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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagttacttacatttcccaaaactgagttgtttagaaatgagctttgtgcattataaggaattgccatcttggttttgatttcatcttcagCCAGCTACTGATTTAATCAAAGACGTTGCGGTGCTCGAAATGGAAGTTATACATTTGGAACAGTATCTTCTTTCATTATACAGAAAAGCCTTTGAGCAGC

Basic information

species Arabidopsis thaliana
transcript AT5G66600.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G66600.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv00s0207g00120.t01 (Vitis vinifera), 3'ss of exon 6
-----gtcagttacttacatttcccaaaactgagttgtttagaa--atgagctttgtg-cattataaggaattgccatcttggttttgatttcatcttcagCCAGCTACTGATTTAATCAAAGACGTTGCGGTGCTCGAAATGGAAGTTATACATTTGGAACAGTATCTTCTTTCATTATACAGAAAAGCCTTTGAGCAGC
      |   ||| |   |         | ||| |||||| |    || | | || |  | || |    |  | | | | | | ||| ||| || || ||||| ||||  ||  |||| || ||  |||| ||| | ||| |||||||| | |||||||||||||||||||||||| | ||| | ||||| ||||| || |
ctttgtttttttagtcttaaactatggtattgacttgttttgcttcatcaccattatttctttgtggttatattctaacattgcttttattgca-ctccagCCTGCTATGGAACTAATTAAGGAAATTGCAGTGTTAGAATTGGAAGTTGTGCATTTGGAACAGTATCTTCTTTCACTGTACCGGAAAGCATTTGATCAAC

upper sequence: AT5G66600.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv00s0207g00150.t01 (Vitis vinifera), 3'ss of exon 3
gtcagttacttacatttccca-----aaactgagttgtttagaa--atgagctttgtg-cattataaggaattgccatcttggttttgatttcatcttcagCCAGCTACTGATTTAATCAAAGACGTTGCGGTGCTCGAAATGGAAGTTATACATTTGGAACAGTATCTTCTTTCATTATACAGAAAAGCCTTTGAGCAGC
 |  |||  |||  | |   |       | ||| |||||| |    || | | || |  | || |    |  | | | ||| | ||| ||| || || ||||| ||||  ||  |||| || ||  |||| ||| | ||| |||||||| | |||||||||||||||||||||||| | ||| | ||||| ||||| || |
ctttgttttttaagtcttaaactatggtattgacttgttttgcttcatcaccattatttctttgtggttatattctaactttgcttttattgca-ctccagCCTGCTATGGAACTAATTAAGGAAATTGCAGTGTTAGAATTGGAAGTTGTGCATTTGGAACAGTATCTTCTTTCACTGTACCGGAAAGCATTTGATCAAC
















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|116429915|gb|EG472507.1|EG472507
EST:     CAGCATCTTCTTACGTACTGACTGAAACAAACGACATTGCCATGCCTAAG                         CCAGCTACTGATTTAATCAAAGACGTTGCGGTGCTCGAAATGGAAGTTATA
genomic: CAGCATCTTCTTACGTACTGACTGAAACAAACGACATTGCCATGCCTAAGgtcagttact ... tcatcttcagCCAGCTACTGATTTAATCAAAGACGTTGCGGTGCTCGAAATGGAAGTTATA
EST: gi|116429913|gb|EG472505.1|EG472505
EST:     CAGCATCTTCTTACGTACTGACTGAAACAAACGACATTGCCATGCCTAAG                         CCAGCTACTGATTTAATCAAAGACGTTGCGGTGCTCGAAATGGAAGTTATA
genomic: CAGCATCTTCTTACGTACTGACTGAAACAAACGACATTGCCATGCCTAAGgtcagttact ... tcatcttcagCCAGCTACTGATTTAATCAAAGACGTTGCGGTGCTCGAAATGGAAGTTATA
EST: gi|116429900|gb|EG472492.1|EG472492
EST:     CAGCATCTTCTTACGTACTGACTGAAACAAACGACATTGCCATGCCTAAG                         CCAGCTACTGATTTAATCAAAGACGTTGCGGTGCTCGAAATGGAAGTTATA
genomic: CAGCATCTTCTTACGTACTGACTGAAACAAACGACATTGCCATGCCTAAGgtcagttact ... tcatcttcagCCAGCTACTGATTTAATCAAAGACGTTGCGGTGCTCGAAATGGAAGTTATA
EST: gi|116429923|gb|EG472515.1|EG472515
EST:     CAGCATCTTCTTACGTACTGACTGAAACAAACGACATTGCCATGCCTAAG                         CCAGCTACTGATTTAATCAAAGACGTTGCGGTGCTCGAAATGGAAGTTATA
genomic: CAGCATCTTCTTACGTACTGACTGAAACAAACGACATTGCCATGCCTAAGgtcagttact ... tcatcttcagCCAGCTACTGATTTAATCAAAGACGTTGCGGTGCTCGAAATGGAAGTTATA
EST: gi|116429925|gb|EG472517.1|EG472517
EST:     CAGCATCTTCTTACGTACTGACTGAAACAAACGACATTGCCATGCCTAAG                         CCAGCTACTGATTTAATCAAAGACGTTGCGGTGCTCGAAATGGAAGTTATA
genomic: CAGCATCTTCTTACGTACTGACTGAAACAAACGACATTGCCATGCCTAAGgtcagttact ... tcatcttcagCCAGCTACTGATTTAATCAAAGACGTTGCGGTGCTCGAAATGGAAGTTATA
EST: gi|116429918|gb|EG472510.1|EG472510
EST:     CAGCATCTTCTTACGTACTGACTGAAACAAACGACATTGCCATGCCTAAG                         CCAGCTACTGATTTAATCAAAGACGTTGCGGTGCTCGAAATGGAAGTTATA
genomic: CAGCATCTTCTTACGTACTGACTGAAACAAACGACATTGCCATGCCTAAGgtcagttact ... tcatcttcagCCAGCTACTGATTTAATCAAAGACGTTGCGGTGCTCGAAATGGAAGTTATA
EST: gi|116429924|gb|EG472516.1|EG472516
EST:     CAGCATCTTCTTACGTACTGACTGAAACAAACGACATTGCCATGCCTAAG                         CCAGCTACTGATTTAATCAAAGACGTTGCGGTGCTCGAAATGGAAGTTATA
genomic: CAGCATCTTCTTACGTACTGACTGAAACAAACGACATTGCCATGCCTAAGgtcagttact ... tcatcttcagCCAGCTACTGATTTAATCAAAGACGTTGCGGTGCTCGAAATGGAAGTTATA
EST: gi|116429922|gb|EG472514.1|EG472514
EST:     CAGCATCTTCTTACGTACTGACTGAAACAAACGACATTGCCATGCCTAAG                         CCAGCTACTGATTTAATCAAAGACGTTGCGGTGCTCGAAATGGAAGTTATA
genomic: CAGCATCTTCTTACGTACTGACTGAAACAAACGACATTGCCATGCCTAAGgtcagttact ... tcatcttcagCCAGCTACTGATTTAATCAAAGACGTTGCGGTGCTCGAAATGGAAGTTATA
EST: gi|116429914|gb|EG472506.1|EG472506
EST:     CAGCATCTTCTTACGTACTGACTGAAACAAACGACATTGCCATGCCTAAG                         CCAGCTACTGATTTAATCAAAG
genomic: CAGCATCTTCTTACGTACTGACTGAAACAAACGACATTGCCATGCCTAAGgtcagttact ... tcatcttcagCCAGCTACTGATTTAATCAAAG
EST: gi|116429904|gb|EG472496.1|EG472496
EST:     CAGCATCTTCTTACGTACTGACTGAAACAAACGACATTGCCATGCCTAAG                         CCAGCTACTGATTTAATCAAAGACGTTGCGGTGCTCGAAATGGAAGTTATA
genomic: CAGCATCTTCTTACGTACTGACTGAAACAAACGACATTGCCATGCCTAAGgtcagttact ... tcatcttcagCCAGCTACTGATTTAATCAAAGACGTTGCGGTGCTCGAAATGGAAGTTATA
EST: gi|116429902|gb|EG472494.1|EG472494
EST:     CAGCATCTTCTTACGTACTGACTGAAACAAACGACATTGCCATGCCTAAG                         CCAGCTACTGATTTAATCAAAGACGTTGCGGTGCTCGAAATGGAAGTTATA
genomic: CAGCATCTTCTTACGTACTGACTGAAACAAACGACATTGCCATGCCTAAGgtcagttact ... tcatcttcagCCAGCTACTGATTTAATCAAAGACGTTGCGGTGCTCGAAATGGAAGTTATA
EST: gi|116429907|gb|EG472499.1|EG472499
EST:     CAGCATCTTCTTACGTACTGACTGAAACAAACGACATTGCCATGCCTAAG                         CCAGCTACTGATTTAATCAAAGACGTTGCGGTGCTCGAAATGGAAGTTATA
genomic: CAGCATCTTCTTACGTACTGACTGAAACAAACGACATTGCCATGCCTAAGgtcagttact ... tcatcttcagCCAGCTACTGATTTAATCAAAGACGTTGCGGTGCTCGAAATGGAAGTTATA
EST: gi|116429909|gb|EG472501.1|EG472501
EST:     CAGCATCTTCTTACGTACTGACTGAAACAAACGACATTGCCATGCCTAAG                         CCAGCTACTGATTTAATCAAAGACGTTGCGGTGCTCGAAATGGAAGTTATA
genomic: CAGCATCTTCTTACGTACTGACTGAAACAAACGACATTGCCATGCCTAAGgtcagttact ... tcatcttcagCCAGCTACTGATTTAATCAAAGACGTTGCGGTGCTCGAAATGGAAGTTATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatgagctttgtgcattataaggaattgccatcttggttttgatttcatcttcagCCAGCTACTGATTTAATCAAAGACGTTGCGGTGCTCGAAATGGAAGTTATACATTTGGAACAGTATCTTCTTTCATTATACAGAAAAGCCTTTGAGCAGC
                                     ttttgat  putative branch site (score: 4)
                                           tttcatcttc  CT-rich tract
                                     ttttgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagttacttacatttcccaaaactgagttgtttagaaatgagctttgtgcattataaggaattgccatcttggttttgatttcatcttcagCCAGCTACTGATTTAATCAAAGACGTTGCGGTGCTCGAAATGGAAGTTATACATTTGGAACAGTATCTTCTTTCATTATACAGAAAAGCCTTTGAGCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG