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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaatgggagtaatttcatatggattctcattcactcttagtatcaaataagatgttgtgaaaatcttagattgttctcgaatttgtttttgatgtgtagATTCAAAGTTTTGAAGCTGATATCTTAGTACCTCAACTAACATCTCAAGAAGGTGGGCCAGAGACATACAGGGGAGTGTTCATACGTGCTCCAGCTGTTC

Basic information

species Arabidopsis thaliana
transcript AT5G60540.1
intron # 3
splice site 3'
intron type U2

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|86052475|gb|DR348232.1|DR348232
EST:     TAGTTGGTGGCCTTGATTGCACCGTACATAGGAACTTCTTCGGTAGCCAG                         ATTCAAAGTTTTGAAGCTGATATCTTAGTACCTCAACTAACATCTCAAGAA
genomic: TAGTTGGTGGCCTTGATTGCACCGTACATAGGAACTTCTTCGGTAGCCAGgttatgtctc ... tgatgtgtagATTCAAAGTTTTGAAGCTGATATCTTAGTACCTCAACTAACATCTCAAGAA
EST: gi|124863235|gb|EH947672.1|EH947672
EST:     AGTTTGGTGGCCTTGATTGCACCGTACATAGGAACTTCTTCGGTAGCCAG                         ATTCAAAGTTTTGAAGCTGATATCTTAGTACCTCAACTAACAT
genomic: AG-TTGGTGGCCTTGATTGCACCGTACATAGGAACTTCTTCGGTAGCCAGgttatgtctc ... tgatgtgtagATTCAAAGTTTTGAAGCTGATATCTTAGTACCTCAACTAACAT
EST: gi|47828146|gb|CK117830.1|CK117830
EST:     TAGTTGGTGGCCTTGATTGCACCGTACATAGGAACTTCTTCGGTAGCCAG                         ATTCAAAGTTTTGAAGCTGATATCTTAGTACCTCAACTAACATCTCAAGAA
genomic: TAGTTGGTGGCCTTGATTGCACCGTACATAGGAACTTCTTCGGTAGCCAGgttatgtctc ... tgatgtgtagATTCAAAGTTTTGAAGCTGATATCTTAGTACCTCAACTAACATCTCAAGAA
EST: gi|86052480|gb|DR348237.1|DR348237
EST:     TAGTTGGTGGCCTTGATTGCACCGTACATAGGAACTTCTTCGGTAGCCAG                         ATTCAAAGTTTT
genomic: TAGTTGGTGGCCTTGATTGCACCGTACATAGGAACTTCTTCGGTAGCCAGgttatgtctc ... tgatgtgtagATTCAAAGTTTT
EST: gi|86052481|gb|DR348238.1|DR348238
EST:     TAGTTGGTGGCCTTGATTGCACCGTACATAGGAACTTCTTCGGTAGCCAG                         ATTCAAAGTTTTGAAGCTGATATCTTAGTACCTCAACTAACATCTCAAGAA
genomic: TAGTTGGTGGCCTTGATTGCACCGTACATAGGAACTTCTTCGGTAGCCAGgttatgtctc ... tgatgtgtagATTCAAAGTTTTGAAGCTGATATCTTAGTACCTCAACTAACATCTCAAGAA
EST: gi|19877313|gb|AU238144.1|AU238144
EST:     TAGTTGGTGGCCTTGATTGCACCGTACATAGGAACTTCTTCGGTAGCCAG                         ATTCAAAGTTTTGAAGCTGATATCTTAGTACCTCAACTAACATCTCAAGAA
genomic: TAGTTGGTGGCCTTGATTGCACCGTACATAGGAACTTCTTCGGTAGCCAGgttatgtctc ... tgatgtgtagATTCAAAGTTTTGAAGCTGATATCTTAGTACCTCAACTAACATCTCAAGAA
EST: gi|124977200|gb|EL050551.1|EL050551
EST:     TAGTTGGTGGCCTTGATTGCACCGTACATAGGAACTTCTTCGGTAGCCAG                         ATTCAAAGTTTTGAAGCTGATATCTTAGTACCTCAACT
genomic: TAGTTGGTGGCCTTGATTGCACCGTACATAGGAACTTCTTCGGTAGCCAGgttatgtctc ... tgatgtgtagATTCAAAGTTTTGAAGCTGATATCTTAGTACCTCAACT
EST: gi|86052478|gb|DR348235.1|DR348235
EST:     TAGTTGGTGGCCTTGATTGCACCGTACATAGGAACTTCTTCGGTAGCCAG                         ATTCAAAGTTTTGAAGCTGATATCTTAGTACCTCAACTAACATCTCAAGAA
genomic: TAGTTGGTGGCCTTGATTGCACCGTACATAGGAACTTCTTCGGTAGCCAGgttatgtctc ... tgatgtgtagATTCAAAGTTTTGAAGCTGATATCTTAGTACCTCAACTAACATCTCAAGAA
EST: gi|86052482|gb|DR348239.1|DR348239
EST:     TAGTTGGTGGCCTTGATTGCACCGTACATAGGAACTTCTTCGGTAGCCAG                         ATTCAAAGTTTTGAAGCTGATATCTTAGTACCACAACTAACATCTCAAGAA
genomic: TAGTTGGTGGCCTTGATTGCACCGTACATAGGAACTTCTTCGGTAGCCAGgttatgtctc ... tgatgtgtagATTCAAAGTTTTGAAGCTGATATCTTAGTACCTCAACTAACATCTCAAGAA
EST: gi|86052484|gb|DR348241.1|DR348241
EST:     TAGTTGGTGGCCTTGATTGCACCGTACATAGGAACTTCTTCGGTAGCCAG                         ATTCAAAGTTTTGAAGCTGATATCTTAGTACCTCAACTAACATCTCAAGAA
genomic: TAGTTGGTGGCCTTGATTGCACCGTACATAGGAACTTCTTCGGTAGCCAGgttatgtctc ... tgatgtgtagATTCAAAGTTTTGAAGCTGATATCTTAGTACCTCAACTAACATCTCAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaataagatgttgtgaaaatcttagattgttctcgaatttgtttttgatgtgtagATTCAAAGTTTTGAAGCTGATATCTTAGTACCTCAACTAACATCTCAAGAAGGTGGGCCAGAGACATACAGGGGAGTGTTCATACGTGCTCCAGCTGTTC
                                          ttttgat  putative branch site (score: 4)
                                     tttgttttt  CT-rich tract
                                   aatttgtttttgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaatgggagtaatttcatatggattctcattcactcttagtatcaaataagatgttgtgaaaatcttagattgttctcgaatttgtttttgatgtgtagATTCAAAGTTTTGAAGCTGATATCTTAGTACCTCAACTAACATCTCAAGAAGGTGGGCCAGAGACATACAGGGGAGTGTTCATACGTGCTCCAGCTGTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - ctcttag
- - - - - - - - - - - - - - - - - - - - - - caaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaatc