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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGGGGGATCTCCTTATTGATGGCCACTCAACTGGCTTCTGTGCAAAAGGCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACAgtatgtattattaatatcttcaaattaaggatccagatcgcctttatatttgtttgttcatggttactgagctcaaagtttccatgctaagataaagtag...

Basic information

species Oryza sativa
transcript LOC_Os05g04630.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g04630.5 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G123029_T01 (Zea mays), 5'ss of exon 2
CATGGGGGATCTCCTTATTGATGGCCACTCAACTGGCTTCTGTGCAAAAGGCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACAgtatgt-attattaatatcttcaaattaaggatccagatcgcctttatattt--gtttgttcatggtt--actgagctcaaagtttccatgctaagataaagtag------------------
||||||||| || || || || |||||||| || || ||||| || || || || ||||| || ||||||||||| ||||||||||| ||||| ||||| ||||||  || |   | ||  |         || | |||   | |  |  |   |||| |   |  ||  |||  |    |||||  |   |  | |  |   |                   
CATGGGGGACCTTCTCATCGACGGCCACTCCACCGGTTTCTGCGCCAAGGGGTGCGCTGCCATCGTCGACTCCGGGACTTCCTTGCTCGCTGGCCCAACGgtatgtcgttctctgtctccactctccgtccataccgatgatcctcctcctcaagtttctctgtacttgtactttggatgaagttctctaacagacagcagacatgtctgatgtttcttgcag

upper sequence: LOC_Os05g04630.5 (Oryza sativa), 5'ss of exon 6
lower sequence: EFJ34434 (Selaginella moellendorffii), 5'ss of exon 6
CATGGGGGATCTCCTTATTGATGGCCACTCAACTGGCTTCTGTGCAAAAGGCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACAgtatgtatta--ttaatatcttcaaattaaggatccagatcgcctttatatttgtttgttcatggttactgagctcaaagtttccatgctaagataaagtag
                                   | |||||||| ||||| |||||||| ||||  || || ||||||||  ||||||||||||| || ||||||   |    || | |  | |  |||   |     | |  || | |                                                    
-----------------------------------GGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACGgtatgttacaagccaaaagcagccatctaacagtt---gttgttttgacag---------------------------------------------------

upper sequence: LOC_Os05g04630.5 (Oryza sativa), 5'ss of exon 6
lower sequence: EFJ06917 (Selaginella moellendorffii), 5'ss of exon 6
CATGGGGGATCTCCTTATTGATGGCCACTCAACTGGCTTCTGTGCAAAAGGCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACAgtatgtattattaatatcttcaaattaaggatccagatcgcctttatatttgtttgttcatggttactgagctcaaagtttccatgctaagataaagtag
                                   | |||||||| ||||| |||||||| ||||  || || ||||||||  ||||||||||||| || ||||||       | |     |||  |   ||| | |  |   || | ||||   |                                            
-----------------------------------GGTTCTGTGCTAAAGGATGTGCTGCAATTGCAGATTCTGGAACTTCACTGCTTGCTGGTCCTACGgtatgt------tacaagccaaaagcagtcatcta-acagttgttgt-tttgacag--------------------------------------------

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|157652007|gb|EX451641.1|EX451641
EST:     CTTGCTGGT-CAACA                         GCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
genomic: CTTGCTGGTCCAACAgtatgtatta ... ttatttccagGCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
EST: gi|218480797|gb|FG967575.1|FG967575
EST:     GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACA                         GCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
genomic: GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACAgtatgtatta ... ttatttccagGCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
EST: gi|218495527|gb|FG960510.1|FG960510
EST:     GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACA                         GCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
genomic: GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACAgtatgtatta ... ttatttccagGCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
EST: gi|218501520|gb|FG954804.1|FG954804
EST:     GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACA                         GCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
genomic: GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACAgtatgtatta ... ttatttccagGCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
EST: gi|218504598|gb|FG967437.1|FG967437
EST:     GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACA                         GCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
genomic: GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACAgtatgtatta ... ttatttccagGCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
EST: gi|218486904|gb|FG965174.1|FG965174
EST:     GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACA                         GCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
genomic: GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACAgtatgtatta ... ttatttccagGCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
EST: gi|58672443|gb|CK061129.1|CK061129
EST:     GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACA                         GCTATAGTTGCT
genomic: GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACAgtatgtatta ... ttatttccagGCTATAGTTGCT
EST: gi|29626867|gb|CB631878.1|CB631878
EST:     GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACA                         GCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
genomic: GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACAgtatgtatta ... ttatttccagGCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
EST: gi|29619013|gb|CB624025.1|CB624025
EST:     CTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCNCA-CA                         GCTATAGTTGCTCAGGTGAACCATGCTA
genomic: CTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTC-CAACAgtatgtatta ... ttatttccagGCTATAGTTGCTCAGGTGAACCATGCTA
EST: gi|58695321|gb|CK084008.1|CK084008
EST:     GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACA                         GCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
genomic: GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACAgtatgtatta ... ttatttccagGCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
EST: gi|218491254|gb|FG966852.1|FG966852
EST:     GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACA                         GCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
genomic: GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACAgtatgtatta ... ttatttccagGCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
EST: gi|218487267|gb|FG944918.1|FG944918
EST:     GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACA                         GCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
genomic: GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACAgtatgtatta ... ttatttccagGCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
EST: gi|87012926|gb|CI297153.1|CI297153
EST:     TGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACA                         GCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
genomic: TGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACAgtatgtatta ... ttatttccagGCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
EST: gi|218485577|gb|FG958988.1|FG958988
EST:     GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACA                         GCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
genomic: GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACAgtatgtatta ... ttatttccagGCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
EST: gi|29645305|gb|CB650312.1|CB650312
EST:     GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACA                         GCTATAGTTGCTCAGGTGAACCATGCTAT
genomic: GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACAgtatgtatta ... ttatttccagGCTATAGTTGCTCAGGTGAACCATGCTAT
EST: gi|29678523|gb|CB674798.1|CB674798
EST:     GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACA                         GCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
genomic: GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACAgtatgtatta ... ttatttccagGCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
EST: gi|218492774|gb|FG946027.1|FG946027
EST:     GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACA                         GCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
genomic: GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACAgtatgtatta ... ttatttccagGCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
EST: gi|218501876|gb|FG958335.1|FG958335
EST:     GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACA                         GCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
genomic: GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACAgtatgtatta ... ttatttccagGCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
EST: gi|33793469|gb|CF322617.1|CF322617
EST:     GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACA                         GCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
genomic: GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACAgtatgtatta ... ttatttccagGCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
EST: gi|33684584|gb|CF312823.1|CF312823
EST:     GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACA                         GCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
genomic: GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACAgtatgtatta ... ttatttccagGCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
EST: gi|29675833|gb|CB672108.1|CB672108
EST:     GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACA                         GCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
genomic: GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACAgtatgtatta ... ttatttccagGCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
EST: gi|29643726|gb|CB648733.1|CB648733
EST:     GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACA                         GCTATAGTTGCTCAGGTGAAACATGCTATTG
genomic: GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACAgtatgtatta ... ttatttccagGCTATAGTTGCTCAGGTGAACCATGCTATTG
EST: gi|218488300|gb|FG946413.1|FG946413
EST:     GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACA                         GCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATC
genomic: GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACAgtatgtatta ... ttatttccagGCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATC
EST: gi|38565650|gb|CK085103.1|CK085103
EST:     GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACA                         GCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
genomic: GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACAgtatgtatta ... ttatttccagGCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
EST: gi|58693676|gb|CK082363.1|CK082363
EST:     GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACA                         GCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
genomic: GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACAgtatgtatta ... ttatttccagGCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
EST: gi|29628863|gb|CB633874.1|CB633874
EST:     GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACA                         GCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC
genomic: GCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACAgtatgtatta ... ttatttccagGCTATAGTTGCTCAGGTGAACCATGCTATTGGGGCTGAAGGAATCATCAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGGGGGATCTCCTTATTGATGGCCACTCAACTGGCTTCTGTGCAAAAGGCTGTGCTGCTATTGTCGACTCCGGAACTTCCTTGCTTGCTGGTCCAACAgtatgtattattaatatcttcaaattaaggatccagatcgcctttatatttgtttgttcatggttactgagctcaaagtttccatgctaagataaagtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT