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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCCATCTTTACAAGGAGAACAAAGATACACAAGAGGCCTTGGGATTGATTGGAAAGATGCTAGGCGTTCAGgtgtttcccatcttcttctatccatctataaaggggctgttttatctctagccattgtactttccttgataagctgtgtattgaaatggtttttgaatttacag

Basic information

species Arabidopsis thaliana
transcript AT3G04820.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G04820.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA19G43270.1 (Glycine max), 5'ss of exon 5
GTTCCATCTTTACAAGGAGAACAAAGATACACAAGAGGCCTTGGGATTGATTGGAAAGATGCTAGGCGTTCAGgtgtttcccatcttcttctatccatctataaaggggctgttttatctctagccattgtactttccttgataagctgtgtattgaaatggtttttgaat-ttacag
||| ||||||||||||||||||||||||||||| || ||||||||  | |||||||| |||||  || | ||||| | |    |    |  |    || | |     |||| | | ||     |  | || | |||  ||  |      |  ||| |    ||| ||| || | | | 
GTTTCATCTTTACAAGGAGAACAAAGATACACATGAAGCCTTGGGGGTTATTGGAAATATGCTCAGCATCCAGgtctgtgttgttcattgttggatatgt-tctgtaggctttctgatggactgaaagtgaagttttgtttgttgatgattcattca----gttcttgtatatgataa

upper sequence: AT3G04820.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA03G40600.1 (Glycine max), 5'ss of exon 5
GTTCCATCTTTACAAGGAGAACAAAGATACACAAGAGGCCTTGGGATTGATTGGAAAGATGCTAGGCGTTCAGgtgtttcccatcttcttctatccatctataaaggggctgttttatctctagccattgtactttccttgataagctgtgtattgaaatggtttttgaatttacag-
||| |||||||||||||||||||||||||| || || ||||||||  | |||||||| |||||  | || ||||| | ||   |    |  |    || | |     |||| | | ||     |  | || | |||  ||     ||||   ||| |    ||| ||| || |   | 
GTTTCATCTTTACAAGGAGAACAAAGATACCCACGAAGCCTTGGGGGTTATTGGAAATATGCTCAGTGTCCAGgtctgtcttgttcattgttggatatgt-tctgtaggctttctgatggaccgaaagtgaagttttgttt----gctgatgattcattcagttcttgtatatgagga

upper sequence: AT3G04820.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: Vv14s0030g01840.t01 (Vitis vinifera), 5'ss of exon 5
GTTCCATCTTTACAAGGAGAACAAAGATACACAAGAGGCCTTGGGATTGATTGGAAAGATGCTAGGCGTTCAGgtgtttcccatcttcttctatccatctataaaggggctgtttta--tctctagccattgtactttccttgataagctg-tgtattga------aatggtttttgaatttacag---------------------------------------------------------------------------------------
||| |||||||||||||||||||| ||||| || |||||| | |||||||||||||||||||| ||| | |||||  |||        || || ||||  ||          || |    || |     |  || |     ||  | |  | ||||||        |   ||| ||| || | |                                                                                         
GTTTCATCTTTACAAGGAGAACAAGGATACCCAGGAGGCCATAGGATTGATTGGAAAGATGCTGGGCATCCAGgtaattcatgggaaattatagccattcatttccaaatatttgtgatcctttgtaggtaataatggggatggcaggtggctgtattagtcatatagctgttgttggatgttctatcatattttgaacagtttgtatcggttgtatatgtagaagtgttaaatatcttttatttacattgattgatgtttctgtttcgacag

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|116462950|gb|EG505542.1|EG505542
EST:     AAGATACACAAGAGGCCTTGGGATTGATTGGAAAGATGCTAGGCGTTCAG                         CCAAAGTCATTCGGATTCTCTGGAACAAAAGATAAGCGGTCTGTTTCTACT
genomic: AAGATACACAAGAGGCCTTGGGATTGATTGGAAAGATGCTAGGCGTTCAGgtgtttccca ... gaatttacagCCAAAGTCATTCGGATTCTCTGGAACAAAAGATAAGCGGTCTGTTTCTACT
EST: gi|116431187|gb|EG473779.1|EG473779
EST:     AAGATACACAAGAGGCCTTGGGATTGATTGGAAAGATGCTAGGCGTTCAG                         CCAAAGTCATTCGGATTCTCTGGAACAAAAGATAAGCGGTCTGTTTCTACT
genomic: AAGATACACAAGAGGCCTTGGGATTGATTGGAAAGATGCTAGGCGTTCAGgtgtttccca ... gaatttacagCCAAAGTCATTCGGATTCTCTGGAACAAAAGATAAGCGGTCTGTTTCTACT
EST: gi|116421231|gb|EG463823.1|EG463823
EST:     AAGATACACAAGAGGCCTTGGGATTGATTGGAAAGATGCTAGGCGTTCAG                         CCAAAGTCATTCGGATTCTCTGGAACAAAAGATAAGCGGTCTGTTTCTACT
genomic: AAGATACACAAGAGGCCTTGGGATTGATTGGAAAGATGCTAGGCGTTCAGgtgtttccca ... gaatttacagCCAAAGTCATTCGGATTCTCTGGAACAAAAGATAAGCGGTCTGTTTCTACT
EST: gi|125106890|gb|EL160279.1|EL160279
EST:     TTGGAAAGATGCTAGGCGTTCAG                         CCAAAGTCATTCGGATTCTCTGGAACAAAAGATAAGCGGTCTGTTTCTACT
genomic: TTGGAAAGATGCTAGGCGTTCAGgtgtttccca ... gaatttacagCCAAAGTCATTCGGATTCTCTGGAACAAAAGATAAGCGGTCTGTTTCTACT
EST: gi|116421229|gb|EG463821.1|EG463821
EST:     AAGATACACAAGAGGCCTTGGGATTGATTGGAAAGATGCTAGGCGTTCAG                         CCAAAGTCATTCGGATTCTTTGGAACAAAAGATAAGCGGTCTGTTTCTACT
genomic: AAGATACACAAGAGGCCTTGGGATTGATTGGAAAGATGCTAGGCGTTCAGgtgtttccca ... gaatttacagCCAAAGTCATTCGGATTCTCTGGAACAAAAGATAAGCGGTCTGTTTCTACT
EST: gi|116421230|gb|EG463822.1|EG463822
EST:     AAGATACACAAGAGGCCTTGGGATTGATTGGAAAGATGCTAGGCGTTCAG                         CCAAAGTCATTC
genomic: AAGATACACAAGAGGCCTTGGGATTGATTGGAAAGATGCTAGGCGTTCAGgtgtttccca ... gaatttacagCCAAAGTCATTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCCATCTTTACAAGGAGAACAAAGATACACAAGAGGCCTTGGGATTGATTGGAAAGATGCTAGGCGTTCAGgtgtttcccatcttcttctatccatctataaaggggctgttttatctctagccattgtactttccttgataagctgtgtattgaaatggtttttgaatttacag

- - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG