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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagccattttttgggaatctggtgtgtgtgtgtgtgtgttttgtcttcaaggcttatgtgacggcttgggttctgtctcttaacagGTTGGGTTAATCGCTTTGCTAATGCTGGGGACACAGCCTTGGAAGTGGCAGGAAACACAGCAATGCGG

Basic information

species Arabidopsis thaliana
transcript AT4G25680.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G25680.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G24630.1 (Glycine max), 3'ss of exon 2
gtaaagccatttt-----ttggga-atctggtgtgtgtgtgtgtgtgttttgtcttcaaggcttatgtgacggct-tgggttctg-----tctcttaacagGTTGGGTTAATCGCTTTGCTAATGCTGGGGACACAGCCTTGGAAGTGGCAGGAAACACAGCAATGCGG
|| |||    |||     |||    |||     ||||  |   ||  || |||     |   || |||  |  || ||  ||||      |  | | ||||||||||||||| | ||||| |||||||| || || ||  |||||||||| ||||| |||||| | |||
gtgaaggaggtttaagcattgatccatccaacttgtgaattattgc-ttctgtacattacttttctgtttccactgtgtattcttacaacttccatgacagGTTGGGTTAATAGGTTTGCCAATGCTGGTGATACTGCTATGGAAGTGGCTGGAAATACAGCATTACGG
















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|19874751|gb|AU235582.1|AU235582
EST:     TCACTTCTGCGATGTACTCTGTGACCGGCTTGGTGTGCCAAAGATCCCAG                         GTTGGGTTAATCGCTTTGCTAATGCTGGGGACACAGCCTTGGAAGTGGCAG
genomic: TCACTTCTGCGATGTACTCTGTGACCGGCTTGGTGTGCCAAAGATCCCAGgtaaagccat ... ctcttaacagGTTGGGTTAATCGCTTTGCTAATGCTGGGGACACAGCCTTGGAAGTGGCAG
EST: gi|125158362|gb|EL186995.1|EL186995
EST:     TCACTTCTGCGATGTACTCTGTGACCGGCTTGGTGTGCCAAAGATCCCAG                         GTTGGGTTAATC
genomic: TCACTTCTGCGATGTACTCTGTGACCGGCTTGGTGTGCCAAAGATCCCAGgtaaagccat ... ctcttaacagGTTGGGTTAATC
EST: gi|163973301|gb|ES019803.1|ES019803
EST:     TTCTGCGATGTACTCTGTGACCGGCTTGGTGTGCCAAAGATCCCAG                         GTTGGGTTAATCGCTTTGCTAATGCTGGGGACACAGCCTTGGAAGTGGC
genomic: TTCTGCGATGTACTCTGTGACCGGCTTGGTGTGCCAAAGATCCCAGgtaaagccat ... ctcttaacagGTTGGGTTAATCGCTTTGCTAATGCTGGGGACACAGCCTTGGAAGTGGC
EST: gi|124770594|gb|EH860724.1|EH860724
EST:     CACTTCTGCGATGTACTCTGTGACCGGCTTGGTGTGCCAAAAGATCCCAG                         GTTGGGTTAATCGCTTTGCTAAT
genomic: CACTTCTGCGATGTACTCTGTGACCGGCTTGGTGTGCCAAA-GATCCCAGgtaaagccat ... ctcttaacagGTTGGGTTAATCGCTTTGCTAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtgtgttttgtcttcaaggcttatgtgacggcttgggttctgtctcttaacagGTTGGGTTAATCGCTTTGCTAATGCTGGGGACACAGCCTTGGAAGTGGCAGGAAACACAGCAATGCGG
                                       ttctgtctctt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagccattttttgggaatctggtgtgtgtgtgtgtgtgttttgtcttcaaggcttatgtgacggcttgggttctgtctcttaacagGTTGGGTTAATCGCTTTGCTAATGCTGGGGACACAGCCTTGGAAGTGGCAGGAAACACAGCAATGCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG