac

upper sequence: AT2G41540.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os05g41590.1 (Oryza sativa), 5'ss of exon 2
AAGTTCTTAAGACAACCTCATTTCATTGTTTGGGACAATAGTGATCTTGTGACACATGAAGTAATGGGAGGTCTCAAGAATGTCTACGCCATTGGAGCTGgtaagtttc-tgtatgtagacacggatttgagtg-----ataattatcaagttttcacact-------ttgatccttcttgttgtgttcag---------
|| ||  | || || |||||||| ||||| ||||| |||||||||||  | || |||||||||||||| ||  | |||||  | || |||||||| ||||||||||| | ||     | |   |   ||   ||     || |   | ||  |||   |||       |  | || || ||| |  ||            
AAATTTCTGAGGCAGCCTCATTTTATTGTGTGGGATAATAGTGATCTCATCACTCATGAAGTAATGGGCGGCTTAAAGAACATATATGCCATTGGTGCTGgtaagttccatggtctcatatctgacgttttatgtccatatcaccttgaaaatttttaactgggaaaataaaaccatcatgtggcttttcttgttgaagc

upper sequence: AT2G41540.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G155348_T01 (Zea mays), 5'ss of exon 3
AAGTTCTTAAGACAACCTCATTTCATTGTTTGGGACAATAGTGATCTTGTGACACATGAAGTAATGGGAGGTCTCAAGAATGTCTACGCCATTGGAGCTGgtaa-gtttctgtatgtagacacggatttgagtgataattatcaagttttcacactttgatccttcttgttgtgttcag----------------------
||||| || || || || ||||||||||| |||||||| ||||||||||| || ||||| || ||||| || || ||||||||||| || || || ||||||||   |    | |||        |  |||   ||| |  |  |   |   ||   |  | |||  |||||     |                       
AAGTTTTTGAGGCAGCCACATTTCATTGTCTGGGACAACAGTGATCTTGTCACCCATGAGGTGATGGGTGGCCTGAAGAATGTCTATGCAATCGGTGCTGgtaatactaacttctgtctttttttaactga-caatattattgtacaataggcatcctactacttgatgttgaagaaaacataacaaacatgtaaatgttt

upper sequence: AT2G41540.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G173195_T01 (Zea mays), 5'ss of exon 2
AAGTTCTTAAGACAACCTCATTTCATTGTTTGGGACAATAGTGATCTTGTGACACATGAAGTAATGGGAGGTCTCAAGAATGTCTACGCCATTGGAGCTGgtaagtttctgtatgtagacac---ggatttgagtga----taattatcaagttttcacac----tttgatccttcttgttgtgttcag-----------
|| ||||| || ||||||||||| ||||| |||||||||||||||||  | || |||||||| ||||| ||  | || || || || |||||||| || ||||||||  |  ||  ||| |    | ||||   |      |  ||  | |||| | |        ||| ||  || |    | ||              
AATTTCTTGAGGCAACCTCATTTTATTGTATGGGACAATAGTGATCTCATTACTCATGAAGTCATGGGCGGCTTAAAAAACGTATATGCCATTGGGGCCGgtaagttatttgatccagaaaaatggaatttccatttgctctcttttcccagttcttatgagatacttggtcaatcattgcatatttgatgtttcatcaa

upper sequence: AT2G41540.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv08s0007g09000.t01 (Vitis vinifera), 5'ss of exon 2
AAGTTCTTAAGACAACCTCATTTCATTGTTTGGGACAATAGTGATCTTGTGACACATGAAGTAATGGGAGGTCTCAAGAATGTCTACGCCATTGGAGCTGgtaagtt------tctgtatg-tagacacggatttgagtgataattat---caagttttcacactttgatccttcttgttgtgttcag----------------------------------------------------------------------------------------------------------------
|||||  | || ||||| |||||||| || |||||||| ||||| ||||| || |||||||| ||||| ||  | |||||||| || ||||||||||| ||||||||      ||| |||| | |  |   | | ||| ||| ||| |     |  ||||| | | ||| | | |||||    |  |                                                                                                                 
AAGTTTCTGAGGCAACCCCATTTCATCGTATGGGACAACAGTGACCTTGTCACTCATGAAGTTATGGGTGGCTTAAAGAATGTGTATGCCATTGGAGCCGgtaagttgttatttctttatgatggtaatataatagagggatcattgtgcttgaagtttcata-tatgagcatccttgtcagataaacttcagcaatgatctggttctcattttgacctactaggagaagaaaaccaaaatttaaaaatgttgttattggatttaatcaagagtctcacattttcactttgattttccag

upper sequence: AT2G41540.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S323_18V6.2 (Physcomitrella patens), 5'ss of exon 4
AAGTTCTTAAGACAACCTCATTTCATTGTTTGGGACAATAGTGATCTTGTGACACATGAAGTAATGGGAGGTCTCAAGAATGTCTACGCCATTGGAGCTGgtaagtttctg-tatgtagacacggatttgagtgataattatcaagttttcacactttgatccttcttgttgtgttcag-------------------------------------------------------------------------------------------------------------------------
|||||  |  | || || ||||| ||||| |||||||||  |||  || | |||||||| || ||||||||||| |||||||| ||||||||||| |||||| || | ||   | |    | ||  |||   |  || |   ||| ||||| || | |  |  | || | ||   ||                                                                                                                           
AAGTTTCTGCGCCAGCCACATTTTATTGTGTGGGACAATCCTGACATTATCACACATGAGGTCATGGGAGGTCTTAAGAATGTGTACGCCATTGGTGCTGgtgagctactaacaggactcctcgtgttt---ttctactgtgcaaattttctcattctagttttact-gatggactcgctaaataggagatttcgtttaatataaagaatgaacagaggatggtagtgccaaacgtggaattcggagtgttcaggaaatggtgggcctgtgctgactaagataagttatggcttgtgcag

upper sequence: AT2G41540.2 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S114_190V6.1 (Physcomitrella patens), 5'ss of exon 4
AAGTTCTTAAGACAACCTCATTTCATTGTTTGGGACAATAGTGATCTTGTGACACATGAAGTAATGGGAGGTCTCAAGAATGTCTACGCCATTGGAGCTGgtaagtttctgt-----------atgtagac-----acggatttgagtgataattatcaa--gttttcacactttgatccttcttgttgtgtt-cag---
|||||  |  | || || || || ||||| ||||| |||  |||  |||| |||||||| || ||||| ||||| |||||||| ||||||||||| || ||| ||   ||||            |||         | | |||       |||| ||| |  |||||| || | |   | ||   |||   |  | |   
AAGTTTCTGCGCCAGCCACACTTTATTGTGTGGGATAATCCTGACATTGTCACACATGAGGTCATGGGTGGTCTTAAGAATGTGTACGCCATTGGTGCCGgtgagccactgtcacgatcctctgtgttagtcttctatgcattgagaatgtaatcatctaatgttttctcattctagcctttagagttaaatcactgaat

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGTTCTTAAGACAACCTCATTTCATTGTTTGGGACAATAGTGATCTTGTGACACATGAAGTAATGGGAGGTCTCAAGAATGTCTACGCCATTGGAGCTGgtaagtttctgtatgtagacacggatttgagtgataattatcaagttttcacactttgatccttcttgttgtgttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT