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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgattttttcttgtgttaggcctgttaggccgttaacatagtgtgcttatgatcaattgtacgtgattataattacagCTGTTGTGAGCTTCGGGGGTGTCTCACGTGAACAAAAAGAAGAAGCTGAAACTTTTGGGTTGGTTATATATGCTTGGGATGAATTTTTGAAGCTG

Basic information

species Arabidopsis thaliana
transcript AT4G23850.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G23850.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA11G02030.1 (Glycine max), 3'ss of exon 7
gtgagtgatttt----ttcttgtgttaggcctgttaggccgttaacatagtgtgcttatgatcaattgtacgtgattataattacagCTGTTGTGAGCTTCGGGGGTGTCTCACGTGAACAAAAAGAAGAAGCTGAAACTTTTGGGTTGGTTATATATGCTTGGGATGAATTTTTGAAGCTG
|| |||  | ||     |||| | |    |||   | ||   |    |||   |       ||| || || ||  || |   ||||||  |||| ||||||||    ||  | | |||||||||  |||||| ||||| |||||||||||  |||||| | ||||||||||||||     ||
gtaagttttgttgattctcttctttctttcctaaaatgcttgtgctttagaaagaa-gcattcatttttatgtctttgt---tacagCAATTGTAAGCTTCGGAAAGGTTACCCCTGAACAAAAGCAAGAAGTTGAAAGTTTTGGGTTGGCAATATATTCATGGGATGAATTTTTACTAGTG
















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|125252928|gb|EL267013.1|EL267013
EST:     TTGTTCAAGACATGCCCAAACTCGACAGAGTACATGAAAA                         CTGTTGTGAGCTTCGGGGGTGTCTCACGT
genomic: TTGTTCAAGACATGCCCAAACTCGACAGAGTACATGAAAAgtgagtgatt ... ataattacagCTGTTGTGAGCTTCGGGGGTGTCTCACGT
EST: gi|125018978|gb|EL091247.1|EL091247
EST:     TTGTTCAAGACATGCCCAAACTCGACAGAGTACATGAAAA                         CTGTTGTGAGCTTCGGG
genomic: TTGTTCAAGACATGCCCAAACTCGACAGAGTACATGAAAAgtgagtgatt ... ataattacagCTGTTGTGAGCTTCGGG
EST: gi|125281992|gb|EL296077.1|EL296077
EST:     TTGTTCAAGACATGCCCAAACTCGACAGAGTACATGAAAA                         CTGTTGTGAGCTTC
genomic: TTGTTCAAGACATGCCCAAACTCGACAGAGTACATGAAAAgtgagtgatt ... ataattacagCTGTTGTGAGCTTC
EST: gi|125045108|gb|EL117377.1|EL117377
EST:     ATCTCTGAGTTGTTCAAGACATAGCCCAAACTCGACAGAGTACATGAAAA                         CTGTCGTGAGCTTCGGGGGTGTCTCACGTGAACAAAAAGAAGAAGCTGAAA
genomic: ATCTCTGAGTTGTTCAAGACAT-GCCCAAACTCGACAGAGTACATGAAAAgtgagtgatt ... ataattacagCTGTTGTGAGCTTCGGGGGTGTCTCACGTGAACAAAAAGAAGAAGCTGAAA
EST: gi|125304597|gb|EL318682.1|EL318682
EST:     TTGTTCAAGACATGCCCAAACTCGACAGAGTACATGAAAA                         CTGTTGTGAGCTTCG
genomic: TTGTTCAAGACATGCCCAAACTCGACAGAGTACATGAAAAgtgagtgatt ... ataattacagCTGTTGTGAGCTTCG
EST: gi|125210271|gb|EL225225.1|EL225225
EST:     TTGTTCAAGACATGCCCAAACTCGACAGAGTACATGAAAA                         CTGTTGTGAGCTTCGGGGGTGTCTCACGT
genomic: TTGTTCAAGACATGCCCAAACTCGACAGAGTACATGAAAAgtgagtgatt ... ataattacagCTGTTGTGAGCTTCGGGGGTGTCTCACGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttaggccgttaacatagtgtgcttatgatcaattgtacgtgattataattacagCTGTTGTGAGCTTCGGGGGTGTCTCACGTGAACAAAAAGAAGAAGCTGAAACTTTTGGGTTGGTTATATATGCTTGGGATGAATTTTTGAAGCTG
       cgttaac  putative branch site (score: 3)
                                        tgattataattaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgattttttcttgtgttaggcctgttaggccgttaacatagtgtgcttatgatcaattgtacgtgattataattacagCTGTTGTGAGCTTCGGGGGTGTCTCACGTGAACAAAAAGAAGAAGCTGAAACTTTTGGGTTGGTTATATATGCTTGGGATGAATTTTTGAAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG