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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTTACCGTCCACCTAGAGCTTCTCATTGTTCCATATGCAACAACTGTGTCCAGAGATTTGATCATCACTGCCCTTGGGTTGGCCAGTGCATTGGAGTGgtaagtttactccatgactcttgccatatattcccggttctatgttttgaacttgtttggattcttttgcag

Basic information

species Arabidopsis thaliana
transcript AT3G56930.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G56930.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os11g03910.1 (Oryza sativa), 5'ss of exon 3
GCTTTACCGTCCACCTAGAGCTTCTCATTGTTCCATATGCAACAACTGTGTCCAGAGATTTGATCATCACTGCCCTTGGGTTGGCCAGTGCATTGGAGTGgtaagtttac--tccatgactc-----------ttgccatatattcccggttctatgttttgaacttgt-ttggattcttttgcag--------------
    ||||| |||||  || | || ||||| ||||| ||||||||||| ||  | |  |||||||| |||||||| ||||| ||||||||||||||| | ||||||  ||  || ||||  |           | | |||          ||| ||||   |  |  ||  |   |  ||    ||              
AAGGTACCGCCCACCGCGATCCTCACATTGCTCCATCTGCAACAACTGCGTTGAAAAGTTTGATCACCACTGCCCATGGGTCGGCCAGTGCATTGGACTTgtaagtaaacaatcaatgatgcagcaatcagtatagtcatcagccttaaattcaatgtgcagttccagtactatttgtttccatagtgtttttaggcatc

upper sequence: AT3G56930.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: LOC_Os12g03730.1 (Oryza sativa), 5'ss of exon 3
GCTTTACCGTCCACCTAGAGCTTCTCATTGTTCCATATGCAACAACTGTGTCCAGAGATTTGATCATCACTGCCCTTGGGTTGGCCAGTGCATTGGAGTGgtaagtttac--tccatgactc--ttgcca-tatatt------cccggttctatgttttgaacttgt-ttggattcttttgcag----------------
    ||||| |||||  || | || ||||| ||||| ||||||||||| ||| | |  |||||||| ||||| || ||||| ||||| ||||||||| | ||||||  ||  || ||||  |  |   || |||| |      ||   ||| ||||   |  |  ||  |   |  ||    ||                
AAGGTACCGCCCACCACGATCCTCACATTGCTCCATCTGCAACAACTGCGTCGAAAAGTTTGATCACCACTGTCCATGGGTCGGCCAATGCATTGGACTTgtaagtaaacaatcaatgatgcagtaatcagtatagtcatcagcctaattcaatgtgcagttccagtactatttgtttccatagtgtttttagaaatatg

upper sequence: AT3G56930.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GRMZM2G005834_T01 (Zea mays), 5'ss of exon 3
GCTTTACCGTCCACCTAGAGCTTCTCATTGTTCCATATGCAACAACTGTGTCCAGAGATTTGATCATCACTGCCCTTGGGTTGGCCAGTGCATTGGAGTGgtaagtttactccatgactcttgccatatattcccggttctatgttttgaacttgtttggattcttttgcag--------------------------------
|   |||||||| ||  || | || || || ||||| ||||||||||| ||||| |  ||||| || |||||||| ||||| ||||||||||||||| | ||||||   |  |    ||    | ||  | | |    | |   | ||||| || |  |  |     | |||                                
GAGGTACCGTCCGCCACGATCCTCGCACTGCTCCATCTGCAACAACTGCGTCCACAAGTTTGACCACCACTGCCCATGGGTCGGCCAGTGCATTGGACTTgtaagtaaccgacccagct---actatgcagtacgcaatttgaatgttgaa-ttatcagattctagctccagacctccactgaaaaaggacacgtgcaagtcag

upper sequence: AT3G56930.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA19G30360.1 (Glycine max), 5'ss of exon 3
GCTTTACCGTCCACCTAGAGCTTCTCATTGTTCCATATGCAACAACTGTGTCCAGAGATTTGATCATCACTGCCCTTGGGTTGGCCAGTGCATTGGAGTGgtaagtt---tactccatgactcttgccatatattcccggttctatgttttgaacttgt-ttggattcttttgcag-------------------------
|||||| || || ||| |  ||||||||||||| ||||||||||| |||||||||||||||||||||||||| || ||||||||||||||||||||| | ||||||    ||  |  | |    ||  || ||    |  ||| |||     |  ||   |||  || |    ||                          
GCTTTATCGCCCTCCTCGTACTTCTCATTGTTCTATATGCAACAATTGTGTCCAGAGATTTGATCATCACTGTCCCTGGGTTGGCCAGTGCATTGGAATAgtaagtccagtatactgtaaaaagtgaaatttagaaact-ttcaatgagacaatgttacattgttttatccaacaacttttttcttatgcttcttggaaat

upper sequence: AT3G56930.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA03G27410.1 (Glycine max), 5'ss of exon 3
GCTTTACCGTCCACCTAGAGCTTCTCATTGTTCCATATGCAACAACTGTGTCCAGAGATTTGATCATCACTGCCCTTGGGTTGGCCAGTGCATTGGAGTGgtaagt---ttactccatgactcttg----ccatatattcccggtt---ctatgttttgaacttgtttg----gattcttttgcag--------------
|||||| ||||| ||| |  ||||||||||||| |||||| |||| |||||||||||||||||||||||||| || ||||||||||||||||||||| | ||||||    ||  |  | ||   ||      | | | | ||  |      |||||     ||| | |      ||| ||||                  
GCTTTATCGTCCTCCTCGTACTTCTCATTGTTCTATATGCGACAATTGTGTCCAGAGATTTGATCATCACTGTCCCTGGGTTGGCCAGTGCATTGGAATAgtaagtcctctatactgtaacaagtgaagtttagaaacttccaatgagataatgttacatgcttttatccgacaatttttttcttatacttcttgggaat

upper sequence: AT3G56930.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv08s0040g00380.t01 (Vitis vinifera), 5'ss of exon 3
GCTTTACCGTCCACCTAGAGCTTCTCATTGTTCCATATGCAACAACTGTGTCCAGAGATTTGATCATCACTGCCCTTGGGTTGGCCAGTGCATTGGAGTGgtaagtttactccatgactcttgccatatattcccggttc-tatgttt-tgaacttgtttggattcttttgcag---------------------------
|||||| ||||| ||| | | |||||| || || || |||||||||||||| |||||||||||||||||||| || |||||||| || ||||||||| | ||||||||  |   |   | ||    ||  |       |  ||||| | || |  ||  || | |  | | ||                            
GCTTTATCGTCCTCCTCGTGTTTCTCACTGCTCAATCTGCAACAACTGTGTTCAGAGATTTGATCATCACTGTCCATGGGTTGGTCAATGCATTGGAATAgtaagttt-ttttttttttttttttgtacgtcttaatcttatatgtgtgtgtatgtgcatgtacttgtatccacctagtacccaaatctagtatatctgat

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTTTACCGTCCACCTAGAGCTTCTCATTGTTCCATATGCAACAACTGTGTCCAGAGATTTGATCATCACTGCCCTTGGGTTGGCCAGTGCATTGGAGTGgtaagtttactccatgactcttgccatatattcccggttctatgttttgaacttgtttggattcttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG