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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGTGCCATTTTTACGGCCATGTGTGGTGGTGCTGAAATTGGTGAAGCAATAGCCAAAGACACACGCATTCCCTTAGTATCCTTTACTGGAAGCTCCAGGgtacttccttaactatattccacctcccaaccaaacacactgagcctactggtccatcattgtcttctctttgaatattatgcatag

Basic information

species Arabidopsis thaliana
transcript AT1G54100.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G54100.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA15G19670.3 (Glycine max), 5'ss of exon 8
CGGTGCCATTTTTACGGCCATGTGTGGTGGTGCTGAAATTGGTGAAGCAATAGCCAAAGACACACGCATTCCCTTAGTATCCTTTACTGGAAGCTCCAGGgtacttccttaacta--tattccacctcccaaccaaacacactgagc----ctactggtccatcat--tgtcttctctttgaatattatgcatag-----
 ||||| || || ||  |  | ||||| |||||||| |||||| | |||||||| |||||||| ||||||||| | || || ||||||||||| || | ||||  |  |  ||||  || |    |     |    | |||   | |    | |||  |  |  |   ||| |    ||  | | |||      |     
TGGTGCAATATTCACCTCTTTCTGTGGAGGTGCTGACATTGGTCAGGCAATAGCAAAAGACACCCGCATTCCCCTGGTTTCATTTACTGGAAGTTCAAAGgtatgttatgtactaagtagttggacatgatattttatacaggaaacaattcaactaattgaataggatgtataaatttatagtgttaaaagatgttgat

upper sequence: AT1G54100.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA09G08150.2 (Glycine max), 5'ss of exon 7
CGGTGCCATTTTTACGGCCATGTGTGGTGGTGCTGAAATTGGTGAAGCAATAGCCAAAGACACACGCATTCCCTTAGTATCCTTTACTGGAAGCTCCAGGgtacttccttaacta--tattccacctcccaaccaaacacactgagccta-ctggtccatcattgtcttctctttgaatattatgcatag----------
 ||||| || || ||  |  | ||||| |||||||| |||||| | |||||||| |||||||| ||||||||| | || || ||||||||||| || | ||||  |  |  ||||  || |    |    ||    | |||   | | ||  |   | |   ||      | |      |   |  | |           
TGGTGCAATATTCACCTCTTTCTGTGGAGGTGCTGACATTGGTCAGGCAATAGCAAAAGACACTCGCATTCCCCTGGTTTCATTTACTGGAAGTTCAAAGgtatgttatgtactaagtagttggacatgaaattttaaacaggaaacataattaaactaagtttaatgcatatacactgacggtataaaactgtcttaca

upper sequence: AT1G54100.1 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv11s0016g00900.t01 (Vitis vinifera), 5'ss of exon 8
CGGTGCCATTTTTACGGCCATGTGTGGTGGTGCTGAAATTGGTGAAGCAATAGCCAAAGACACACGCATTCCCTTAGTATCCTTTACTGGAAGCTCCAGGgtacttccttaactatattccacctcccaaccaaacaca-ctgagcctactggtccatcattgtcttctctttgaatattatgcatag-------------
 ||||| || || ||  |  | ||||| |||||||||||||||||||| ||| | |||||| | ||||||||| | || || || ||||| || || | |||||     | || ||| |    | |      ||  ||| ||  |     ||     |  || |||  ||     |   |||||  |              
AGGTGCAATATTCACCTCTTTTTGTGGAGGTGCTGAAATTGGTGAAGCCATATCAAAAGACGCTCGCATTCCCCTGGTTTCATTCACTGGGAGTTCAAAGgtaccctgcttac-atacttgtgcgctattggaattacatctatgtgagatgccaagtttttatctattcaccataatgtatgcggaccttttggtttgtc

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|116486592|gb|EG529184.1|EG529184
EST:     TAGCCAAAGACACACGCATTCCCTTAGTATCCTTTACTGGAAGCTCCAGG                         GTGGGCTCAATGGTACAACAAACAGTGAATGCGAGATCTGGGAAAACTTTG
genomic: TAGCCAAAGACACACGCATTCCCTTAGTATCCTTTACTGGAAGCTCCAGGgtacttcctt ... ttatgcatagGTGGGCTCAATGGTACAACAAACAGTGAATGCGAGATCTGGGAAAACTTTG
EST: gi|116420799|gb|EG463391.1|EG463391
EST:     TAGCCAAAGACACACGCATTCCCTTAGTATCCTTTACTGGAAGCTCCAGG                         GTGGGCTCAATGGTACAACAAACAGTGAATGCGAGATCTGGGAAAACTTTG
genomic: TAGCCAAAGACACACGCATTCCCTTAGTATCCTTTACTGGAAGCTCCAGGgtacttcctt ... ttatgcatagGTGGGCTCAATGGTACAACAAACAGTGAATGCGAGATCTGGGAAAACTTTG
EST: gi|116420807|gb|EG463399.1|EG463399
EST:     TAGCCAAAGACACACGCATTCCCTTAGTATCCTTTACTGGAAGCTCCAGG                         GTGGGCTCAATGGTACAACAAACAGTGAATGCGAGATCTGGGAAAACTTTG
genomic: TAGCCAAAGACACACGCATTCCCTTAGTATCCTTTACTGGAAGCTCCAGGgtacttcctt ... ttatgcatagGTGGGCTCAATGGTACAACAAACAGTGAATGCGAGATCTGGGAAAACTTTG
EST: gi|116420806|gb|EG463398.1|EG463398
EST:     TAGCCAAAGACACACGCATTCCCTTAGTATCCTTTACTGGAAGCTCCAGG                         GTGGGCTCAATGGTACAACAAACAGTGAATGCGAGATCTGGGAAAACTTTG
genomic: TAGCCAAAGACACACGCATTCCCTTAGTATCCTTTACTGGAAGCTCCAGGgtacttcctt ... ttatgcatagGTGGGCTCAATGGTACAACAAACAGTGAATGCGAGATCTGGGAAAACTTTG
EST: gi|116486590|gb|EG529182.1|EG529182
EST:     TAGCCAAAGACACACGCATTCCCTTAGTATCCTTTACTGGAAGCTCCAGG                         GTGGGCTCAATGGTACAACAAACAGTGAATGCGAGATCTGGGAAAACTTTG
genomic: TAGCCAAAGACACACGCATTCCCTTAGTATCCTTTACTGGAAGCTCCAGGgtacttcctt ... ttatgcatagGTGGGCTCAATGGTACAACAAACAGTGAATGCGAGATCTGGGAAAACTTTG
EST: gi|116486594|gb|EG529186.1|EG529186
EST:     TAGCCAAAGACACACGCATTCCCTTAGTATCCTTTACTGGAAGCTCCAGG                         GTGGGCTCAATGGTACAACAAACAGTGAATGCGAGATCTGGGAAAACTTTG
genomic: TAGCCAAAGACACACGCATTCCCTTAGTATCCTTTACTGGAAGCTCCAGGgtacttcctt ... ttatgcatagGTGGGCTCAATGGTACAACAAACAGTGAATGCGAGATCTGGGAAAACTTTG
EST: gi|125242054|gb|EL256139.1|EL256139
EST:     CAAAGACACACGCATTCCCTTAGTATCCTTTACTGGAAGCTCCAGG                         GTGGGCTCAATGGTACAACAAACAGTGAATGCGAGATCTGGGAAAACTTTG
genomic: CAAAGACACACGCATTCCCTTAGTATCCTTTACTGGAAGCTCCAGGgtacttcctt ... ttatgcatagGTGGGCTCAATGGTACAACAAACAGTGAATGCGAGATCTGGGAAAACTTTG
EST: gi|116486591|gb|EG529183.1|EG529183
EST:     TAGCCAAAGACACACGCATTCCCTTAGTATCCTTTACTGGAAGCTCCAGG                         GTGGGCTCAATGGTACAACAAACAGTGAATGCGAGATCTGGGAAAACTTTG
genomic: TAGCCAAAGACACACGCATTCCCTTAGTATCCTTTACTGGAAGCTCCAGGgtacttcctt ... ttatgcatagGTGGGCTCAATGGTACAACAAACAGTGAATGCGAGATCTGGGAAAACTTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGTGCCATTTTTACGGCCATGTGTGGTGGTGCTGAAATTGGTGAAGCAATAGCCAAAGACACACGCATTCCCTTAGTATCCTTTACTGGAAGCTCCAGGgtacttccttaactatattccacctcccaaccaaacacactgagcctactggtccatcattgtcttctctttgaatattatgcatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG