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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacacatcaaaaatctctggtttcttgaataaacccatttcttttttccggattttaaagagagtggtgggactttaaacattgttgcagGCGTTTGCAAGCAAATACAAACTACCGTATACATTGTTAAGCGACGAAGGGAATAAGGTGAGAAAAGATTGGGGAGTGCCTGGAGACCTGTTTGGAGCAT

Basic information

species Arabidopsis thaliana
transcript AT3G26060.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G26060.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv11s0016g00560.t01 (Vitis vinifera), 3'ss of exon 3
--------------------------------------------------gtacacacatcaaaaatctctggt--ttcttgaataaacccatttcttttttccggattttaaagagagtggtgggactt-taaac--attgttgcagGCGTTTGCAAGCAAATACAAACTACCGTATACATTGTTAAGCGACGAAGGGAATAAGGTGAGAAAAGATTGGGGAGTGCCTGGAGACCTGTTTGGAGCAT
                                                  | | | |   | | | | |   ||  ||   || | |||   |  || |   |   | |      ||     | |   || ||||   |||  || |||| |||||||  ||||||| ||| || |  |||||| | ||||| || || || |||||||| ||||||||||||||||| | ||| ||||||||| |||
gtaatacaaaaataattggtcttgaatcgatgtttcctcgttctctcaagggaaaaattcccatagttttcagtagtttcggagttaactggtagctgtggccaaaaatgcttgtagttaactagtgtttgtaaatgaattaatgtagGCATTTGCAAAGAAATACAGACTTCCATTCACATTGCTGAGCGATGACGGAAACAAGGTGAGGAAAGATTGGGGAGTGCCGGCAGATCTGTTTGGAACAT
















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|125150015|gb|EL182899.1|EL182899
EST:     AGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAG                         GCGTTTGCAAGCAAATACAAACTACCGTATACATTGTTAAGCGACGAAG
genomic: AGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAGgtacacacat ... attgttgcagGCGTTTGCAAGCAAATACAAACTACCGTATACATTGTTAAGCGACGAAG
EST: gi|125116719|gb|EL166148.1|EL166148
EST:     CTGGTGCAGAGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAG                         GCGTTTGCAAGCAAATACAAACTACCGTATACATTG
genomic: CTGGTGCAGAGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAGgtacacacat ... attgttgcagGCGTTTGCAAGCAAATACAAACTACCGTATACATTG
EST: gi|125219787|gb|EL233872.1|EL233872
EST:     GAGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAG                         GCGTTTGCAAGCAAATACAAACTACCGTATACATTGTTAAGCGACGAAGGG
genomic: GAGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAGgtacacacat ... attgttgcagGCGTTTGCAAGCAAATACAAACTACCGTATACATTGTTAAGCGACGAAGGG
EST: gi|124906603|gb|EH980683.1|EH980683
EST:     ATGACTCTGCTTCTCACAAG                         GCGTTTGCAAGCAAATACAAACTACCGTATACATTGTTAAGCGACGAAGGG
genomic: ATGACTCTGCTTCTCACAAGgtacacacat ... attgttgcagGCGTTTGCAAGCAAATACAAACTACCGTATACATTGTTAAGCGACGAAGGG
EST: gi|125047117|gb|EL119386.1|EL119386
EST:     CAGAGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAG                         GCGTTTGCAAGCAAATACAAACTACCGTATACATTGTTAAGCGACGAAGGG
genomic: CAGAGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAGgtacacacat ... attgttgcagGCGTTTGCAAGCAAATACAAACTACCGTATACATTGTTAAGCGACGAAGGG
EST: gi|124858870|gb|EH943307.1|EH943307
EST:     CTGGTGCAGAGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAG                         GCGTTTGCAAGCAAATACAAACTACCGT
genomic: CTGGTGCAGAGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAGgtacacacat ... attgttgcagGCGTTTGCAAGCAAATACAAACTACCGT
EST: gi|125155991|gb|EL185823.1|EL185823
EST:     CTGGTGCAGAGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAG                         GCGTTTGCAAGCAAATACAAACTACCGTATACAT
genomic: CTGGTGCAGAGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAGgtacacacat ... attgttgcagGCGTTTGCAAGCAAATACAAACTACCGTATACAT
EST: gi|125317898|gb|EL331983.1|EL331983
EST:     CATTAGTGGAGATGACTCTGCTTCTCACAAG                         GCGTTTGCAAGCAAATACAAACTACCGTATACATTGTTAAGCGACGAAGGG
genomic: CATTAGTGGAGATGACTCTGCTTCTCACAAGgtacacacat ... attgttgcagGCGTTTGCAAGCAAATACAAACTACCGTATACATTGTTAAGCGACGAAGGG
EST: gi|124820523|gb|EH905389.1|EH905389
EST:     CTGGTGCAGAGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAG                         GCGTTTGCAAGCAAATACAAACTACCG
genomic: CTGGTGCAGAGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAGgtacacacat ... attgttgcagGCGTTTGCAAGCAAATACAAACTACCG
EST: gi|124785483|gb|EH875162.1|EH875162
EST:     CTGGTGCAGAAGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAG                         GCGTTTGCAAGCAAATACAAACTACCGTATA
genomic: CTGGTGCAGAGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAGgtacacacat ... attgttgcagGCGTTTGCAAGCAAATACAAACTACCGTATA
EST: gi|124887354|gb|EH966256.1|EH966256
EST:     AGATGACTCTGCTTCTCACAAG                         GCGTTTGTCAAGCAAATACAAACTACCGTATACATTGTTAAGCGACGAAGG
genomic: AGATGACTCTGCTTCTCACAAGgtacacacat ... attgttgcagGCGTTTG-CAAGCAAATACAAACTACCGTATACATTGTTAAGCGACGAAGG
EST: gi|125103144|gb|EL157653.1|EL157653
EST:     CTGGTGCAGAGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAG                         GCGTTTGCAAG
genomic: CTGGTGCAGAGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAGgtacacacat ... attgttgcagGCGTTTGCAAG
EST: gi|125212019|gb|EL226973.1|EL226973
EST:     TAGTGGAGATGACTCTGCTTCTCACAAG                         GCGTTTGCAAGCAAATACAAACTACCGTATACATTGTTAAGCGACGAAGGG
genomic: TAGTGGAGATGACTCTGCTTCTCACAAGgtacacacat ... attgttgcagGCGTTTGCAAGCAAATACAAACTACCGTATACATTGTTAAGCGACGAAGGG
EST: gi|125198036|gb|EL212990.1|EL212990
EST:     TGACTCTGCTTCTCACAAG                         GCGTTTGCAAGCAAATACAAACTACCGTATACATTGTTAAGCGACGAAGGG
genomic: TGACTCTGCTTCTCACAAGgtacacacat ... attgttgcagGCGTTTGCAAGCAAATACAAACTACCGTATACATTGTTAAGCGACGAAGGG
EST: gi|125250370|gb|EL264455.1|EL264455
EST:     TTGGCATTAGTGGAGATGACTCTGCTTCTCACAAG                         GCGTTTGCAAGCAAATACAAACTACCGTATACATTGTTAAGCGACGAAGGG
genomic: TTGGCATTAGTGGAGATGACTCTGCTTCTCACAAGgtacacacat ... attgttgcagGCGTTTGCAAGCAAATACAAACTACCGTATACATTGTTAAGCGACGAAGGG
EST: gi|125076867|gb|EL139863.1|EL139863
EST:     CTGGTGCAGAGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAG                         GCGTTTGCAAGCAAATACAAACTACCG
genomic: CTGGTGCAGAGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAGgtacacacat ... attgttgcagGCGTTTGCAAGCAAATACAAACTACCG
EST: gi|125033951|gb|EL106220.1|EL106220
EST:     CTGGTGCAGAGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAG                         GCGTTTGCAAGCAAATACAAACTACCGTATACATTGTTAAGCGACG
genomic: CTGGTGCAGAGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAGgtacacacat ... attgttgcagGCGTTTGCAAGCAAATACAAACTACCGTATACATTGTTAAGCGACG
EST: gi|86080940|gb|DR376697.1|DR376697
EST:     CTGGTGCAGAGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAG                         GCGTTTGCAAGCAAATACAAACTACCGTATACATTGTTAAGCGACGAAGGG
genomic: CTGGTGCAGAGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAGgtacacacat ... attgttgcagGCGTTTGCAAGCAAATACAAACTACCGTATACATTGTTAAGCGACGAAGGG
EST: gi|124728569|gb|EH819971.1|EH819971
EST:     TAGTGGAGATGACTCTGCTTCTCTACAAG                         GCGTTTGCAAGCAAATACAAACTACCGTATACATTGTTAAGCGACGAAGG
genomic: TAGTGGAGATGACTCTGCTTCTC-ACAAGgtacacacat ... attgttgcagGCGTTTGCAAGCAAATACAAACTACCGTATACATTGTTAAGCGACGAAGG
EST: gi|124909777|gb|EH983857.1|EH983857
EST:     CTGGTGCAGAGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAG                         GCGTTTGCAAGCAAATACAAACTACCGTATA
genomic: CTGGTGCAGAGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAGgtacacacat ... attgttgcagGCGTTTGCAAGCAAATACAAACTACCGTATA
EST: gi|124824991|gb|EH909857.1|EH909857
EST:     TCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAG                         GCGTTTGCAAGCAAATACAAACTACCGTNTACATTGTTAAGCGACGAAGGG
genomic: TCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAGgtacacacat ... attgttgcagGCGTTTGCAAGCAAATACAAACTACCGTATACATTGTTAAGCGACGAAGGG
EST: gi|125255227|gb|EL269312.1|EL269312
EST:     AGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAG                         GCGTTTGCAAGCAAATACAAACTACCGTATACATTGTTAAGCGAC
genomic: AGGTCATTGGCATTAGTGGAGATGACTCTGCTTCTCACAAGgtacacacat ... attgttgcagGCGTTTGCAAGCAAATACAAACTACCGTATACATTGTTAAGCGAC
EST: gi|125011093|gb|EL083362.1|EL083362
EST:     CTTCTCACAAG                         GCGTTTGCAAGCAAATACAAACTACCGTATACATTGTTAAGCGACGAAGGG
genomic: CTTCTCACAAGgtacacacat ... attgttgcagGCGTTTGCAAGCAAATACAAACTACCGTATACATTGTTAAGCGACGAAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttcttttttccggattttaaagagagtggtgggactttaaacattgttgcagGCGTTTGCAAGCAAATACAAACTACCGTATACATTGTTAAGCGACGAAGGGAATAAGGTGAGAAAAGATTGGGGAGTGCCTGGAGACCTGTTTGGAGCAT
                attttaaaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacacacatcaaaaatctctggtttcttgaataaacccatttcttttttccggattttaaagagagtggtgggactttaaacattgttgcagGCGTTTGCAAGCAAATACAAACTACCGTATACATTGTTAAGCGACGAAGGGAATAAGGTGAGAAAAGATTGGGGAGTGCCTGGAGACCTGTTTGGAGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA