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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagattcatcaagttttcacattttcgaaaatattttgtagtctttgttactcgttgttagctgctattatcatgctaatcgtaaccaaattttgtttttttatagGAGAGCTCTAATGGTGAAGAGAGCAGTGAGAGTGAAACCACAATTGAATTCACACAAGAGATTTGCTAATGCATTCCCAAAGTATTGTGAGCTTGTTGAT

Basic information

species Arabidopsis thaliana
transcript AT1G04280.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G04280.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA20G34760.1 (Glycine max), 3'ss of exon 5
gtaaagattcatcaagttttcacattttcgaaaa-tattttgtagtc--tttgttactcgttgttagctgctat-tatcatgctaatcgtaaccaaattttgtttttttatagGAGAGCTCTAATGGTGAAGAGAGCAGTGAGAGTGAAACCACAATTGAATTCACACAAGAGATTTGCTAATGCATTCCCAAAGTATTGTGAGCTTGTTGAT
               || || |   ||  |||   |    |||      ||||  | | |   || |  | ||| ||| |   | | | |  || |  || |  |||| | ||||||||| | |||     ||| |||||||| |||||  |||||||||| || ||||| ||||||||||||||||| ||||  | |||  | |||||||||
---------------gtatttatgcttgtgaattctgccatgttactagtttgggaattga-atttgtggatatatatgaaagttaacatttccca--ttggaattttgacagGAGAGCTATTATGACAGGGAGGGCAGTGAGGGTGAATTCACAATTGAAATCTCACAAAAGATTTGCTAATGCATTTCCAAGATTTTGCAAACTTGTTGAT

upper sequence: AT1G04280.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA20G34750.1 (Glycine max), 3'ss of exon 6
gtaaagattcatcaagttttcacattttcgaaaatattt-tgtagtc--tttgttactcgttgttagctgctattatcatgctaatcgtaaccaaattttgtttttttatagGAGAGCTCTAATGGTGAAGAGAGCAGTGAGAGTGAAACCACAATTGAATTCACACAAGAGATTTGCTAATGCATTCCCAAAGTATTGTGAGCTTGTTGAT
               || |  |   ||  | ||  ||   |||      | ||  | | | | || | || ||| |  |||    |    |  | |||  |  |||| | ||||||||| | |||     ||| ||||||||||||||  ||||| |||| || ||||| ||||||||||||||||| ||||  |||||  | |||||||||
---------------gtatgtatgcttgtggaatcatccatgttactagtctgggaattggtttt-gttgatatgagtatgactgttaacatgacattg-gaattttgacagGAGAGCTATTATGACAGGGAGGGCAGTGAGAGTGAATTCACAACTGAAATCTCACAAAAGATTTGCTAATGCATTTCCAAGATATTGCAAACTTGTTGAT
















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|125236851|gb|EL250936.1|EL250936
EST:     GCTTATCTTGCCGTAGCAAGAGGCATACG                         GAGAGCTCTAATGGTGAAGAGAGCAGTGAGAGTG
genomic: GCTTATCTTGCCGTAGCAAGAGGCATACGgtaaagattc ... ttttttatagGAGAGCTCTAATGGTGAAGAGAGCAGTGAGAGTG
EST: gi|124773413|gb|EH863542.1|EH863542
EST:     CTGGTCGGTGTGGTTTGTGACGCTTATCTTGCCGTAGCAAGAGGCATACG                         GAGAGCTCTAATGGTGAAGAGAG
genomic: CTGGTCGGTGTGGTTTGTGACGCTTATCTTGCCGTAGCAAGAGGCATACGgtaaagattc ... ttttttatagGAGAGCTCTAATGGTGAAGAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgttgttagctgctattatcatgctaatcgtaaccaaattttgtttttttatagGAGAGCTCTAATGGTGAAGAGAGCAGTGAGAGTGAAACCACAATTGAATTCACACAAGAGATTTGCTAATGCATTCCCAAAGTATTGTGAGCTTGTTGAT
                            tcgtaac  putative branch site (score: 2)
                                       ttttgtttttttat  putative PPT
                               taaccaaattttgttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagattcatcaagttttcacattttcgaaaatattttgtagtctttgttactcgttgttagctgctattatcatgctaatcgtaaccaaattttgtttttttatagGAGAGCTCTAATGGTGAAGAGAGCAGTGAGAGTGAAACCACAATTGAATTCACACAAGAGATTTGCTAATGCATTCCCAAAGTATTGTGAGCTTGTTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT