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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttagagaaatacatacctagagaaagagaggagaaggtttaaagtatgttgacactgatggtcgtgttatgttgttatagGTGCCTTACCTGGAAGATCCAAACACTGGAGTCGCGATGTTTGAGAGTGCAGAAATTGTTGAGTATCTCAAGCAAACTTATGCTGCCTAAGTGTTCGTCT

Basic information

species Arabidopsis thaliana
transcript AT5G03880.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G03880.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv08s0007g03250.t01 (Vitis vinifera), 3'ss of exon 11
-------------------------------gtgagttagagaaatacat--acctagagaaagagaggagaaggtttaaagtatgttgacactgatggtcgtgttatgttgttatagGTGCCTTACCTGGAAGATCCAAACACTGGAGTCGCGATGTTTGAGAGTGCAGAAATTGTTGAGTATCTCAAGCAAACTTATGCTGCCTAAGTGTTCGTCT-
                                | |  ||  | | |   |  |  ||  |    | | |  |  |  |     | | |     | |   || |  |||| | | | |||  |||||  | ||||||||||||||||||||    |||||||| |||||||||||||| || ||||| ||   ||| |||||| | | | |   |     
gtatcctcctttttgttctgtgacaattattctcatctatggcatttttttcatttattgtgtcatatggcatagaatggtaaaagattgttttaac--tcctactatggt-tgacagGCACCTTATTTAGAAGATCCAAACACTGGAGTGAAAATGTTTGAAAGTGCAGAAATTGTGGAATATCTAAAAGCAACATATGCT-CTTCAATAAGCAAAAA
















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|125050172|gb|EL122441.1|EL122441
EST:     GGTAGCCCCAAACGGCAGGTATTGCTTGAAGAAAAGCTGGTCACTTTCAG                         GTGCCTTACCTGG
genomic: GGTAGCCCCAAACGGCAGGTATTGCTTGA-GAAA-GCTGGTCACTTTCAGgtgagttaga ... gttgttatagGTGCCTTACCTGG
EST: gi|124787842|gb|EH877521.1|EH877521
EST:     GTGGTAGCCCCAAACGGCAGGTATTGCTTGAGAAAGCTGGTCACTTTCAG                         GTGCCTTACCTGGAAGATCCAAACACTGG
genomic: GTGGTAGCCCCAAACGGCAGGTATTGCTTGAGAAAGCTGGTCACTTTCAGgtgagttaga ... gttgttatagGTGCCTTACCTGGAAGATCCAAACACTGG
EST: gi|86080278|gb|DR376035.1|DR376035
EST:     GTGGTAGCCCCAAACGGCAGGTATTGCTTGAGAAAGCTGGTCACTTTCAG                         GTGCCTTACCTGGAAGATCCAAACACTGGAGTCGCGATGTTTGAGAGTGCA
genomic: GTGGTAGCCCCAAACGGCAGGTATTGCTTGAGAAAGCTGGTCACTTTCAGgtgagttaga ... gttgttatagGTGCCTTACCTGGAAGATCCAAACACTGGAGTCGCGATGTTTGAGAGTGCA
EST: gi|124728425|gb|EH819827.1|EH819827
EST:     GTGGTAGCCCCAAACGGCAGGTATTGCTTGAGAAAGCTGGTCACTTTCAG                         GTGCCTTACCTGGAAGATCCAAACACTG
genomic: GTGGTAGCCCCAAACGGCAGGTATTGCTTGAGAAAGCTGGTCACTTTCAGgtgagttaga ... gttgttatagGTGCCTTACCTGGAAGATCCAAACACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagaggagaaggtttaaagtatgttgacactgatggtcgtgttatgttgttatagGTGCCTTACCTGGAAGATCCAAACACTGGAGTCGCGATGTTTGAGAGTGCAGAAATTGTTGAGTATCTCAAGCAAACTTATGCTGCCTAAGTGTTCGTCT
                           cactgat  putative branch site (score: 3)
            tttaaagtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttagagaaatacatacctagagaaagagaggagaaggtttaaagtatgttgacactgatggtcgtgttatgttgttatagGTGCCTTACCTGGAAGATCCAAACACTGGAGTCGCGATGTTTGAGAGTGCAGAAATTGTTGAGTATCTCAAGCAAACTTATGCTGCCTAAGTGTTCGTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC