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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtcaatacagtggttttcactaatggtcataagctgtagaacagaatgtcggcatatatatagttcactgatcctaatacttcattttattttcacagCGCGAGAAGAGGGAGGATATATTTACCACAAGATGAACTTGCAGAGGCAGGGCTCTCTGATGAGGACATCTTCAATGGCGTTGTGACTAACAAATGGAGA

Basic information

species Oryza sativa
transcript LOC_Os06g51290.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g51290.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G300348_T01 (Zea mays), 3'ss of exon 1
gtaagtgtcaatacagtggttttcactaatggtcataagctgtagaacagaatgtcggcatatatatagttcactgatcctaatacttcattttattttcacagCGCGAGAAGAGGGAGGATATATTTACCACAAGATGAACTTGCAGAGGCAGGGCTCTCTGATGAGGACATCTTCAATGGCGTTGTGACTAACAAATGGAGA
||||||  || || |     || |    |  | ||  | |  |  |   |       ||| | || |  |     |||   | |   |||   | | ||   || || |||||||| ||||||||||||||||||||||| |||||| ||||||||||||||||||||||||||||||| || || || || |||   ||||||
gtaagtaaca-tatatattcttcctgcgacaggcacgaac-atgcatgtgttcaatagcacagatgtgat-----gatatgactg--tcaccatgtcttt-tagTGCTAGAAGAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGGGCTCTCTGATGAGGACATCTTCAAAGGGGTCGTCACGAACCGGTGGAGA

upper sequence: LOC_Os06g51290.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G300348_T03 (Zea mays), 3'ss of exon 4
gtaagtgtcaatacagtggttttcactaatggtcataagctgtagaacagaatgtcggcatatatatagttcactgatcctaatacttcattttattttcacagCGCGAGAAGAGGGAGGATATATTTACCACAAGATGAACTTGCAGAGGCAGGGCTCTCTGATGAGGACATCTTCAATGGCGTTGTGACTAACAAATGGAGA---------
||||||  || || |     || |    |  | ||  | |  |  |   |       ||| | || |  |     |||   | |   |||   | | ||   || || |||||||| ||||||||||||||||||||||| |||||| ||||||||||||||||||||||||||||||| || || || || |||   ||||||         
gtaagtaaca-tatatattcttcctgcgacaggcacgaac-atgcatgtgttcaatagcacagatgtgat-----gatatgactg--tcaccatgtcttt-tagtgctagaagAGGAAGGATATATTTACCACAAGATGAGCTTGCACAGGCAGGGCTCTCTGATGAGGACATCTTCAAAGGGGTCGTCACGAACCGGTGGAGAAACTTCATG

upper sequence: LOC_Os06g51290.3 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv04s0079g00680.t01 (Vitis vinifera), 3'ss of exon 5
gtaagtgtcaatacagtggttttc-actaatggtcataagctgtagaacagaatgtcggcatatatatagttcactgatcctaatacttc--attttattttca--cagCGCGAGAAGAGGGAGGATATATTTACCACAAGATGAACTTGCAGAGGCAGGGCTCTCTGATGAGGACATCTTCAATGGCGTTGTGACTAACAAATGGAGA
        | | | |  || |||  | | | |  |        ||  |  || | | |   | |   |  ||||||  || |||| |||      ||||||| |  ||| || || ||||| ||||| ||||||||||| ||||| || ||| | ||||||||||| ||||||||||| || |  ||    || ||  | |||||||||
-------gccacatatcggcttttgattgaagaactctctaattattagtgacttttgagttttcctt--ttcacttttcataattcttttgggattattttgattcagTGCAAGGAGAGGAAGGATTTATTTACCACAGGATGAGCTGGCACAAGCAGGGCTCTCAGATGAGGACATTTTTATGGGAAGGGTAACAGATAAATGGAGA

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|29619022|gb|CB624034.1|CB624034
EST:     CTCGGCATTGCAAACCAGCTCACGAATATACTCCGTGACGTTGGAGAGGA                         CGCGAGAAGAGGGAGGATATATTTACCACAAGATGAACTTGCAGAGGCAGG
genomic: CTCGGCATTGCAAACCAGCTCACAAATATACTCCGTGACGTTGGAGAGGAgtaagtgtca ... attttcacagCGCGAGAAGAGGGAGGATATATTTACCACAAGATGAACTTGCAGAGGCAGG
EST: gi|86601906|gb|CI258582.1|CI258582
EST:     AACCAGCTCACAAATATACTCCGTGACGTTGGAGAGGA                         CGCGAGAAGAGGGAGGATATATTTACCACAAGATGAACTTGCAGAGGCAGG
genomic: AACCAGCTCACAAATATACTCCGTGACGTTGGAGAGGAgtaagtgtca ... attttcacagCGCGAGAAGAGGGAGGATATATTTACCACAAGATGAACTTGCAGAGGCAGG
EST: gi|29617651|gb|CB622663.1|CB622663
EST:     GTGACGTTGGAGAGGA                         CGCGAGAAGAGGGAGGATATATTTACCACAAGATGAACTTGCAGAGGCAGG
genomic: GTGACGTTGGAGAGGAgtaagtgtca ... attttcacagCGCGAGAAGAGGGAGGATATATTTACCACAAGATGAACTTGCAGAGGCAGG
EST: gi|29617544|gb|CB622556.1|CB622556
EST:     CATTGCAAACCAGCTCACGAATATACTCCGTGACGTTGGAGAGGA                         CGCGAGAAGAGGGAGGATATATTTACCACAAGATGAACTTGCAGAGGCAGG
genomic: CATTGCAAACCAGCTCACAAATATACTCCGTGACGTTGGAGAGGAgtaagtgtca ... attttcacagCGCGAGAAGAGGGAGGATATATTTACCACAAGATGAACTTGCAGAGGCAGG
EST: gi|29613195|gb|CB618208.1|CB618208
EST:     CTCGGCATTGCAAACCAGCTCACGAATATACTCCGTGACGTTGGAGAGGA                         CGCGAGAAGAGGGAGGATATATTTACCACAAGATGAACTTGCAGAGGCAGG
genomic: CTCGGCATTGCAAACCAGCTCACAAATATACTCCGTGACGTTGGAGAGGAgtaagtgtca ... attttcacagCGCGAGAAGAGGGAGGATATATTTACCACAAGATGAACTTGCAGAGGCAGG
EST: gi|38476677|gb|CF960810.1|CF960810
EST:     CTCGGCATTGCAAACCAGCTCACGAATATACTCCGTGACGTTGGAGAGGA                         CGCGAGAAGAGGGAGGATATATTTACCACAAGATGAACTTGCAGAGGCAGG
genomic: CTCGGCATTGCAAACCAGCTCACAAATATACTCCGTGACGTTGGAGAGGAgtaagtgtca ... attttcacagCGCGAGAAGAGGGAGGATATATTTACCACAAGATGAACTTGCAGAGGCAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaatgtcggcatatatatagttcactgatcctaatacttcattttattttcacagCGCGAGAAGAGGGAGGATATATTTACCACAAGATGAACTTGCAGAGGCAGGGCTCTCTGATGAGGACATCTTCAATGGCGTTGTGACTAACAAATGGAGA
                            tcctaat  putative branch site (score: 2)
                                    cttcattttattttc  CT-rich tract
                               taatacttcattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgtcaatacagtggttttcactaatggtcataagctgtagaacagaatgtcggcatatatatagttcactgatcctaatacttcattttattttcacagCGCGAGAAGAGGGAGGATATATTTACCACAAGATGAACTTGCAGAGGCAGGGCTCTCTGATGAGGACATCTTCAATGGCGTTGTGACTAACAAATGGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA