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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCCTGTGCTTGAGACTCCTGAAGGTCCCATATTTGAGAGCAATGCCATTGCCCGATATGgtataacttcatttccttctgtttctctttgatgcacctatctataacttggtattaattggatatgatgattgttttgttatcccccttcag

Basic information

species Arabidopsis thaliana
transcript AT1G57720.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G57720.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os02g12794.3 (Oryza sativa), 5'ss of exon 3
---------------------------------------GTTCCTGTGCTTGAGACTCCTGAAGGTCCCATATTTGAGAGCAATGCCATTGCCCGATATGgtata-acttcatttccttctgtttctctttgatgcacctatctataacttggtattaattggatatgatgattgttttgttatcccccttcag
                                        ||||||| || ||||||||||| |||||  | |||||||||||||| ||||| ||||||||||     | |||  |      ||    ||   |  | || | | || | |  | | | || | | | |   |   |  || ||   |||  ||
CATTCGCACAGAATCTTATTTGGACACGTTTTCTTTCAGATTCCTGTTCTAGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCGATTGCACGATATGgtaagtgatacatagcaaggaattggagttctcttaatctttttctatcata-tctgatttagttctaa--gtcact--gtcattttcctgaag

upper sequence: AT1G57720.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G134582_T01 (Zea mays), 5'ss of exon 4
GTTCCTGTGCTTGAGACTCCTGAAGGTCCCATATTTGAGAGCAATGCCATTGCCCGATATGgta---taacttcatttccttctgtttctctttgatgcacctatctataacttggtattaattggatatgatgattgttttgttatcccccttcag
 ||||||| || ||||||||||| |||||  | |||||||||||||| |||||  |||||||||    || |  |    |   ||  | | || |   | ||| | |  |  |    |||  ||    |   |||   || ||| |||    |  ||
ATTCCTGTCCTGGAGACTCCTGATGGTCCTGTTTTTGAGAGCAATGCAATTGCAAGATATGgtaattcaaatgtagcaaccattgggttttttagt--ctcctgtttgcattt----atttttttagcac--tga--attctgtcatctttttgaag
















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|152035102|gb|BP844635.2|BP844635
EST:     TGAGACTCCTGAAGGTCCCATATTTGAGAGCAATGCCATTGCCCGATATG                         TGAGCCGTAAGAATGGTGACAACTCTTTGAATGGATCCTCCCTTATTGAAT
genomic: TGAGACTCCTGAAGGTCCCATATTTGAGAGCAATGCCATTGCCCGATATGgtataacttc ... cccccttcagTGAGCCGTAAGAATGGTGACAACTCTTTGAATGGATCCTCCCTTATTGAAT
EST: gi|124763202|gb|EH853332.1|EH853332
EST:     TTGCCCGATATG                         TGAGCCGTAAGAATGGTGACAACTCTTTGAATGGATCCTCCCTTATTGAAT
genomic: TTGCCCGATATGgtataacttc ... cccccttcagTGAGCCGTAAGAATGGTGACAACTCTTTGAATGGATCCTCCCTTATTGAAT
EST: gi|124711169|gb|EH802571.1|EH802571
EST:     TGAGACTCCTGAAGGTCCCATATTTGAGAGCAATGCCATTGCCCGATATG                         TGAGCCGTAAGAATGGTGACAACTCTTTGAATGGATCCTCCCTTAT
genomic: TGAGACTCCTGAAGGTCCCATATTTGAGAGCAATGCCATTGCCCGATATGgtataacttc ... cccccttcagTGAGCCGTAAGAATGGTGACAACTCTTTGAATGGATCCTCCCTTAT
EST: gi|124956219|gb|EL031166.1|EL031166
EST:     TGCCATTGCCCGATATG                         TGAGCCGTAAGAATGGTGACAACTCTTTGAATGGATCCTCCCTTATTGAAT
genomic: TGCCATTGCCCGATATGgtataacttc ... cccccttcagTGAGCCGTAAGAATGGTGACAACTCTTTGAATGGATCCTCCCTTATTGAAT
EST: gi|124821159|gb|EH906025.1|EH906025
EST:     CAATGCCATTGCCCGATATG                         TGAGCCGTAAGAATGGTGACAACTCTTTGAATGGATCCTCCCTTATTGAAT
genomic: CAATGCCATTGCCCGATATGgtataacttc ... cccccttcagTGAGCCGTAAGAATGGTGACAACTCTTTGAATGGATCCTCCCTTATTGAAT
EST: gi|125234252|gb|EL248337.1|EL248337
EST:     CCTGAAGGTCCCATATTTGAGAGCAATGCCATTGCCCGATATG                         TGAGCCGTAAGAATGGTGACAACTCTTTGAATGGATCCTCCCTTATTGAAT
genomic: CCTGAAGGTCCCATATTTGAGAGCAATGCCATTGCCCGATATGgtataacttc ... cccccttcagTGAGCCGTAAGAATGGTGACAACTCTTTGAATGGATCCTCCCTTATTGAAT
EST: gi|164140036|gb|ES035059.1|ES035059
EST:     TGCCATTGCCCGATACG                         TGAGCCGTAAGAATGGTGACAACTCTTTGAATGGATCCTCCCTTATTGAAT
genomic: TGCCATTGCCCGATATGgtataacttc ... cccccttcagTGAGCCGTAAGAATGGTGACAACTCTTTGAATGGATCCTCCCTTATTGAAT
EST: gi|116473109|gb|EG515701.1|EG515701
EST:     TGAGACTCCTGAAGGTCCCATATTTGAGAGCAATGCCATTGCCCGATATG                         TGAGCCGTAAGAATGGTGACAACTCTTTGAATGGATCCTCCCTTATTGAAT
genomic: TGAGACTCCTGAAGGTCCCATATTTGAGAGCAATGCCATTGCCCGATATGgtataacttc ... cccccttcagTGAGCCGTAAGAATGGTGACAACTCTTTGAATGGATCCTCCCTTATTGAAT
EST: gi|125193807|gb|EL208761.1|EL208761
EST:     CCATTGCCCGATATG                         TGAGCCGTAAGAATGGTGACAACTCTTTGAATGGATCCTCCCTTATTGAAT
genomic: CCATTGCCCGATATGgtataacttc ... cccccttcagTGAGCCGTAAGAATGGTGACAACTCTTTGAATGGATCCTCCCTTATTGAAT
EST: gi|152035939|gb|BP865394.2|BP865394
EST:     TGAGACTCCTGAAGGTCCCATATTTGAGAGCAATGCCATTGCCCGATATG                         TGAGCCGTAAGAATGGTGACAACT
genomic: TGAGACTCCTGAAGGTCCCATATTTGAGAGCAATGCCATTGCCCGATATGgtataacttc ... cccccttcagTGAGCCGTAAGAATGGTGACAACT
EST: gi|116410809|gb|EG453401.1|EG453401
EST:     TGAGACTCCTGAAGGTCCCATATTTGAGAGCAATGCCATTGCCCGATATG                         TGAGCCGTAAGAATGGTGACAACTCTTTGAATGGATCCTCCCTTATTGAAT
genomic: TGAGACTCCTGAAGGTCCCATATTTGAGAGCAATGCCATTGCCCGATATGgtataacttc ... cccccttcagTGAGCCGTAAGAATGGTGACAACTCTTTGAATGGATCCTCCCTTATTGAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCCTGTGCTTGAGACTCCTGAAGGTCCCATATTTGAGAGCAATGCCATTGCCCGATATGgtataacttcatttccttctgtttctctttgatgcacctatctataacttggtattaattggatatgatgattgttttgttatcccccttcag

- - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - -  AGAGCA