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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgttgatattcttcattcgtgcttttggcgtttcgcattgtaaagataaaatgaatcgttctgttgcttatttgttcgtcttctgccaccatgtagGATTCAAACACGCCCCTTTCCGAAGCTGAAGCAGTTGACTTGGTTAAAACTGTTTTCGCATCTGCCACAGAGAGGGATATCTACACTGTAA

Basic information

species Arabidopsis thaliana
transcript AT3G60820.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G60820.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA08G39420.2 (Glycine max), 3'ss of exon 3
gtttgttgatattcttca-ttcgtgcttttggcgtttcgcattgtaaagataaaatgaatcgttctgt-tgcttatttgttcgtcttctgccaccatgtagGATTCAAACACGCCCCTTTCCGAAGCTGAAGCAGTTGACTTGGTTAAAACTGTTTTCGCATCTGCCACAGAGAGGGATATCTACACTGTAA
      |||  ||||  | || | ||||||  | |     |||  |    | || |  || |       ||| ||  | |      | ||    | | |||||| |    || ||  | || ||||| |||||||||||  |||| ||||||||||| |||||||| || ||||| ||||| |||||     
-----gtgaggttctgaaattggcgctttt--cttgaaatatttgattcttcaactttattgactgacatgcctacat-taaaaaatatgatttcttttagGATGCTGTTACTCCATTGTCTGAAGCAGAAGCAGTTGATCTGGTCAAAACTGTTTTTGCATCTGCAACTGAGAGAGATATATACACC----

upper sequence: AT3G60820.2 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv15s0048g00900.t01 (Vitis vinifera), 3'ss of exon 5
gtttgttgatattcttcattcgtgcttttggcgtttcgcattgtaaagataaaatgaatcgttctgt-tgcttatttgttcgtcttctgccaccatgtagGATTCAAACACGCCCCTTTCCGAAGCTGAAGCAGTTGACTTGGTTAAAACTGTTTTCGCATCTGCCACAGAGAGGGATATCTACACTGTAA
         | ||||| |  | || |  |    |    ||||      |     | |       ||| ||| |  |      ||           || ||||| |    || || || || ||  | ||||||||||| || || |||||||| || |||||||| || ||||||||||| ||||||    
------gtgtgttcttaaagcttgttgctttgttgatacatttgctccactggttaatcttccatgtgtgcctgctctaaaatccaaactacttgtgcagGATGCTGTTACTCCTCTCTCTGAGCCAGAAGCAGTTGATTTAGTGAAAACTGTCTTTGCATCTGCAACTGAGAGGGATATATACACT----
















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|86020238|gb|DR315984.1|DR315984
EST:     TCCTTGACA-TCAGCTCAAGTCTCCAAGTCCTCTTTTGCTACCTAAACAG                         GGAT-CAAACACGCCCCTTTCCGAAGCTGAAAGCAGT-GACTTG
genomic: TCCTTGACAATCAGCTCAAGTCTCCAAGTCCTCTTTTGCTACCTAAACAGgtttgttgat ... caccatgtagG-ATTCAAACACGCCCCTTTCCGAAGCTGAA-GCAGTTGACTTG
EST: gi|125094587|gb|EL152029.1|EL152029
EST:     CCTTGACAATCAGCTCAAGTCTCCTAAGTCCTCTTTTGCTACCTAAACAG                         GATTCAAACACGCCCCTTTCCGAAGCTGAAGCAGTTGACTTGGTTAAAACT
genomic: CCTTGACAATCAGCTCAAGTCTCC-AAGTCCTCTTTTGCTACCTAAACAGgtttgttgat ... caccatgtagGATTCAAACACGCCCCTTTCCGAAGCTGAAGCAGTTGACTTGGTTAAAACT
EST: gi|124986015|gb|EL058564.1|EL058564
EST:     TACCTAAACAG                         GATTCAAACACGCCCCTTTCCGAAGCTGAAGCAGTTGACTTGGTTAAAACT
genomic: TACCTAAACAGgtttgttgat ... caccatgtagGATTCAAACACGCCCCTTTCCGAAGCTGAAGCAGTTGACTTGGTTAAAACT
EST: gi|164212305|gb|EL977040.1|EL977040
EST:     CCTTGACAATCAGCTCAAGTCTCCAAGTACCTCTTTTGCTACCTAAACAG                         GATTCAAACACG
genomic: CCTTGACAATCAGCTCAAGTCTCCAAGT-CCTCTTTTGCTACCTAAACAGgtttgttgat ... caccatgtagGATTCAAACACG
EST: gi|86020250|gb|DR315996.1|DR315996
EST:     GCTCAAGTCTCCAAGTCCTCTTTTGCTACCTAAACAG                         GATTCAAACACGCCCCTTTCCGAAGCTGAAGCAGTTGACTTGGTTAAAACT
genomic: GCTCAAGTCTCCAAGTCCTCTTTTGCTACCTAAACAGgtttgttgat ... caccatgtagGATTCAAACACGCCCCTTTCCGAAGCTGAAGCAGTTGACTTGGTTAAAACT
EST: gi|124790177|gb|EH879856.1|EH879856
EST:     TACCTAAACAG                         GATTCAAACACGCCCCTTTCCGAAGCNGAAGCAGTTGACTTGGTTAAAACT
genomic: TACCTAAACAGgtttgttgat ... caccatgtagGATTCAAACACGCCCCTTTCCGAAGCTGAAGCAGTTGACTTGGTTAAAACT
EST: gi|86078317|gb|DR374074.1|DR374074
EST:     TCCTTGACAATCAGCTCAAGTCTCCAAGTCCTCTTTTGCTACCTAAACAG                         GATTCAAACACGCCCCTTTCCGAAGCTGAAGCAGTTGACTTGGTTAAAACT
genomic: TCCTTGACAATCAGCTCAAGTCTCCAAGTCCTCTTTTGCTACCTAAACAGgtttgttgat ... caccatgtagGATTCAAACACGCCCCTTTCCGAAGCTGAAGCAGTTGACTTGGTTAAAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaagataaaatgaatcgttctgttgcttatttgttcgtcttctgccaccatgtagGATTCAAACACGCCCCTTTCCGAAGCTGAAGCAGTTGACTTGGTTAAAACTGTTTTCGCATCTGCCACAGAGAGGGATATCTACACTGTAA
                                     tcttctgcc  CT-rich tract
     taaaatgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgttgatattcttcattcgtgcttttggcgtttcgcattgtaaagataaaatgaatcgttctgttgcttatttgttcgtcttctgccaccatgtagGATTCAAACACGCCCCTTTCCGAAGCTGAAGCAGTTGACTTGGTTAAAACTGTTTTCGCATCTGCCACAGAGAGGGATATCTACACTGTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG