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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcctctcgatttggaaaactgtgattatgcagtgtgtcttgtaacctatgatatgatgatccttatgtggacttgtcttctctaatcctcacaccttatttactctatatggtggcttag

Basic information

species Arabidopsis thaliana
transcript AT3G52880.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G52880.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv08s0007g03610.t01 (Vitis vinifera), 5'ss of exon 2
GGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcctctcgatttggaaaactgtgattatgcagtgtgtcttgtaacctatgatatgatgatccttatgtggacttgtct-tctctaatcctcacaccttatttactctatatggtggcttag
||||| ||||||| |||||||||||| ||||||||| | ||||| ||| ||||  |||| || |||||||||||| || |  |      |    | | | | || ||    | ||  || | |  ||  || |||||||   | | |||  |  | | | | | ||| |   ||                          
GGATATGCAGCTAGGGAGTTTGCCAAGCAAGGGGTTAAGCCAGGGGAACTGGCAATTATTTCCAAAGAGGCGgtatgcatttttgtatatctttatattcttatgat----tttgatttttgaattaacatttgatgattgctttatgggttattttgtttttgatcattcaacgc------------------------
















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|86038366|gb|DR334121.1|DR334121
EST:     CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCG                         GTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
genomic: CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcc ... ggtggcttagGTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
EST: gi|124929182|gb|EL006753.1|EL006753
EST:     CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCG                         GTGGCTCCATATGAACGCC
genomic: CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcc ... ggtggcttagGTGGCTCCATATGAACGCC
EST: gi|86038353|gb|DR334108.1|DR334108
EST:     CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCG                         GTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
genomic: CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcc ... ggtggcttagGTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
EST: gi|86038384|gb|DR334139.1|DR334139
EST:     CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCG                         GTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
genomic: CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcc ... ggtggcttagGTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
EST: gi|86038379|gb|DR334134.1|DR334134
EST:     CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCG                         GTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
genomic: CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcc ... ggtggcttagGTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
EST: gi|86038373|gb|DR334128.1|DR334128
EST:     CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCG                         GTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
genomic: CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcc ... ggtggcttagGTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
EST: gi|86038364|gb|DR334119.1|DR334119
EST:     CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAANAGGCG                         GTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
genomic: CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcc ... ggtggcttagGTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
EST: gi|86038359|gb|DR334114.1|DR334114
EST:     CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCG                         GTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
genomic: CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcc ... ggtggcttagGTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
EST: gi|86038370|gb|DR334125.1|DR334125
EST:     CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAANAGGCG                         GTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
genomic: CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcc ... ggtggcttagGTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
EST: gi|86038368|gb|DR334123.1|DR334123
EST:     CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCG                         GTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
genomic: CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcc ... ggtggcttagGTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
EST: gi|124764747|gb|EH854877.1|EH854877
EST:     CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCG                         GTGGCTCCATATG
genomic: CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcc ... ggtggcttagGTGGCTCCATATG
EST: gi|86038377|gb|DR334132.1|DR334132
EST:     CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCG                         GTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
genomic: CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcc ... ggtggcttagGTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
EST: gi|164165133|gb|ES049422.1|ES049422
EST:     CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCG                         GTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
genomic: CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcc ... ggtggcttagGTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
EST: gi|152033821|gb|BP816817.2|BP816817
EST:     CCAATCAAGGGGTTCAACCAGGAGAATTGGGTGTTATCTCGAAAGAGGCG                         GTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
genomic: CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcc ... ggtggcttagGTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
EST: gi|86038378|gb|DR334133.1|DR334133
EST:     CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCG                         GTGGCTCCATATGAACGCCCTGCACTTMGCAAGGGGTATTTGTTTCCTGAA
genomic: CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcc ... ggtggcttagGTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
EST: gi|86038374|gb|DR334129.1|DR334129
EST:     CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCG                         GTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
genomic: CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcc ... ggtggcttagGTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
EST: gi|86038367|gb|DR334122.1|DR334122
EST:     CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCG                         GNGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
genomic: CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcc ... ggtggcttagGTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
EST: gi|86038358|gb|DR334113.1|DR334113
EST:     CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCG                         GNGGCTCCATATGAACGCCCTGCACTTA
genomic: CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcc ... ggtggcttagGTGGCTCCATATGAACGCCCTGCACTTA
EST: gi|86038380|gb|DR334135.1|DR334135
EST:     CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCG                         GTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
genomic: CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcc ... ggtggcttagGTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
EST: gi|86038376|gb|DR334131.1|DR334131
EST:     CCAATCAAGGGGTN-AACCAGGAGAATTGGCTGTTATCTCGAAANAGGCG                         GTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTMCTGAA
genomic: CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcc ... ggtggcttagGTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
EST: gi|86038355|gb|DR334110.1|DR334110
EST:     CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCG                         GTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
genomic: CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcc ... ggtggcttagGTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
EST: gi|86038356|gb|DR334111.1|DR334111
EST:     CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCG                         GTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
genomic: CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcc ... ggtggcttagGTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
EST: gi|86038354|gb|DR334109.1|DR334109
EST:     CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCG-AANAGGCG                         GTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
genomic: CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcc ... ggtggcttagGTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
EST: gi|86038381|gb|DR334136.1|DR334136
EST:     CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCG                         GTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
genomic: CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcc ... ggtggcttagGTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
EST: gi|86038383|gb|DR334138.1|DR334138
EST:     CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCG                         GTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
genomic: CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcc ... ggtggcttagGTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
EST: gi|86038357|gb|DR334112.1|DR334112
EST:     CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCG                         GTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
genomic: CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcc ... ggtggcttagGTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
EST: gi|86038369|gb|DR334124.1|DR334124
EST:     CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCG                         GTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
genomic: CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcc ... ggtggcttagGTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
EST: gi|86038361|gb|DR334116.1|DR334116
EST:     CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCG                         GTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
genomic: CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcc ... ggtggcttagGTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
EST: gi|86038362|gb|DR334117.1|DR334117
EST:     CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCG                         GTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
genomic: CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcc ... ggtggcttagGTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
EST: gi|86038382|gb|DR334137.1|DR334137
EST:     CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAANAGGCG                         GTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTMCTGAA
genomic: CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcc ... ggtggcttagGTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
EST: gi|301501396|gb|HO206936.1|HO206936
EST:     CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCG                         GTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
genomic: CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcc ... ggtggcttagGTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
EST: gi|86038375|gb|DR334130.1|DR334130
EST:     CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCG                         GTGGCTCCATATGAACGCMCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA
genomic: CCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcc ... ggtggcttagGTGGCTCCATATGAACGCCCTGCACTTAGCAAGGGGTATTTGTTTCCTGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATACGCAGCTAAGGAGTTTGCCAATCAAGGGGTTCAACCAGGAGAATTGGCTGTTATCTCGAAAGAGGCGgtaagcttcctctcgatttggaaaactgtgattatgcagtgtgtcttgtaacctatgatatgatgatccttatgtggacttgtcttctctaatcctcacaccttatttactctatatggtggcttag

- - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG