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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGGAAGGTCCAAAAGAAGATGAGGAATCTGACAAGTCAGTGTCAGAGGTCAATGACGAGGATGATGCTGAGGATGGTAGTGAAGAGgttagtggtctgagtttttaatgttaacgtcatagcatatataaagagctttgattttaactcttgttactttggtgtgtaattaaattgcag

Basic information

species Arabidopsis thaliana
transcript AT1G20693.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G20693.1 (Arabidopsis thaliana), 5'ss of exon 7
lower sequence: GRMZM5G834758_T01 (Zea mays), 5'ss of exon 6
----------------GAGGAAGGTCCAAAAGAAGATGAGGAATCTGACAAGTCAGTGTCAGAGGTCAATGACGAGGATGATGCTGAGGATGGTAGTGAAGAGgttagtggtctgagtttttaatgttaacgt---catagcatatataaagagct--ttgatttta-actcttgttactttggtgtgt-aattaaattgcag
                |||||||      |||| || ||||| |||||||||||   ||| ||||||||||||||||||||||   | || |||||||| |||||        |   ||  |    |   | |     |  | || | |||   |   || ||     |  | |   |  ||  ||  | ||  || ||||  
GAAGGCTCCTGCCAAGGAGGAAGAGGAGGAAGATGAAGAGGAGTCTGACAAGTCCAAGTCGGAGGTCAATGACGAGGATGATG---AAGAGGGTAGTGAGGAGgtatacaaaatctattcctgtcttctccatattttttccttagacaaaataccaattaatccaggatacatagcatgttcatgcattaagcaagttgcta
















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|124710568|gb|EH801970.1|EH801970
EST:     CAGTGTCAGAGGTCAATGGCGAGGATGATGCTGAGGATGGTAGTGAAGAG                         GAGGAGGACGA
genomic: CAGTGTCAGAGGTCAATGACGAGGATGATGCTGAGGATGGTAGTGAAGAGgttagtggtc ... taaattgcagGAGGAGGACGA
EST: gi|164173515|gb|ES004362.1|ES004362
EST:     GACGAGGATGATGCTGAGGATGGTAGTGAAGAG                         GAGGAGGACGATGACTAAGAAGCTGAATGTTGGTAGCATTAGTATAGATGG
genomic: GACGAGGATGATGCTGAGGATGGTAGTGAAGAGgttagtggtc ... taaattgcagGAGGAGGACGATGACTAAGAAGCTGAATGTTGGTAGCATTAGTATAGATGG
EST: gi|116450036|gb|EG492628.1|EG492628
EST:     CAATGACGAGGATGATGCTGAGGATGGTAGTGAAGAG                         GAGGAGGACGATGACTAAGAAGCTGAATGTTGGTAGCATTAGTATAGATGG
genomic: CAATGACGAGGATGATGCTGAGGATGGTAGTGAAGAGgttagtggtc ... taaattgcagGAGGAGGACGATGACTAAGAAGCTGAATGTTGGTAGCATTAGTATAGATGG
EST: gi|86076071|gb|DR371828.1|DR371828
EST:     CAGTGTCAGAGGTCAATGACGAGGATGATGCTGAGGATGGTAGTGAAGAG                         GAGGAGGACGATGACTAAGAAGCTGAATGTTGGTAGCATTAGTATAGATGG
genomic: CAGTGTCAGAGGTCAATGACGAGGATGATGCTGAGGATGGTAGTGAAGAGgttagtggtc ... taaattgcagGAGGAGGACGATGACTAAGAAGCTGAATGTTGGTAGCATTAGTATAGATGG
EST: gi|116450037|gb|EG492629.1|EG492629
EST:     AGTGTCAGAGGTCAATGACGAGGATGATGCTGAGGATGGTAGTGAAGAG                         GAGGAGGACGATGACTAAGAAGCTGAATGTTGGTAGCATTAGTATA
genomic: AGTGTCAGAGGTCAATGACGAGGATGATGCTGAGGATGGTAGTGAAGAGgttagtggtc ... taaattgcagGAGGAGGACGATGACTAAGAAGCTGAATGTTGGTAGCATTAGTATA
EST: gi|125098772|gb|EL154800.1|EL154800
EST:     TGACGAGGATGATGCTGAGGATGGTAGTGAAGAG                         GAGGAGGACGATGACTAAGAAGCTGAATGTTAGGTAGCATTAGTATAGATG
genomic: TGACGAGGATGATGCTGAGGATGGTAGTGAAGAGgttagtggtc ... taaattgcagGAGGAGGACGATGACTAAGAAGCTGAATGTT-GGTAGCATTAGTATAGATG
EST: gi|19799425|gb|AU230715.1|AU230715
EST:     CAGTGTCAGAGGTCAATGACGAGGATGATGCTGAGGATGGTAGTGAAGAG                         GAGGAGGACGATGACTAAGAAGCTGAATCTTGGTAGCATTAGTATAGATGG
genomic: CAGTGTCAGAGGTCAATGACGAGGATGATGCTGAGGATGGTAGTGAAGAGgttagtggtc ... taaattgcagGAGGAGGACGATGACTAAGAAGCTGAATGTTGGTAGCATTAGTATAGATGG
EST: gi|164059202|gb|ES199715.1|ES199715
EST:     AGTGTCAGAGGTCTAATGACGAGGATGATGCTGAGGATGGTAGTGAAGAG                         GAGGAGGACGATGACTAAGA
genomic: AGTGTCAGAGGTC-AATGACGAGGATGATGCTGAGGATGGTAGTGAAGAGgttagtggtc ... taaattgcagGAGGAGGACGATGACTAAGA
EST: gi|163989638|gb|ES173834.1|ES173834
EST:     AGTGTCAGAGGTCAATGACGAGGATGATGCTGAGGATGGTAGTAGAAGAG                         GAGGAGGACGATGACTAAGAAGC
genomic: AGTGTCAGAGGTCAATGACGAGGATGATGCTGAGGATGGTAGT-GAAGAGgttagtggtc ... taaattgcagGAGGAGGACGATGACTAAGAAGC
EST: gi|164111162|gb|ES189848.1|ES189848
EST:     CAGTGTCAGAGGTCAATGACGAGGATGATGCTGAGGATGGTAGTGAAGAG                         GAGGAGGACGATGACTAAGA
genomic: CAGTGTCAGAGGTCAATGACGAGGATGATGCTGAGGATGGTAGTGAAGAGgttagtggtc ... taaattgcagGAGGAGGACGATGACTAAGA
EST: gi|86082340|gb|DR378099.1|DR378099
EST:     CAGTGTCAGAGGTCAATGACGAGGATGATGCTGAGGATGGTAGTGAAGAG                         GAGGAGGACGATGACTAAGAAGCTGAAT-TTGGTAGCATTAGTATAGATGG
genomic: CAGTGTCAGAGGTCAATGACGAGGATGATGCTGAGGATGGTAGTGAAGAGgttagtggtc ... taaattgcagGAGGAGGACGATGACTAAGAAGCTGAATGTTGGTAGCATTAGTATAGATGG
EST: gi|164185042|gb|ES205790.1|ES205790
EST:     CAGTGTCAGAGGTCAATGACGAGGATGATGCTGAGGATGGTAGTGAAGAG                         GAGGAAGGACGATGACTAAGAAGC
genomic: CAGTGTCAGAGGTCAATGACGAGGATGATGCTGAGGATGGTAGTGAAGAGgttagtggtc ... taaattgcagGAGGA-GGACGATGACTAAGAAGC
EST: gi|164058987|gb|EL990983.1|EL990983
EST:     CAGTGTCAGAGGTCAATGACGAGGATGATGCTGAGGATGATAGTGAAGAG                         GAGGAGGACGATGACTAAGAAGCTGAATGTTGGTAGC
genomic: CAGTGTCAGAGGTCAATGACGAGGATGATGCTGAGGATGGTAGTGAAGAGgttagtggtc ... taaattgcagGAGGAGGACGATGACTAAGAAGCTGAATGTTGGTAGC
EST: gi|163986727|gb|ES208771.1|ES208771
EST:     CAGTGTCAGAGGTCAATGACGAGGATGATGCTGAGGATGGTAGTGAAGAG                         GAGGAGGACGATGAACTAAGAAGC
genomic: CAGTGTCAGAGGTCAATGACGAGGATGATGCTGAGGATGGTAGTGAAGAGgttagtggtc ... taaattgcagGAGGAGGACGATGA-CTAAGAAGC
EST: gi|86081548|gb|DR377305.1|DR377305
EST:     CAGTGTCAGAGGTCAATGACGAGGATGATGCTGAGGATGGTAGTGAAGAG                         GAGGAGGACGATGACTAAGAAGCTGAATGTTGGTAGCATTAGTATAGATGG
genomic: CAGTGTCAGAGGTCAATGACGAGGATGATGCTGAGGATGGTAGTGAAGAGgttagtggtc ... taaattgcagGAGGAGGACGATGACTAAGAAGCTGAATGTTGGTAGCATTAGTATAGATGG
EST: gi|124851349|gb|EH935786.1|EH935786
EST:     TCAATGACGAGGATGATGCTGAGGATGGTAGTGAAGAG                         GAGGAGGACGATGACTAAGAAGCTGAATGTTGGTAGCATTAGTATAGATGG
genomic: TCAATGACGAGGATGATGCTGAGGATGGTAGTGAAGAGgttagtggtc ... taaattgcagGAGGAGGACGATGACTAAGAAGCTGAATGTTGGTAGCATTAGTATAGATGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGGAAGGTCCAAAAGAAGATGAGGAATCTGACAAGTCAGTGTCAGAGGTCAATGACGAGGATGATGCTGAGGATGGTAGTGAAGAGgttagtggtctgagtttttaatgttaacgtcatagcatatataaagagctttgattttaactcttgttactttggtgtgtaattaaattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA