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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGAAGAACCCGTGGCCAAATGTTGATGCTCACAGTGGGGTCTTGCTGAACCACTATGGTCTAACCGAAGCAAGgtaagaagtagacacctccttcaagtatcattgagccttaggatagcactcaaatataatatctgtgcgttttatag

Basic information

species Arabidopsis thaliana
transcript AT2G44350.2
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G44350.2 (Arabidopsis thaliana), 5'ss of exon 18
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 5'ss of exon 18
GTGAAGAACCCGTGGCCAAATGTTGATGCTCACAGTGGGGTCTTGCTGAACCACTATGGTCTAACCGAAGCAAGgtaagaagtagacacctccttcaagta--tcattgagc---cttaggatagcactca-aatataata-tctgtgcgttttatag------------------------------------
|| || ||||| ||||| |||||||||||||||||||| ||  |||||||||||| |||  || | |||||  |||| |   ||     |    | || ||  | | | | |    |||   | | || ||  ||  |||| |   ||   || | |                                     
GTCAAAAACCCATGGCCTAATGTTGATGCTCACAGTGGAGTTCTGCTGAACCACTTTGGATTATCTGAAGCTCGgtatgtt-tacctgtcctggttaaataatttagtaaccaaatttaatcttgaacccatgatggaatagtaaatgtacttcagaacgagtacttaataaaagcggccatctaattacgcag

upper sequence: AT2G44350.2 (Arabidopsis thaliana), 5'ss of exon 18
lower sequence: GRMZM2G064023_T01 (Zea mays), 5'ss of exon 19
GTGAAGAACCCGTGGCCAAATGTTGATGCTCACAGTGGGGTCTTGCTGAACCACTATGGTCTAACCGAAGCAAGgtaagaagtagacacctccttcaagtatca------ttgagccttaggatagcactcaaatataatatctgtgcgttttatag-----------------------
|| |||||||||||||| |||||||||||||||||||| || ||||||||||||| ||| ||| | |||||| |||| |     |     || || |  |  ||      |   |  ||    ||      ||||| | | ||||   |     |                         
GTCAAGAACCCGTGGCCGAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttatgctttgtcatttagattccaatttagtgatgtttttatttacttagtaaataaagt-tctgaatgagcactcatgtctggaacactaactgtgcag

upper sequence: AT2G44350.2 (Arabidopsis thaliana), 5'ss of exon 18
lower sequence: GRMZM2G063851_T05 (Zea mays), 5'ss of exon 4
GTGAAGAACCCGTGGCCAAATGTTGATGCTCACAGTGGGGTCTTGCTGAACCACTATGGTCTAACCGAAGCAAGgtaag----aagtagacacctccttcaagtatca--ttgagccttaggatagcactcaaatataatatctgtgcgttttatag-----------------------
|| |||||||| |||||||||||||||||||||||||| || ||||||||||||| ||| ||| | |||||| |||| |       | |  |  |  |  |  || ||  ||   |||     ||     ||||| || | |||| | |     ||                        
GTCAAGAACCCATGGCCAAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttatgcttgtgatttagtctagatagcaatttagtcctctttttacttagcaaatctagt-tctgagtgagcactaatgtttggaacactaactgtgcag

upper sequence: AT2G44350.2 (Arabidopsis thaliana), 5'ss of exon 18
lower sequence: GRMZM2G063909_T03 (Zea mays), 5'ss of exon 17
GTGAAGAACCCGTGGCCAAATGTTGATGCTCACAGTGGGGTCTTGCTGAACCACTATGGTCTAACCGAAGCAAGgtaagaagtagacacctccttcaagtatca-ttgagccttaggatagcactcaaatataatatct-gtgcgttttatag-------------------------------------------
|| |||||||| ||||| |||||||| |||||||||||  ||||||||||||||| ||| ||| | ||| || |||| |   |   |   |  || |  || || || || | |    |     |    ||   |     |   ||| |  |                                            
GTCAAGAACCCATGGCCCAATGTTGACGCTCACAGTGGACTCTTGCTGAACCACTTTGGACTATCTGAAACACGgtatgtt-tgtgcttgtagtttagataccaattcagtcatgtttttttttttttttactttgcaaagctagttctgaatgagcacagagcactcactcatgtctgggacaccaactgtgcag

upper sequence: AT2G44350.2 (Arabidopsis thaliana), 5'ss of exon 18
lower sequence: GLYMA08G16770.1 (Glycine max), 5'ss of exon 18
GTGAAGAACCCGTGGCCAAATGTTGATGCTCACAGTGGGGTCTTGCTGAACCACTATGGTCTAACCGAAGCAAGgtaagaagtagacacctcc-----------ttcaagta----tcattgagc--------cttaggatagcactcaaatataat-atctgtgcgttttatag----
|| || || || ||||| |||||||||||||||||||| ||  | |||||| | ||||||||||| || | || ||| |  ||     |   |           || || ||    |||||  ||         ||||| |   | || ||| |||| |||| |   | || | |    
GTTAAAAATCCATGGCCTAATGTTGATGCTCACAGTGGAGTGCTACTGAACTATTATGGTCTAACTGAGGAAAAgtatggggttacttctctcacttgttccacttgaaatagttttcattttgcaattattttttagggtg--aatctaatctaatgatctattaatattgtggacag

upper sequence: AT2G44350.2 (Arabidopsis thaliana), 5'ss of exon 18
lower sequence: GLYMA15G42300.1 (Glycine max), 5'ss of exon 18
GTGAAGAACCCGTGGCCAAATGTTGATGCTCACAGTGGGGTCTTGCTGAACCACTATGGTCTAACCGAAGCAAGgtaagaagtagacacctccttcaagtatca-ttgagccttaggatagcactcaaatataatatctgtgcgttttatag---------------------------
|| || || || ||||| ||||||||||| |||||||| ||  | |||||| ||||||||||||| || | || ||| |  ||  ||  |||   |  ||  || ||||          |     ||| |||  | |  | | |  ||  |                            
GTTAAAAATCCATGGCCGAATGTTGATGCGCACAGTGGAGTGCTACTGAACTACTATGGTCTAACTGAGGAAAAgtatggggtt-acttctctcacctgttccacttgaaatagttttcattttgcaattatttttttagggtgaatttcatctaatgatctattaacatcgtggacag

upper sequence: AT2G44350.2 (Arabidopsis thaliana), 5'ss of exon 18
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 5'ss of exon 18
GTGAAGAACCCGTGGCCAAATGTTGATGCTCACAGTGGGGTCTTGCTGAACCACTATGGTCTAACCGAAGCAAGgtaagaagtagacacctccttcaagtatcattgag----ccttaggatagcactcaaatataatatctgtgcgttttatag----------------------------
|| || ||||| ||||| ||||| ||||||||||||||||||||||||||||| | |||| ||  ||||||| |||||  |||   | |   |    | ||| ||||       ||||   | ||  |  ||||  || | || |    |  ||                             
GTTAAAAACCCATGGCCCAATGTCGATGCTCACAGTGGGGTCTTGCTGAACCATTTTGGTTTACACGAAGCACGgtaaagagttctctctcacaatcattataattggagatttcttaatttggctatttaatagtatct-tgggtagatggtaaaaatcctttaacaattgatcccttgcag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|116471055|gb|EG513647.1|EG513647
EST:     GATGCTCACAGTGGGGTCTTGCTGAACCACTATGGTCTAACCGAAGCAAG                         GTACTACACCGTGCTCTTTGGTGTTTCAAGGAGTCTTGGCATCTGCTCTCA
genomic: GATGCTCACAGTGGGGTCTTGCTGAACCACTATGGTCTAACCGAAGCAAGgtaagaagta ... cgttttatagGTACTACACCGTGCTCTTTGGTGTTTCAAGGAGTCTTGGCATCTGCTCTCA
EST: gi|124734316|gb|EH825718.1|EH825718
EST:     TCTTGCTGAACCACTATGGTCTAACCGAAGCAAG                         GTACTACACCGTGCTCTTTGGTGTTTCAAGGAGTCTTGGCATCTGCTCTCA
genomic: TCTTGCTGAACCACTATGGTCTAACCGAAGCAAGgtaagaagta ... cgttttatagGTACTACACCGTGCTCTTTGGTGTTTCAAGGAGTCTTGGCATCTGCTCTCA
EST: gi|116453292|gb|EG495884.1|EG495884
EST:     GATGCTCACAGTGGGGTCTTGCTGAACCACTATGGTCTAACCGAAGCAAG                         GTACTACACCGTGCTCTTTGGTG
genomic: GATGCTCACAGTGGGGTCTTGCTGAACCACTATGGTCTAACCGAAGCAAGgtaagaagta ... cgttttatagGTACTACACCGTGCTCTTTGGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGAAGAACCCGTGGCCAAATGTTGATGCTCACAGTGGGGTCTTGCTGAACCACTATGGTCTAACCGAAGCAAGgtaagaagtagacacctccttcaagtatcattgagccttaggatagcactcaaatataatatctgtgcgttttatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG