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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcaagattgaagcaaattatgtccacactaaataaatgatggttttttataaaaagttttcctctcttccaatagGGCCTTGGAGGTGGTTTGATGAATCAATGTTGGATTGCTGCGAACCTCTGGAAGTAGTGAAGGAAAAAGGCATTTCATTTGGAAAAGTTGTCTGTTTGGC

Basic information

species Arabidopsis thaliana
transcript AT5G44070.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G44070.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA03G32200.1 (Glycine max), 3'ss of exon 3
---------------------gtatgcaagattga---agcaaattatgtccacactaaataaatgat--ggttttttataaaaagttttcctctct-tccaatagGGCCTTGGAGGTGGTTTGATGAATCAATGTTGGATTGCTGCGAACCTCTGGAAGTAGTGAAGGAAAAAGGCATTTCATTTGGAAAAGTTGTCTGTTTGGC
                     |  | ||  | | |   |   |||||||   |   |   | ||| ||    |   || |    |||| |  | | |  |    ||| |||||||| |||||||||||||| |||||||| ||||| || ||||| |||  ||| ||||  | ||||||  | || || ||  |||| ||||||||
gtacataacaaacaatctaatgcttccatcactaacctaattaattatgaatat-ttgcttgaatcatttaatcaattgtctcgagttctattatttgccttgcagGACCTTGGAGATGGTTTGATGAATCTATGTTGGACTGCTGTGAGCCTCTAGAAACAGTCAAGGCTAGAGGCATCACGTTCGGGAAGCTTGTGTGTTTGGC
















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|86051282|gb|DR347037.1|DR347037
EST:     CTCAGTGGTGTTGAATGCTCTTTCTATCGATCCTGGACGTAAATGGAAAG                         GGCCTTGGAGGTGGTTTGATGAATCAATGATGGATTGCTGCGAACCTCTGG
genomic: CTCAGTGGTGTTGAATGCTCTTTCTATCGATCCTGGACGTAAATGGAAAGgtatgcaaga ... cttccaatagGGCCTTGGAGGTGGTTTGATGAATCAATGTTGGATTGCTGCGAACCTCTGG
EST: gi|125029059|gb|EL101328.1|EL101328
EST:     CTCAGTGGTGTTGAATGCTCTTTCTATCGATCCTGGACGTAAATGGAAAG                         GGCCTTGGAGGTGGTTTGATGAATCAATGT
genomic: CTCAGTGGTGTTGAATGCTCTTTCTATCGATCCTGGACGTAAATGGAAAGgtatgcaaga ... cttccaatagGGCCTTGGAGGTGGTTTGATGAATCAATGT
EST: gi|86051284|gb|DR347039.1|DR347039
EST:     CTCAGTGGTGTTGAATGCTCTTTCTATCGATCCTGGACGTAAATGGAAAG                         GGCCTTGGAGGTGGTTTGATGAATCAATGTTGGATTGCTGCGAACCTCTGG
genomic: CTCAGTGGTGTTGAATGCTCTTTCTATCGATCCTGGACGTAAATGGAAAGgtatgcaaga ... cttccaatagGGCCTTGGAGGTGGTTTGATGAATCAATGTTGGATTGCTGCGAACCTCTGG
EST: gi|86051290|gb|DR347045.1|DR347045
EST:     CTCAGTGGTGTTGAATGCTCTTTCTATCGATCCTGGACGTAAATGGAAAG                         GGCCTTGGAGGTGGTTTGATGAATCAATGTTGGATTGCTGCGAACCTCTGG
genomic: CTCAGTGGTGTTGAATGCTCTTTCTATCGATCCTGGACGTAAATGGAAAGgtatgcaaga ... cttccaatagGGCCTTGGAGGTGGTTTGATGAATCAATGTTGGATTGCTGCGAACCTCTGG
EST: gi|86051294|gb|DR347049.1|DR347049
EST:     CTCAGTGGTGTTGAATGCTCTTTCTATCGATCCTGGACGTAAATGGAAAG                         GGCCTTGGAGGTGGTTTGATGAATCAATGTTGGATTGCTGCGAACCTCTGG
genomic: CTCAGTGGTGTTGAATGCTCTTTCTATCGATCCTGGACGTAAATGGAAAGgtatgcaaga ... cttccaatagGGCCTTGGAGGTGGTTTGATGAATCAATGTTGGATTGCTGCGAACCTCTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtccacactaaataaatgatggttttttataaaaagttttcctctcttccaatagGGCCTTGGAGGTGGTTTGATGAATCAATGTTGGATTGCTGCGAACCTCTGGAAGTAGTGAAGGAAAAAGGCATTTCATTTGGAAAAGTTGTCTGTTTGGC
     cactaaa  putative branch site (score: 2)
                                    ttttcctctcttccaa  putative PPT
      actaaataaatgatgg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcaagattgaagcaaattatgtccacactaaataaatgatggttttttataaaaagttttcctctcttccaatagGGCCTTGGAGGTGGTTTGATGAATCAATGTTGGATTGCTGCGAACCTCTGGAAGTAGTGAAGGAAAAAGGCATTTCATTTGGAAAAGTTGTCTGTTTGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA