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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtttggtttggtttcctttttctgccatcatcttgtttagaatgcaattatcaatcaactcactgactggtactatctacttgtgatgacttaatgcagGTGTAGATGTTAGCATGAACACTCATTTAAAAGCTGTGAAACTCACTCTGAAAGGGAAGAATCCAGTTACATTAGACCACTTAAGTGTCAGGGGAAACAA

Basic information

species Arabidopsis thaliana
transcript AT4G02840.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G02840.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os02g37430.1 (Oryza sativa), 3'ss of exon 2
tgtttggtttggtttcctttttctgccatcatcttgtttagaat-gcaattatcaatcaactcactg------actggtactatctacttgtgatgact-taatgcagGTGTAGATGTTAGCATGAACACTCATTTAAAAGCTGTGAAACTCACTCTGAAAGGGAAGAATCCAGTTACATTAGACCACTTAAGTGTCAGGGGAAACAA
        |  |      | ||||       || ||  || |||  |    || | | |   || |       |   | ||   |||  |   | | || |  || |||||| ||| | ||||||||||| ||  | ||| |||||||||||||  |||||||||| ||||| ||||| || || ||| | ||||| |||||||||||
--------tcagcagagctattctcatgcggtcatgcctataatcacctccataagtgactccattatactccatatgcacatcctaacttccaggtctattttgtagGTGTTGATATCAGCATGAACACGCACCTGAAAACTGTGAAACTCACATTGAAAGGGAAAAATCCTGTTACCTTTGATCACCTCAGTGTGAGGGGAAACAA

upper sequence: AT4G02840.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G10640.1 (Glycine max), 3'ss of exon 3
tgtttggtttggtttcctttttctgccatcatcttgtttagaatgcaattatcaatcaactcactgactggtactatctacttg-tgat-----gactt--aatgcagGTGTAGATGTTAGCATGAACACTCATTTAAAAGCTGTGAAACTCACTCTGAAAGGGAAGAATCCAGTTACATTAGACCACTTAAGTGTCAGGGGAAACAA
    | ||  |   ||||||| ||  | |  |  | | |||  || | |   | | |||||    ||  || | | |   |||  ||||     |||||      ||||||| ||| | || |||||||| ||||| ||| | || ||||| |||||||||||||| |||||||| ||  |||| ||  | ||||| ||||| |||||
----tagtcag---tccttttactatcttgcttctttctagt-tgaactacaccagcaactttaagagaggaagtcttagcttactgattctgggacttttgccacagGTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAAAGGGAAAAATCCAGTCACTCTAGATCATCTCAGTGTGAGGGGTAACAA

upper sequence: AT4G02840.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA18G52210.1 (Glycine max), 3'ss of exon 3
tgtttggtttggtttcctttttctgccatca--tcttgtttagaatgcaattatcaatc-aactcactgactggta--ctatctacttgtgatgacttaatgcagGTGTAGATGTTAGCATGAACACTCATTTAAAAGCTGTGAAACTCACTCTGAAAGGGAAGAATCCAGTTACATTAGACCACTTAAGTGTCAGGGGAAACAA-
        |  ||   |||  | |         || |  ||  | | ||   |  | |  ||  ||   | |  ||   ||   | |   |     ||    ||||||| ||| | || |||||||| ||||| ||| | || ||||| |||||||||||||| |||||||| ||  | || ||  | ||||| ||||| ||||| 
------agtgagtcctcttactatattgctgcttcctagttgaactacaccaacaactttaagacaggaagtcttagcttactgattctgggatttttgccacaggTGTTGATATCAGTATGAACACACATTTGAAAACAGTTAAACTAACTCTGAAAGGGAAAAATCCAGTGACTCTGGATCATCTCAGTGTGAGGGGTAACAAC

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|164187199|gb|ES052565.1|ES052565
EST:     TCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTG                         GTGTAGATGTTAGCATGAACACTCATTTAAAAGCTGTGAAACTCACTTTGA
genomic: TCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTGgtacgcttct ... cttaatgcagGTGTAGATGTTAGCATGAACACTCATTTAAAAGCTGTGAAACTCACTCTGA
EST: gi|164062250|gb|ES072763.1|ES072763
EST:     GCTTAAGAACGGAACCATTGTTCATGGAACCATTACTG                         GTGTAGATGTTAGCATGAACACTCATTTAAAAGCTGTGAAACTCACTTTGA
genomic: GCTTAAGAACGGAACCATTGTTCATGGAACCATTACTGgtacgcttct ... cttaatgcagGTGTAGATGTTAGCATGAACACTCATTTAAAAGCTGTGAAACTCACTCTGA
EST: gi|125118423|gb|EL167152.1|EL167152
EST:     AGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTG                         GTGTAGATGTTAGCAT
genomic: AGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTGgtacgcttct ... cttaatgcagGTGTAGATGTTAGCAT
EST: gi|152034269|gb|BP823720.2|BP823720
EST:     AGTTTCAATCGAGCTTAAGAACGGAACCATTGATCATGGAACCATTACTG                         GTGTAGATGTTAGCATGAACACTCATTTAAAAGCTGTGAAACTCACTCTGA
genomic: AGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTGgtacgcttct ... cttaatgcagGTGTAGATGTTAGCATGAACACTCATTTAAAAGCTGTGAAACTCACTCTGA
EST: gi|164217352|gb|ES063004.1|ES063004
EST:     CAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTG                         GTGTAGATGTTAGCATGAACACTCATTTAAAAGCTGTGAAACTCACTTTGA
genomic: CAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTGgtacgcttct ... cttaatgcagGTGTAGATGTTAGCATGAACACTCATTTAAAAGCTGTGAAACTCACTCTGA
EST: gi|116418470|gb|EG461062.1|EG461062
EST:     GCTTAAGAACGGAACCATTGTTCATGGAACCATTACTG                         GTGTAGATGTTAGCATGAACACTCATTTAAAAGCTGTGAAACTCACTCTGA
genomic: GCTTAAGAACGGAACCATTGTTCATGGAACCATTACTGgtacgcttct ... cttaatgcagGTGTAGATGTTAGCATGAACACTCATTTAAAAGCTGTGAAACTCACTCTGA
EST: gi|19877683|gb|AU238514.1|AU238514
EST:     AGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTG                         GTGTAGATGTTAGCATGAACACTCATTTAAAAGCTGTGAAACTCACTCTGA
genomic: AGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTGgtacgcttct ... cttaatgcagGTGTAGATGTTAGCATGAACACTCATTTAAAAGCTGTGAAACTCACTCTGA
EST: gi|86076061|gb|DR371818.1|DR371818
EST:     AGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTG                         GTGTAGATGTTAGCATGAACACTCATTTAAAAGCTGTGAAACTCACTCTGA
genomic: AGTTTCAATCGAGCTTAAGAACGGAACCATTGTTCATGGAACCATTACTGgtacgcttct ... cttaatgcagGTGTAGATGTTAGCATGAACACTCATTTAAAAGCTGTGAAACTCACTCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caattatcaatcaactcactgactggtactatctacttgtgatgacttaatgcagGTGTAGATGTTAGCATGAACACTCATTTAAAAGCTGTGAAACTCACTCTGAAAGGGAAGAATCCAGTTACATTAGACCACTTAAGTGTCAGGGGAAACAA
                                            acttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtttggtttggtttcctttttctgccatcatcttgtttagaatgcaattatcaatcaactcactgactggtactatctacttgtgatgacttaatgcagGTGTAGATGTTAGCATGAACACTCATTTAAAAGCTGTGAAACTCACTCTGAAAGGGAAGAATCCAGTTACATTAGACCACTTAAGTGTCAGGGGAAACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - -ggtttgg
- - - - - - - - - - - - - - - - - tgtttag
- - - - - - - - - - - - - - - - - - - - - - - - - - caatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctcactg