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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctatgtcactttgctagcatgcacttgagtgtgctcctagagctctgatttcccaccccttttgaggtttgtcatattcaaacttcacagattgaactttccatctatctgcagGGCGGGTTCCCTCATTGCAGGAAGGTAATATCCAAGAAAAGATATTCACTTTTCCATGGGTGGATGATCGGCCAGTGATGCTTG

Basic information

species Arabidopsis thaliana
transcript AT5G49820.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G49820.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv12s0035g01870.t01 (Vitis vinifera), 3'ss of exon 8
-----------------------------------------gtaagctat-gtcactttgctagcatgcacttgagtgtgctcctagagctctgatttcccaccccttt-tgaggtttgtcat-attcaaacttcacagattgaactttccatctatctgcagGGCGGGTTCCCTCATTGCAGGAAGGTAATATCCAAGAAAAGATATTCACTTTTCCATGGGTGGATGATCGGCCAGTGATGCTTG
                                          |||| ||   |    ||       |    || | | |  | |||||  ||  ||     | | || | || |  || |||| | || ||   |  | ||||  || |   ||  | ||||||||| || |||||||||||||| || |||||  | ||||| ||||||| |||||||||| |||| |||   ||  |  | ||||
gttaggatggttttttttcctttaaagattcatttttctccttaagttaccatggtcttatggttctttgattaaat-tcttactagaattcctatacgtgagcactatatgggcattttcattaatctaatggctta-attgtgctatatttccttttgcagGGCGAGTACCCTCATTGCAGGAGGGCAATATGAAGGAAAACATATTCAGTTTTCCATGGTTGGAAGATAAACCTATCGTTCTTG
















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|86038682|gb|DR334437.1|DR334437
EST:     ACTAAACCGTGCTAGATTTACAGTAGCAGTGGAGTCCTTTCTTAAGACGG                         GACGGGGTTCCCTCATTGCAGGAAGGTAATATCCAAGAAAAGATATTCACT
genomic: ACTAAACCGTGCTAGATTTACAGTAGCAGTGGAGTCCTTTCTTAAGACGGgtaagctatg ... ctatctgcagGGCGGG-TTCCCTCATTGCAGGAAGGTAATATCCAAGAAAAGATATTCACT
EST: gi|125104280|gb|EL158404.1|EL158404
EST:     ACTAAACCGTGCTAGATTTACAG-AGCAGTGGAGTCCTTTCTTAAGACGG                         GGCGGGTTCCCTCATTGCAGGAAGG
genomic: ACTAAACCGTGCTAGATTTACAGTAGCAGTGGAGTCCTTTCTTAAGACGGgtaagctatg ... ctatctgcagGGCGGGTTCCCTCATTGCAGGAAGG
EST: gi|124824431|gb|EH909297.1|EH909297
EST:     CTAAACCGTGCTAGATTTACAGTAGCTAGTGGAGTCCTTTCTTAAGACGG                         GGCGGGTTCCCTCATTGCAGGAAGGTAATATCCAAGAAAAGATATTCACTT
genomic: CTAAACCGTGCTAGATTTACAGTAGC-AGTGGAGTCCTTTCTTAAGACGGgtaagctatg ... ctatctgcagGGCGGGTTCCCTCATTGCAGGAAGGTAATATCCAAGAAAAGATATTCACTT
EST: gi|125195799|gb|EL210753.1|EL210753
EST:     ACTAAACCGTGCTAGATTTACAGTAGCAGTGGAGTCCTTTCTTAAGACGG                         GGCGGGTTCCCTCATTGCAGGAAGGTAATATCCAAGAAAAGATATTCAC
genomic: ACTAAACCGTGCTAGATTTACAGTAGCAGTGGAGTCCTTTCTTAAGACGGgtaagctatg ... ctatctgcagGGCGGGTTCCCTCATTGCAGGAAGGTAATATCCAAGAAAAGATATTCAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgaggtttgtcatattcaaacttcacagattgaactttccatctatctgcagGGCGGGTTCCCTCATTGCAGGAAGGTAATATCCAAGAAAAGATATTCACTTTTCCATGGGTGGATGATCGGCCAGTGATGCTTG
                                     ctttccatctatct  CT-rich tract
              atattcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctatgtcactttgctagcatgcacttgagtgtgctcctagagctctgatttcccaccccttttgaggtttgtcatattcaaacttcacagattgaactttccatctatctgcagGGCGGGTTCCCTCATTGCAGGAAGGTAATATCCAAGAAAAGATATTCACTTTTCCATGGGTGGATGATCGGCCAGTGATGCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA