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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagctcaataacatcacacaaagcaatcttcctcttatctctcttgcttctaatggttatgttccattggattcacatactcacagATTGTAGATGGAAGGCAGAGGCGGGCGATGTTTGTGTGGCCTCATTCGAATGGAGCTGTAGTGGGATTTGCAAGTCCGTAGAGAGAATGAAGATAGTGCA

Basic information

species Arabidopsis thaliana
transcript AT1G77810.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G77810.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ30358 (Selaginella moellendorffii), 3'ss of exon 10
gtaaagctcaataacatcacacaaagcaatcttcctcttatctctcttgcttctaatggttatgttccattggattcacatactcacagATTGTAGATGGAAGGCAGAGGCGGGCGATGTTTGTGTGGCCTCATTCGAATGGAGCTGTAGTGGGATTTGCAAGTCCGTAGAGAGAATGAAGATAGTGCA
                             |  ||     ||  |||| |  || | ||| |        ||   ||  | | ||  |||||||    ||| | ||  | || ||| | |||||||| ||||| ||||| ||||| ||||| || |||||||| ||||| || ||||||||||| |||||
------------------------gtttgttctcgatcgattgctctcgtatcgattggatgaagaatttttcttttgc-tcctggcagATTGCGAGTGGCAAGCTCAAGCAGGCAACGTTTGTGTTGCCTCGTTCGATTGGAGTTGTAGCGGCATTTGCAAATCCGTGGAAAGAATGAAGATCGTGCA

upper sequence: AT1G77810.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ28470 (Selaginella moellendorffii), 3'ss of exon 10
gtaaagctcaataacatcacacaaagcaatcttcctcttatctctcttgcttctaatggttatgttccattggattcacatactcacagATTGTAGATGGAAGGCAGAGGCGGGCGATGTTTGTGTGGCCTCATTCGAATGGAGCTGTAGTGGGATTTGCAAGTCCGTAGAGAGAATGAAGATAGTGCA
                             |||   ||   |  |||| |  || | ||| |        ||   ||  | | ||  |||||||    ||| | ||  | || ||| | |||||||| ||||| ||||| ||||| ||||| || |||||||| ||||| || ||||||||||| |||||
-----------------------gtttgttctcgatcgatttgctctcgtatcgattggatgaagaatttttcttttgc-tcctggcagATTGCGACTGGCAAGCTCAAGCAGGCAACGTTTGTGTTGCCTCGTTCGATTGGAGTTGTAGCGGCATTTGCAAATCCGTGGAAAGAATGAAGATCGTGCA
















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|86075540|gb|DR371297.1|DR371297
EST:     TGAGGTTGAACATATTGATGACCGCAACTTCTGTTGTGGGACTCCTCCAG                         ATTGTAGATGGAAGGCAGAGGCGGGCGATGTTTGTGTGGCCTCATTCGAAT
genomic: TGAGGTTGAACATATTGATGACCGCAACTTCTGTTGTGGGACTCCTCCAGgtaaagctca ... atactcacagATTGTAGATGGAAGGCAGAGGCGGGCGATGTTTGTGTGGCCTCATTCGAAT
EST: gi|163983189|gb|ES114369.1|ES114369
EST:     AACATATTGATGACCGCAACTTCTGTTGTGGGACTCCTCCAG                         ATTGTAGATGGAAGGCAGAGGCGGGCGATGTTTGTGTGGCCTCATTCGAA
genomic: AACATATTGATGACCGCAACTTCTGTTGTGGGACTCCTCCAGgtaaagctca ... atactcacagATTGTAGATGGAAGGCAGAGGCGGGCGATGTTTGTGTGGCCTCATTCGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcttatctctcttgcttctaatggttatgttccattggattcacatactcacagATTGTAGATGGAAGGCAGAGGCGGGCGATGTTTGTGTGGCCTCATTCGAATGGAGCTGTAGTGGGATTTGCAAGTCCGTAGAGAGAATGAAGATAGTGCA
                ttctaat  putative branch site (score: 2)
                ttctaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagctcaataacatcacacaaagcaatcttcctcttatctctcttgcttctaatggttatgttccattggattcacatactcacagATTGTAGATGGAAGGCAGAGGCGGGCGATGTTTGTGTGGCCTCATTCGAATGGAGCTGTAGTGGGATTTGCAAGTCCGTAGAGAGAATGAAGATAGTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA