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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCGCTGATCTTGGTGGCACCGAGATTGACTTGAGATTTGCTAGTCCTAAAGAAGGCCGTTTGTCTGTTATTGTAGCTCCTGTTCTTAGATTTGCAGATAgtaagttgtctctgctattaaagattcatcaactttactcttttgagttatataggcaatgcaatcttgtctatttgtactcgtagattgattgatttgtgtgttccacttatacag

Basic information

species Arabidopsis thaliana
transcript AT1G77090.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G77090.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA04G42010.1 (Glycine max), 5'ss of exon 3
ATCGCTGATCTTGGTGGCACCGAGATTGACTTGAGATTTGCTAGTCCTAAAGAAGGCCGTTTGTCTGTTATTGTAGCTCCTGTTCTTAGATTTGCAGATAgtaag--ttgtctctgctat-taaagattcatcaactttactcttttgag----------------ttatataggcaatgcaatc--ttgtctatttgta---ctcgtagattgattgatttgtgtgttc-cacttatacag-------------
|| || |||||||||||||| ||||| || ||||||||||| ||  |||| ||||| ||||||| ||| ||||| |||||||||||||||||  | ||| || ||  |||  | |||    |     |||  || |||  || | | |||                | | | ||  |   ||||      ||||  ||||     | |  |||  ||| ||| | || |  |  || |||               
ATAGCAGATCTTGGTGGCACAGAGATAGATTTGAGATTTGCCAGCTCTAAGGAAGGACGTTTGTTTGTCATTGTTGCTCCTGTTCTTAGATTCTCCGATGgtgagtattgagtttgccccattttctttctccatcttagctttctagagacaaggagaataaagttgaaacagaaagaacaatgaaacttctaggtgtaacttccatttattacttgttttatatgataacttttttactatacatctatacag

upper sequence: AT1G77090.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA06G12760.1 (Glycine max), 5'ss of exon 3
ATCGCTGATCTTGGTGGCACCGAGATTGACTTGAGATTTGCTAGTCCTAAAGAAGGCCGTTTGTCTGTTATTGTAGCTCCTGTTCTTAGATTTGCAGATAgtaag--ttgtctctgc-tattaaagattcatcaactttactcttttgagttatataggcaatgcaatcttgtc--------tatttgtactcgtagattgattg---atttgtgtgttccacttatacag---------------------------
|| || |||||||||||||| ||||| || ||||||||||| ||  |||| ||||| ||||||| ||| ||||| |||||||||||||||||  | ||| || ||  |||  | ||| ||||     |||  || |||  || |   |||  | |  |  |||  |||     |         | |   |||  ||| | | |     |||| | || |    |||||                              
ATAGCAGATCTTGGTGGCACAGAGATAGATTTGAGATTTGCCAGCTCTAAGGAAGGACGTTTGTTTGTCATTGTTGCTCCTGTTCTTAGATTCTCTGATGgtgagtattgagtttgcctatttttctttctccatcttagctttccagag--acaaggagaataaaattgaaacagaaagaacaatgaaacttctaggtggttcttccatttat-tgcttgctttatatgataacttttttactatacatctatacag

upper sequence: AT1G77090.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv18s0001g15360.t01 (Vitis vinifera), 5'ss of exon 3
ATCGCTGATCTTGGTGGCACCGAGATTGACTTGAGATTTGCTAGTCCTAAAGAAGGCCGTTTGTCTGTTATTGTAGCTCCTGTTCTTAGATTTGCAGATAgtaagttgtctctgctattaaagattcatcaactttactcttttgagttatataggcaatgcaatcttgtctatttgtactcgtagat--tga--ttgatttgtgtgttccacttatacag------------------------------
|| || ||||| ||||| || |||||||| ||||| ||||| | | |||| ||||| ||||| | ||| ||||| || || ||||| ||||||||||| |||||||| |||     ||     ||| |  | ||| ||   |       |     | |||| |||   ||      ||| |  |  ||  |||  ||| ||     |   ||  ||| ||                               
ATTGCAGATCTAGGTGGGACAGAGATTGATTTGAGGTTTGCCAATTCTAAGGAAGGGCGTTTATTTGTCATTGTTGCCCCAGTTCTCAGATTTGCAGACAgtaagtt-tctgacagatcttgtatttaagaccttgacaagtggacaggaatcttgaaatgaaatgcagttctcaagtagttttccatggtgaacttggttcactagcctcagatattcatttcttatcatagtgttgctatgatgtacag

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|125295346|gb|EL309431.1|EL309431
EST:     TTATTGTAGCTCCTGTTCTTAGATTTGCAGATA                         ACCTCGGGGACGATGTTAAGATTGAAAATATTGGACAACCAGCGAAGGTGA
genomic: TTATTGTAGCTCCTGTTCTTAGATTTGCAGATAgtaagttgtc ... acttatacagACCTCGGGGACGATGTTAAGATTGAAAATATTGGACAACCAGCGAAGGTGA
EST: gi|124785291|gb|EH874970.1|EH874970
EST:     AGAAGGCCGTTTGTCTGTTATTGTAGCTCCTGTTCTTAGATTTGCAGATA                         ACCTCGGGGACGATGTTAAGATTGAAAATATTGGACAACCAGCGAAGGTGA
genomic: AGAAGGCCGTTTGTCTGTTATTGTAGCTCCTGTTCTTAGATTTGCAGATAgtaagttgtc ... acttatacagACCTCGGGGACGATGTTAAGATTGAAAATATTGGACAACCAGCGAAGGTGA
EST: gi|86075038|gb|DR370795.1|DR370795
EST:     AGAAGGCCGTTTGTCTGTTATTGTAGCTCCTGTTCTTAGATTTGCAGATA                         ACCTCGGGGACGATGTTAAGATTGAAAATATTGGACAACCAGCGAAGGTGA
genomic: AGAAGGCCGTTTGTCTGTTATTGTAGCTCCTGTTCTTAGATTTGCAGATAgtaagttgtc ... acttatacagACCTCGGGGACGATGTTAAGATTGAAAATATTGGACAACCAGCGAAGGTGA
EST: gi|125325991|gb|EL340071.1|EL340071
EST:     TTGTAGCTCCTGTTCTTAGATTTGCAGATA                         ACCTCGGGGACGATGTTAAGATTGAAAATATTGGACAACCAGCGAAGGTGA
genomic: TTGTAGCTCCTGTTCTTAGATTTGCAGATAgtaagttgtc ... acttatacagACCTCGGGGACGATGTTAAGATTGAAAATATTGGACAACCAGCGAAGGTGA
EST: gi|125082010|gb|EL143029.1|EL143029
EST:     ATTTGCAGATA                         ACCTCGGGGACGATGTTAAGATTGAAAATATTGGACAACCAGCGAAGGTGA
genomic: ATTTGCAGATAgtaagttgtc ... acttatacagACCTCGGGGACGATGTTAAGATTGAAAATATTGGACAACCAGCGAAGGTGA
EST: gi|124997111|gb|EL069380.1|EL069380
EST:     AGAAGGCCGTTTGTCTGTTATTGTAGCTCCTGTTCTTAGATTTGCAGATA                         ACCTCGGGGACGATGTTAAGATTGAAAATATTGGACAACCAGCGAAGGTG
genomic: AGAAGGCCGTTTGTCTGTTATTGTAGCTCCTGTTCTTAGATTTGCAGATAgtaagttgtc ... acttatacagACCTCGGGGACGATGTTAAGATTGAAAATATTGGACAACCAGCGAAGGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCGCTGATCTTGGTGGCACCGAGATTGACTTGAGATTTGCTAGTCCTAAAGAAGGCCGTTTGTCTGTTATTGTAGCTCCTGTTCTTAGATTTGCAGATAgtaagttgtctctgctattaaagattcatcaactttactcttttgagttatataggcaatgcaatcttgtctatttgtactcgtagattgattgatttgtgtgttccacttatacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT