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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtaatgcttttgttcaaaaacactatttttaaaagtattttgctggatgttgaacttgtgaatgttcttattcagGATATAAACGAAGAATGGATATCTGACAAAACCCGATTCTGTTATGACGGCCTGAAAAGACAAAGGCTGAGCGACCCTATGATCCGAGATTCCGATGGAC

Basic information

species Arabidopsis thaliana
transcript AT5G37510.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G37510.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g50540.1 (Oryza sativa), 3'ss of exon 3
-------------------gtatgtaatgcttttgttca--aaaacactatttttaaaagtattttgctggatgttgaacttgtgaatgttcttatt-cagGATATAAACGAAGAATGGATATCTGACAAAACCCGATTCTGTTATGACGGCCTGAAAAGACAAAGGCTGAGCGACCCTATGATCCGAGATTCCGATGGAC
                     |  |  | | || ||     |   |||   | |   || ||     |||  |      | |||    ||  |  || |||||||| || || |||||||||||||||||||| || || |||||||| || ||||| || ||||| || | |||||| |||||||| | | | |||||  
gttcaacagcgtgttgatgaaactttttcccttcgtctgttatgtcacatctgtctgaaataaac-actgagtaagcttcctgttttcgtgatacttgcagGATATCAATGAGGAATGGATATCTGACAAAACACGGTTTTGTTATGATGGTCTGAAGAGGCAAAGACTAAACGACCCCATGATCCGTGGTACTGATGGCA

upper sequence: AT5G37510.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA11G33480.1 (Glycine max), 3'ss of exon 3
---------------gtatgtaatgctttt----gttcaaaaacactatttttaaaagtattttgctggatgttgaacttgtga-atgttcttatt-cagGATATAAACGAAGAATGGATATCTGACAAAACCCGATTCTGTTATGACGGCCTGAAAAGACAAAGGCTGAGCGACCCTATGATCCGAGATTCCGATGGAC
                 |   |||  | ||    |   || |       || |     || ||||||   | |  | |||||      | |  ||| ||||| ||||| ||||||||||| || ||||||||||| || |||||||| ||  ||||||| || ||| | |  ||||| ||||| || | ||| |||||||
tctaaaaagaaaagaaaaaaaaatcttcttagggggagaagaggttggcttctttccatagtttgctatttttaaagcttgttctgcttgcccattgcagGACATAAATGAAGAATGGATTTCAGACAAAACCCGCTTTTGTTATGATGGTTTGAAAAGGCAGAGGTTAAATGACCCCATGATTCGTGGTTCTGATGGAC

upper sequence: AT5G37510.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G04730.1 (Glycine max), 3'ss of exon 3
-------------gtatgtaatgctttt----gttcaaaaacacta-tttttaaaagtattttgctggatgttgaacttgtga-atgttcttatt-cagGATATAAACGAAGAATGGATATCTGACAAAACCCGATTCTGTTATGACGGCCTGAAAAGACAAAGGCTGAGCGACCCTATGATCCGAGATTCCGATGGAC-
             | |   ||  ||| |    | |  || |   |   || |     || ||||||   | |  | |||||      | |  ||| ||||| ||||| ||||||||||| || || |||||||| || |||||||| ||  ||||||| |||||| | |  || || ||||| || | ||| ||||||| 
tttttccaaaaaagaaaaaaaaacttcttagggatagaagaggttggcttctttccatagtttgctatttttaaagcttgttctgcttgcccattgcaggAGATAAATGAAGAATGGATTTCGGATAAAACCCGCTTTTGTTATGATGGTTTGAAAAGGCAAAGGTTAAATGATCCCATGATACGTGGTTCTGATGGACG

upper sequence: AT5G37510.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv14s0006g02020.t01 (Vitis vinifera), 3'ss of exon 3
------gtatgtaatgcttttgttcaaaaacactatttttaaaagtattttgctggatgttgaacttgtgaatgtt----------------cttattcagGATATAAACGAAGAATGGATATCTGACAAAACCCGATTCTGTTATGACGGCCTGAAAAGACAAAGGCTGAGCGACCCTATGATCCGAGATTCCGATGGAC
       | |||  |  |||   |     | | | | ||| |   | |||| ||| |   | |  |  | ||| |                 ||  | ||||| ||||| || ||||||||||| |||||||| || ||||||||||| || ||||| || || ||| | |  || |||||||| || | | | |||||||
gaggatctttgtgtttttttaacttgttcaga-tgtcttttagcatcttttactgaaatgtaagatcatcaatttcagctggctttgctgaactgttgcagGACATAAATGAGGAATGGATATCAGACAAAACACGTTTCTGTTATGATGGTCTGAAGAGGCAGAGGTTAAATGATCCTATGATTCGTGGTGCTGATGGAC

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|124911626|gb|EH985706.1|EH985706
EST:     GACCAGAAGT-ATGCGTATCATTCCACGCCTGAATGAG                         GATATAAACGAAGAATGGATATCTGACAAAACCCGATTCTGTTATGACGGC
genomic: GACCAGAAGTAATGCGTATCATTCCACGCCTGAATGAGgtatgtaatg ... tcttattcagGATATAAACGAAGAATGGATATCTGACAAAACCCGATTCTGTTATGACGGC
EST: gi|116446466|gb|EG489058.1|EG489058
EST:     TTGATAGTAGAGGACCAGAAGTAATGCGTATCATTCCACGCCTGAATGAG                         GATATAAACGAAGAATGGATATCTGACAAAACCCGATTCTGTTATGACGGC
genomic: TTGATAGTAGAGGACCAGAAGTAATGCGTATCATTCCACGCCTGAATGAGgtatgtaatg ... tcttattcagGATATAAACGAAGAATGGATATCTGACAAAACCCGATTCTGTTATGACGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactatttttaaaagtattttgctggatgttgaacttgtgaatgttcttattcagGATATAAACGAAGAATGGATATCTGACAAAACCCGATTCTGTTATGACGGCCTGAAAAGACAAAGGCTGAGCGACCCTATGATCCGAGATTCCGATGGAC
                                            ttcttattc  CT-rich tract
     tttttaaaagtatttt  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtaatgcttttgttcaaaaacactatttttaaaagtattttgctggatgttgaacttgtgaatgttcttattcagGATATAAACGAAGAATGGATATCTGACAAAACCCGATTCTGTTATGACGGCCTGAAAAGACAAAGGCTGAGCGACCCTATGATCCGAGATTCCGATGGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA