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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagaccaaatacaggcacttttctttgattatttgtatgaagaacatgcttttctctgtcagttttattataagtgtttctggtctgtgttagGATCCTCGACAACCTTCCTCTGGTTGTTCCAATTGAAAGAGTCGACCAGGGTTCTCCCTCTGTTGTTTATCAGCTTGGTTATCATGTTGGTCTTAAAGGC

Basic information

species Arabidopsis thaliana
transcript AT5G10840.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G10840.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv04s0008g06640.t01 (Vitis vinifera), 3'ss of exon 3
------gtaagaccaaatacaggcacttttctttgattatttgtatgaagaacatgcttttctctgtcagttttattataagtgtttctggtc-tgtgttagGATCCTCGACAACCTTCCTCTGGTTGTTCCAATTGAAAGAGTCGACCAGGGTTCTCCCTCTGTTGTTTATCAGCTTGGTTATCATGTTGGTCTTAAAGGC---
      | |    |  ||   |   | |   |   |||| |  | |  |  | |   || | |    |   | | ||||        |   || ||||  ||||| || || ||||||||||| |||||||| ||    ||  | || || |  |||||  || |   |||||||||||| ||||||||||| |||||||     
gtgggggcaccctcttatttggatccataattcaaattactaatttccatgaga-atttctttgaaccgcatcttttattgaatcaaccattcatgtgacagGATTCTGGATAACCTTCCTCTTGTTGTTCCCATAAGGAGGCTTGATCAAGAATCTCCTCCTCT---TTATCAGCTTGGATATCATGTTGGGCTTAAAGCACAA
















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|124767608|gb|EH857738.1|EH857738
EST:     ACAGCTAAAGCGTTTAAAGAAAAGATCGATGATGAGTACCGGGTCAACAT                         GATCCTCGACAACCTTCCTCTGGTTGTTCCAATTGAAAGA
genomic: ACAGCTAAAGCGTTTAAAGAAAAGATCGATGATGAGTACCGGGTCAACATgtaagaccaa ... tctgtgttagGATCCTCGACAACCTTCCTCTGGTTGTTCCAATTGAAAGA
EST: gi|124973099|gb|EL046754.1|EL046754
EST:     CTAAAGCGTTTAAAGAAAAGATCGATGATGAGTACCGGGTCAACAT                         GATCCTCGACAACCTTCCTCTGGTTGTTCCAATTGAAAGAGTCGACCAGGG
genomic: CTAAAGCGTTTAAAGAAAAGATCGATGATGAGTACCGGGTCAACATgtaagaccaa ... tctgtgttagGATCCTCGACAACCTTCCTCTGGTTGTTCCAATTGAAAGAGTCGACCAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagaacatgcttttctctgtcagttttattataagtgtttctggtctgtgttagGATCCTCGACAACCTTCCTCTGGTTGTTCCAATTGAAAGAGTCGACCAGGGTTCTCCCTCTGTTGTTTATCAGCTTGGTTATCATGTTGGTCTTAAAGGC
                        ttttattataagtgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagaccaaatacaggcacttttctttgattatttgtatgaagaacatgcttttctctgtcagttttattataagtgtttctggtctgtgttagGATCCTCGACAACCTTCCTCTGGTTGTTCCAATTGAAAGAGTCGACCAGGGTTCTCCCTCTGTTGTTTATCAGCTTGGTTATCATGTTGGTCTTAAAGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT