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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtttattatatccagtacatttgacttttgtagacatgtttatatacaatgttgatggttacttttaagcttggtatgacttacaacagGTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG

Basic information

species Arabidopsis thaliana
transcript AT4G25070.2
intron # 4
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|116426385|gb|EG468977.1|EG468977
EST:     AAGAAAGACGCGAAGCTGCAGAAGCAAGGGCTAAAGAGCTCGAGAAACAG                         GTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
genomic: AAGAAAGACGCGAAGCTGCAGAAGCAAGGGCTAAAGAGCTTGAGAAACAGgtgtttatta ... cttacaacagGTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
EST: gi|116426422|gb|EG469014.1|EG469014
EST:     CGCGAAGCTGCAGAAGCAAGGGCTAAAGAGCTTGAGAAACAG                         GTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
genomic: CGCGAAGCTGCAGAAGCAAGGGCTAAAGAGCTTGAGAAACAGgtgtttatta ... cttacaacagGTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
EST: gi|116426389|gb|EG468981.1|EG468981
EST:     AAGAAAGACGCGAAGCTGCAGAAGCAAGGGCTAAAGAGCTTGAGAAACAG                         GTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
genomic: AAGAAAGACGCGAAGCTGCAGAAGCAAGGGCTAAAGAGCTTGAGAAACAGgtgtttatta ... cttacaacagGTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
EST: gi|116426396|gb|EG468988.1|EG468988
EST:     AAGAAAGACGCGAAGCTGCAGAAGCAAGGGCTAAAGAGCTTGAGAAACAG                         GTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
genomic: AAGAAAGACGCGAAGCTGCAGAAGCAAGGGCTAAAGAGCTTGAGAAACAGgtgtttatta ... cttacaacagGTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
EST: gi|116426415|gb|EG469007.1|EG469007
EST:     CGCGAAGCTGCAGAAGCAAGGGCTAAAGAGCTTGAGAAACAG                         GTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
genomic: CGCGAAGCTGCAGAAGCAAGGGCTAAAGAGCTTGAGAAACAGgtgtttatta ... cttacaacagGTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
EST: gi|116426404|gb|EG468996.1|EG468996
EST:     AAGAAAGACGCGAAGCTGCAGAAGCAAGGGCTAAAGAGCTTGAGAAACAG                         GTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
genomic: AAGAAAGACGCGAAGCTGCAGAAGCAAGGGCTAAAGAGCTTGAGAAACAGgtgtttatta ... cttacaacagGTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
EST: gi|116426393|gb|EG468985.1|EG468985
EST:     AAGAAAGACGCGAAGCTGCAGAAGCAAGGGCTAAAGAGCTTGAGAAACAG                         GTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
genomic: AAGAAAGACGCGAAGCTGCAGAAGCAAGGGCTAAAGAGCTTGAGAAACAGgtgtttatta ... cttacaacagGTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
EST: gi|116426400|gb|EG468992.1|EG468992
EST:     AAGAAAGACGCGAAGCTGCAGAAGCAAGGGCTAAAGAGCTTGAGAAACGG                         GTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
genomic: AAGAAAGACGCGAAGCTGCAGAAGCAAGGGCTAAAGAGCTTGAGAAACAGgtgtttatta ... cttacaacagGTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
EST: gi|116426413|gb|EG469005.1|EG469005
EST:     CGCGATGCTGCAGAAGCAAGGGCTAAAGAGCTTGAGAAACAG                         GTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
genomic: CGCGAAGCTGCAGAAGCAAGGGCTAAAGAGCTTGAGAAACAGgtgtttatta ... cttacaacagGTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
EST: gi|116426386|gb|EG468978.1|EG468978
EST:     AAGAAAGACGCGAAGCTGCAGAAGCAAGGGCTAAAGAGCTTGAGAAACGG                         GTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
genomic: AAGAAAGACGCGAAGCTGCAGAAGCAAGGGCTAAAGAGCTTGAGAAACAGgtgtttatta ... cttacaacagGTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
EST: gi|116426401|gb|EG468993.1|EG468993
EST:     AAGAAAGACGCGAAGCTGCAGAAGCAAGGGCTAAAGAGCTTGAGAAACGG                         GTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
genomic: AAGAAAGACGCGAAGCTGCAGAAGCAAGGGCTAAAGAGCTTGAGAAACAGgtgtttatta ... cttacaacagGTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
EST: gi|116426402|gb|EG468994.1|EG468994
EST:     AAGAAAGACGCGAAGCTGCAGAAGCAAGGGCTAAAGAGCTTGAGAAACAG                         GTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
genomic: AAGAAAGACGCGAAGCTGCAGAAGCAAGGGCTAAAGAGCTTGAGAAACAGgtgtttatta ... cttacaacagGTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
EST: gi|116426395|gb|EG468987.1|EG468987
EST:     AAGAAAGACGCGAAGCTGCAGAAGCAAGGGCTAAAGAGCTTGAGAAACAG                         GTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
genomic: AAGAAAGACGCGAAGCTGCAGAAGCAAGGGCTAAAGAGCTTGAGAAACAGgtgtttatta ... cttacaacagGTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
EST: gi|116426388|gb|EG468980.1|EG468980
EST:     AGAAGCAAGGGCTAAAGAGCTTGAGAAACAG                         GTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
genomic: AGAAGCAAGGGCTAAAGAGCTTGAGAAACAGgtgtttatta ... cttacaacagGTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
EST: gi|116426391|gb|EG468983.1|EG468983
EST:     AAGAAAGACGCGAAGCTGCAGAAGCAAGGGCTAAAGAGCTTGAGAAACAG                         GTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
genomic: AAGAAAGACGCGAAGCTGCAGAAGCAAGGGCTAAAGAGCTTGAGAAACAGgtgtttatta ... cttacaacagGTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
EST: gi|116426384|gb|EG468976.1|EG468976
EST:     GCAGAAGCAAGGGCTAAAGAGCTCGAGAAACAG                         GTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
genomic: GCAGAAGCAAGGGCTAAAGAGCTTGAGAAACAGgtgtttatta ... cttacaacagGTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
EST: gi|116426407|gb|EG468999.1|EG468999
EST:     AAGAAAGACGCGAAGCTGCAGAAGCAAGGGCTAAAGAGCTTGAGAAACAG                         GTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
genomic: AAGAAAGACGCGAAGCTGCAGAAGCAAGGGCTAAAGAGCTTGAGAAACAGgtgtttatta ... cttacaacagGTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgtttatatacaatgttgatggttacttttaagcttggtatgacttacaacagGTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG
                                           gacttac  putative branch site (score: 2)
     ttatatacaatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtttattatatccagtacatttgacttttgtagacatgtttatatacaatgttgatggttacttttaagcttggtatgacttacaacagGTTGCTTCTCTAGGTGAAGGAGCAAATTTTGATGTCAAGCTCTTGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA