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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGCATGATGCTATTGGATATACAGAAGAGCAAATATCTGAATTGAAAAAGGAGATCCAGAGAACTCGGGATGAACAGCTTGCAAACATTACCAACATGgtaagtgcaactccatgtagttgaactgttgaagaagagcatatgtgtgcttatatcatttactcaagcagtagtttgtattaaatatatacatttaaat...

Basic information

species Oryza sativa
transcript LOC_Os02g35130.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g35130.2 (Oryza sativa), 5'ss of exon 5
lower sequence: AC217665.3_FGT005 (Zea mays), 5'ss of exon 4
GGTGCATGATGCTATTGGATATACAGAAGAGCAAATATCTGAATTGAAAAAGGAGATCCAGAGAACTCGGGATGAACAGCTTGCAAACATTACCAACATGgtaagtgcaactccatgtagttgaactgttgaagaag---agcatatgtgtgcttatatcatttactcaagcagtagtttgtattaaatatatacatttaaat
 | |    || |    |||||| |||| ||||| ||||||||||||||||||||||| || |||||| ||||||||||||||||  |||| ||||||||||||||  |   ||| |||    | ||   | | |||    || || | | |      |   | |    |||||  |  || |  |   | ||| || | |   
AGAGGTGCATACCTCGGGATATTCAGATGAGCAGATATCTGAATTGAAAAAGGAGATTCATAGAACTAGGGATGAACAGCTTGCGCACATAACCAACATGgtaagaacttatcc-tgttcaaggacacattaggaattttaggatctatatagaatgaatgtgttgcaaagcaacacctttt--tcgttgtattcaatcatga

upper sequence: LOC_Os02g35130.2 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G136178_T01 (Zea mays), 5'ss of exon 5
GGTGCATGATGCTATTGGATATACAGAAGAGCAAATATCTGAATTGAAAAAGGAGATCCAGAGAACTCGGGATGAACAGCTTGCAAACATTACCAACATGgtaagtgca-actccatgtagttgaact-gttgaagaagagcatatgtgtgcttatatcatttactcaagcagtagtttgtattaaatat-atacatttaaat
 | |    || |  | |||||| |||| ||||| |||||||| |||||  ||||||| || |||||| ||||||||||||||||| | || |||| ||||||||| ||  |  | ||  |     | | | |     ||    |||   |      | | | |    |||||  |     | |||    | ||  || |    
AGAGGTGCATACCTTGGGATATTCAGATGAGCAGATATCTGAGTTGAAGGAGGAGATTCATAGAACTAGGGATGAACAGCTTGCACAGATAACCAGCATGgtaagagcttatcctattcaaaaacatttggtattttaggatctatacctagaatgaacgtgttgcaaagcaacaaacctttttagtcgtgatcgatctg---
















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|88551918|gb|CI482015.1|CI482015
EST:     CAAACATTACCAACATG                         GTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
genomic: CAAACATTACCAACATGgtaagtgcaa ... atgttcatagGTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
EST: gi|88535512|gb|CI464316.1|CI464316
EST:     ACAGCTTGCAAACATTACCAACATG                         GTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
genomic: ACAGCTTGCAAACATTACCAACATGgtaagtgcaa ... atgttcatagGTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
EST: gi|88484430|gb|CI421701.1|CI421701
EST:     CGGGATGAACAGCTTGCANACATTACCAACATG                         GTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
genomic: CGGGATGAACAGCTTGCAAACATTACCAACATGgtaagtgcaa ... atgttcatagGTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
EST: gi|88503264|gb|CI430770.1|CI430770
EST:     AAACATTACCAACATG                         GTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
genomic: AAACATTACCAACATGgtaagtgcaa ... atgttcatagGTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
EST: gi|88366308|gb|CI551140.1|CI551140
EST:     AGGAGATCCAGAGAACTCGGGATGAACAGCTTGCAAACATTACCAACATG                         GTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
genomic: AGGAGATCCAGAGAACTCGGGATGAACAGCTTGCAAACATTACCAACATGgtaagtgcaa ... atgttcatagGTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
EST: gi|33684042|gb|CF312281.1|CF312281
EST:     GGAGATCCAGAGAACTCGGGATGAACAGCTTGCAAACATNTACCAACATG                         GTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
genomic: GGAGATCCAGAGAACTCGGGATGAACAGCTTGCAAACAT-TACCAACATGgtaagtgcaa ... atgttcatagGTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
EST: gi|86893473|gb|CI313495.1|CI313495
EST:     AGGAGATCCAGAGAACTCGGGATGAACAGCTTCCAAACATTACCAACATG                         GTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
genomic: AGGAGATCCAGAGAACTCGGGATGAACAGCTTGCAAACATTACCAACATGgtaagtgcaa ... atgttcatagGTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
EST: gi|33683950|gb|CF312189.1|CF312189
EST:     AGGAGATCCAGAGAACTCGGGATGAACAGCTTGCAAACATTACCAACATG                         G-GGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
genomic: AGGAGATCCAGAGAACTCGGGATGAACAGCTTGCAAACATTACCAACATGgtaagtgcaa ... atgttcatagGTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
EST: gi|88283138|gb|CI404584.1|CI404584
EST:     GAGAACTCGGGATGAACAGCTTGCAAACATTACCAACATG                         GTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
genomic: GAGAACTCGGGATGAACAGCTTGCAAACATTACCAACATGgtaagtgcaa ... atgttcatagGTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
EST: gi|88275782|gb|CI396386.1|CI396386
EST:     AGCTTGCAAACATTACCAACATG                         GTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
genomic: AGCTTGCAAACATTACCAACATGgtaagtgcaa ... atgttcatagGTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
EST: gi|9864918|gb|AU100668.1|AU100668
EST:     AGGAGATCCAGAGAACTCGGGATGAACAGCTTGCAAACATTACCAACATG                         GTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
genomic: AGGAGATCCAGAGAACTCGGGATGAACAGCTTGCAAACATTACCAACATGgtaagtgcaa ... atgttcatagGTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
EST: gi|88408289|gb|CI551418.1|CI551418
EST:     AGAACTCGGGATGAACAGCTTGCAAACATTACCAACATG                         GTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
genomic: AGAACTCGGGATGAACAGCTTGCAAACATTACCAACATGgtaagtgcaa ... atgttcatagGTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
EST: gi|33684158|gb|CF312397.1|CF312397
EST:     CTCGGGATGAACAGCTTGCAAACATTACCAACATG                         GTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
genomic: CTCGGGATGAACAGCTTGCAAACATTACCAACATGgtaagtgcaa ... atgttcatagGTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
EST: gi|88456420|gb|CI561023.1|CI561023
EST:     GGATGAACAGCTTGCAAACATTACCAACATG                         GTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
genomic: GGATGAACAGCTTGCAAACATTACCAACATGgtaagtgcaa ... atgttcatagGTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
EST: gi|29678307|gb|CB674582.1|CB674582
EST:     AGGAGATCCAGAGAACTCGGGATGAACAGCTTGCAAACATTACCAACATG                         GTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
genomic: AGGAGATCCAGAGAACTCGGGATGAACAGCTTGCAAACATTACCAACATGgtaagtgcaa ... atgttcatagGTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
EST: gi|88289325|gb|CI553301.1|CI553301
EST:     GAGATCCAGAGAACTCGGGATGAACAGCTTGCAAACATTACCAACATG                         GTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
genomic: GAGATCCAGAGAACTCGGGATGAACAGCTTGCAAACATTACCAACATGgtaagtgcaa ... atgttcatagGTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
EST: gi|33683949|gb|CF312188.1|CF312188
EST:     AGGAGATCCAGAGAACTCGGGATGAACAGCTTGCAAACATTACCAACATG                         GTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
genomic: AGGAGATCCAGAGAACTCGGGATGAACAGCTTGCAAACATTACCAACATGgtaagtgcaa ... atgttcatagGTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
EST: gi|86873899|gb|CI334431.1|CI334431
EST:     AGGAGATCCAGAGAACTCGGGATGAACAGCTTGCAAACATTACCAACATG                         GTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
genomic: AGGAGATCCAGAGAACTCGGGATGAACAGCTTGCAAACATTACCAACATGgtaagtgcaa ... atgttcatagGTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
EST: gi|88533777|gb|CI460441.1|CI460441
EST:     AGAGAACTCGGGATGAACAGCTTGCAAACATTACCAACATG                         GTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG
genomic: AGAGAACTCGGGATGAACAGCTTGCAAACATTACCAACATGgtaagtgcaa ... atgttcatagGTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 72 (upstream exon), 61 (downstream exon)
Score: 28

GGTGCATGATGCTATTGGATATACAGAAGAGCAAATATCTGAATTGAAAAAGGAGATCCAGAGAACTCGGGATGAACAGCTTGCAAACATTACCAACATGgtaagtgcaa ... atgttcatagGTGGAGGAAAAGCTGAATATCACTGTTGACAAGCTGCAACAGCAACTCATGGAAGAACAGAATGCAAGGCTAGAAGCAGAGAGGTTGGCAGCTGAAGCTA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTGCATGATGCTATTGGATATACAGAAGAGCAAATATCTGAATTGAAAAAGGAGATCCAGAGAACTCGGGATGAACAGCTTGCAAACATTACCAACATGgtaagtgcaactccatgtagttgaactgttgaagaagagcatatgtgtgcttatatcatttactcaagcagtagtttgtattaaatatatacatttaaat

- - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC