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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGCAAAGAAACGAGAACAGGAACGCCAAAGGCAGGAAAAACTTGCGGAGGTAGGTCGGTACAGGGGTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAGgtaattgaattgaatcagtattcatcacatcaatgcaatcttggacatgaaactgtagggctgtgatagaatctgcttgcttcctaaataattcaagctg...

Basic information

species Oryza sativa
transcript LOC_Os03g27840.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g27840.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G022061_T03 (Zea mays), 5'ss of exon 11
TAGCAAAGAAACGAGAACAGGAACGCCAAAGGCAGGAAAAACTTGCGGAGGTAGGTCGGTACAGGGGTCGAAGC------AGGAGCCTTAGCCGATCTCCACCAAGgtaattgaattgaatcagtatt-catcacatcaatgcaatc-ttggacatgaaactgtagggctgtg-atagaatctgcttgcttcctaaataattcaagctg
      ||||||||||||||||||| |||||||||||||||||||| || || ||||| |||| | |||| |||      || || |||||||| || |||||||||||||| ||   ||||| | ||   |||  |   |    || ||   |||   |   | | |||  | ||      |  |||    | | | || |||     
------AGAAACGAGAACAGGAACGACAAAGGCAGGAAAAACTTGCTGAAGTTGGTCGATACAAGCGTCGTAGCCGCAGTAGAAGTCTTAGCCGTTCCCCACCAAGgtaattaaacc-aatcatttttatgtcagtttgtttttttccttcttcattggataattgtgctaagcatgtggatttgttgacctcaatagaagtcattt--
















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|86494603|gb|CI137236.1|CI137236
EST:     GTAGGTCGGTACAGGGGTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAG                         AAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
genomic: GTAGGTCGGTACAGGGGTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAGgtaattgaat ... cctggtgcagAAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
EST: gi|88850975|gb|CI096365.1|CI096365
EST:     GTAGGTCGGTACAGGGGTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAG                         AAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
genomic: GTAGGTCGGTACAGGGGTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAGgtaattgaat ... cctggtgcagAAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
EST: gi|88541031|gb|CI469115.1|CI469115
EST:     AGCCTTAGCCGATCTCCACCAAG                         AAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
genomic: AGCCTTAGCCGATCTCCACCAAGgtaattgaat ... cctggtgcagAAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
EST: gi|58659672|gb|CK048352.1|CK048352
EST:     GTAGGTCGGTACAGGGGTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAG                         AAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
genomic: GTAGGTCGGTACAGGGGTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAGgtaattgaat ... cctggtgcagAAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
EST: gi|86842263|gb|CI335196.1|CI335196
EST:     GTAGGTCGGTACAGGGGTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAG                         AAGGCGACATTATAGCAGAAGTCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
genomic: GTAGGTCGGTACAGGGGTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAGgtaattgaat ... cctggtgcagAAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
EST: gi|15856484|gb|BI809296.1|BI809296
EST:     GTAGGTCGGTACAGGGGTCGAAGCAGGA-CCTTA-CCGATCTCCACCAAG                         AAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
genomic: GTAGGTCGGTACAGGGGTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAGgtaattgaat ... cctggtgcagAAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
EST: gi|86896295|gb|CI330171.1|CI330171
EST:     GTAGGTCGGTACAGGGGTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAG                         AAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
genomic: GTAGGTCGGTACAGGGGTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAGgtaattgaat ... cctggtgcagAAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
EST: gi|88554487|gb|CI484670.1|CI484670
EST:     GTANGTCGGTACAGGGGTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAG                         AAGGCNACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
genomic: GTAGGTCGGTACAGGGGTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAGgtaattgaat ... cctggtgcagAAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
EST: gi|88451276|gb|CI536669.1|CI536669
EST:     AGGGTTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAG                         AAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGGAGTCCAAGGAGGTA
genomic: AGGGGTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAGgtaattgaat ... cctggtgcagAAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
EST: gi|88561976|gb|CI492693.1|CI492693
EST:     TAGGTC-GTACAGGGGGTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAG                         AAGGCGACATTATAGCAGAAGCCGTATTAGGAGTAGAAGTCCAAGGAGGTA
genomic: TAGGTCGGTACA-GGGGTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAGgtaattgaat ... cctggtgcagAAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
EST: gi|66924446|gb|CX111294.1|CX111294
EST:     GTAGGTCGGTACAGGGGTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAG                         AAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
genomic: GTAGGTCGGTACAGGGGTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAGgtaattgaat ... cctggtgcagAAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
EST: gi|88961858|gb|CI097011.1|CI097011
EST:     GTAGGTCGGTACAGGGGTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAG                         AAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
genomic: GTAGGTCGGTACAGGGGTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAGgtaattgaat ... cctggtgcagAAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
EST: gi|86595093|gb|CI260332.1|CI260332
EST:     GTAGGTCGGTACAGGGGTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAG                         AAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
genomic: GTAGGTCGGTACAGGGGTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAGgtaattgaat ... cctggtgcagAAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
EST: gi|88906142|gb|CI375214.1|CI375214
EST:     TAGGTCGGTACACGGGTCGAAGCAGTGAGCCTTAGCCGATCTCCACCAAG                         AAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
genomic: TAGGTCGGTACAGGGGTCGAAGCAG-GAGCCTTAGCCGATCTCCACCAAGgtaattgaat ... cctggtgcagAAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
EST: gi|87031743|gb|CI272444.1|CI272444
EST:     GTAGGTCGGTACAGGGGTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAG                         AAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
genomic: GTAGGTCGGTACAGGGGTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAGgtaattgaat ... cctggtgcagAAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
EST: gi|88530682|gb|CI459096.1|CI459096
EST:     GTAGGTCGGTACA-GGGTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAG                         AAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAATTCCAAGGAGGTA
genomic: GTAGGTCGGTACAGGGGTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAGgtaattgaat ... cctggtgcagAAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
EST: gi|33655396|gb|CF278010.1|CF278010
EST:     GTAGGTCGGTACAGGGGTCGAAGCAGGAGCTTTAGCCGATCTCCACCAAG                         AAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
genomic: GTAGGTCGGTACAGGGGTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAGgtaattgaat ... cctggtgcagAAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
EST: gi|86598342|gb|CI354959.1|CI354959
EST:     GTAGGTCGCTACACGGGTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAT                         AAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
genomic: GTAGGTCGGTACAGGGGTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAGgtaattgaat ... cctggtgcagAAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
EST: gi|88449120|gb|CI560581.1|CI560581
EST:     GTAGGTCGGTACAGGGGTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAG                         AAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA
genomic: GTAGGTCGGTACAGGGGTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAGgtaattgaat ... cctggtgcagAAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTA

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: 64 (upstream exon), 63 (downstream exon)
Score: 23

TAGCAAAGAAACGAGAACAGGAACGCCAAAGGCAGGAAAAACTTGCGGAGGTAGGTCGGTACAGGGGTCGAAGCAGGAGCCTTAGCCGATCTCCACCAAGgtaattgaat ... cctggtgcagAAGGCGACATTATAGCAGAAGCCGTAGTAGGAGTAGAAGTCCAAGGAGGTACCATTCACGATCCCAGTCTCATTCCCGTTCGCCTTCTCGCTCTCCAAG




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