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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgtttatccagatgcacacttattggcttgcaaataactaatcttctcctcttaattcaatcttcatagTTTCTATTGGTAGACCTGCGTTGCCATGGGGATTCAACATCTCTCAAGAAGAGAGGTCCACACTCGGTTGCTACTACTGCTTCTGATGTTCTAAAACTT

Basic information

species Arabidopsis thaliana
transcript AT4G10030.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G10030.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G01670.1 (Glycine max), 3'ss of exon 5
--------------gtatttgtttat-----ccagatgcacacttatt---ggcttgcaaataact-aatcttctcctcttaattcaatc---ttcatagTTTCTATTGGTAGACCTGCGTTGCCATGGGGATTCAACATCTCTCAAGAAGAGAGGTCCACACTCGGTTGCTACTACTGCTTCTGATGTTCTAAAACTT
                 |||| || |      |  |||||     |||   |  || || | | || |||| | |    ||| ||   |    || | ||||||| || ||||||||||| || ||||| |||||| ||||  |||||||||||| ||| ||  | |||||  || |||||   |||||| | ||||| 
tactgggtatcttaaattttgattgtaggggtccaatgcaagaacattttggatttacataaatctgaatcctgtttgtttattttgtttgcattgacagTTTCTTTTAGTAGACCTGCGATGTCATGGCGATTCAGCATCAATCAAGAAGAGAGATCCCCATACTGTTGCATCTGCTGCTATGGATGTTTTGAAACTG
















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|125289117|gb|EL303202.1|EL303202
EST:     TTGGCTCATGAATTCCCAACGTGGCAG                         TTTCTATTGGTAGACCTGCGTTGCCATGGGGATTCAACATCTCTCAAGAAG
genomic: TTGGCTCATGAATTCCCAACGTGGCAGgtatttgttt ... atcttcatagTTTCTATTGGTAGACCTGCGTTGCCATGGGGATTCAACATCTCTCAAGAAG
EST: gi|86019776|gb|DR315522.1|DR315522
EST:     GCACTTTTGCTCGTAGATTGGCTCATGAATTCCCAACGTGGCAG                         TTTCTATTGGTAGACCTGCGTTGCCATGGGGATTCAACATCTCTCAAGAAG
genomic: GCACTTTTGCTCGTAGATTGGCTCATGAATTCCCAACGTGGCAGgtatttgttt ... atcttcatagTTTCTATTGGTAGACCTGCGTTGCCATGGGGATTCAACATCTCTCAAGAAG
EST: gi|86019779|gb|DR315525.1|DR315525
EST:     GCACTTTTGCTCGTAGATTGGCTCATGAATTCCCAACGTGGCAG                         TT-CTATTGGTAGA
genomic: GCACTTTTGCTCGTAGATTGGCTCATGAATTCCCAACGTGGCAGgtatttgttt ... atcttcatagTTTCTATTGGTAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacacttattggcttgcaaataactaatcttctcctcttaattcaatcttcatagTTTCTATTGGTAGACCTGCGTTGCCATGGGGATTCAACATCTCTCAAGAAGAGAGGTCCACACTCGGTTGCTACTACTGCTTCTGATGTTCTAAAACTT
                                              tcttcat  CT-rich tract
                 aaataactaatctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttgtttatccagatgcacacttattggcttgcaaataactaatcttctcctcttaattcaatcttcatagTTTCTATTGGTAGACCTGCGTTGCCATGGGGATTCAACATCTCTCAAGAAGAGAGGTCCACACTCGGTTGCTACTACTGCTTCTGATGTTCTAAAACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG