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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAGgttagtatgatgcacatggttcaacgtttcactgcctgtggacattccttgaactctggtaattattgaattgccatgactttgaatttccaacag

Basic information

species Oryza sativa
transcript LOC_Os01g43540.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g43540.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G149704_T02 (Zea mays), 5'ss of exon 8
CTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAGgttagtatgatgcacatggttcaacgtttcactgcctgtggacattccttgaactctggtaattattgaattgccatgac-tttgaatttccaacag
||||| | ||||  || || ||||| || || ||||| || || || |||||||||||||||||||||||||| |||||||||||| |    |    |    ||  | |  |||||          | | |   ||||  |||  || |  |||    | |   ||||  |   ||||||
CTGAAACAGCCCCAAGACCTTCATACCCATCTTCAAAGTCAAAAAAGGACTGGGATAAACTGGAAGCTGAAGTAAAAAAGGAGgtttgatcaagatgcccacttttaggcatcactttt-------acttcagcaacttgggt--ttctcaaatatgaacggtgtttgtgtcggcaacag

upper sequence: LOC_Os01g43540.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G105019_T01 (Zea mays), 5'ss of exon 8
CTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAGgttagt--atgatgcacatggttcaacgtttcactgcctgtggacattccttgaactc--tggtaattattgaattgccatgactttgaatttccaacag
||||| | ||||  || || ||||| || || |||||  | || ||||||||||||||||||||||||||||| |||||||||||| |   | ||| | ||    |  | || ||  | | | | |  |   ||||   |    |   || | ||   |  ||||| ||||  | | || |||
CTGAAACAGCCCCAAGACCTTCATACCCATCTTCAAAGGCGAAAAAAGACTGGGATAAACTGGAAGCTGAAGTCAAAAAGGAGgtttgatgaagatcctcacttatatatgtatcgat-cttattgctagaacttgggtttatcgaatatgaatggggtttcatga-tttgtgtctgcatcag
















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|218485287|gb|FG957632.1|FG957632
EST:     CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAG                         GAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
genomic: CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAGgttagtatga ... tttccaacagGAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
EST: gi|86523660|gb|CI163866.1|CI163866
EST:     ACTGGAAGCTGAAGTTAAAAAGGAG                         GAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
genomic: ACTGGAAGCTGAAGTTAAAAAGGAGgttagtatga ... tttccaacagGAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
EST: gi|25803427|gb|CA759388.1|CA759388
EST:     CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAG                         GAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
genomic: CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAGgttagtatga ... tttccaacagGAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
EST: gi|8857468|gb|AU094786.1|AU094786
EST:     CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAG                         GAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
genomic: CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAGgttagtatga ... tttccaacagGAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
EST: gi|29661449|gb|CB657724.1|CB657724
EST:     CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAG                         GAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
genomic: CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAGgttagtatga ... tttccaacagGAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
EST: gi|88980111|gb|CI026400.1|CI026400
EST:     CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAG                         GAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
genomic: CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAGgttagtatga ... tttccaacagGAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
EST: gi|13805768|gb|AU181196.1|AU181196
EST:     TTAAAAAGGAG                         GAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
genomic: TTAAAAAGGAGgttagtatga ... tttccaacagGAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
EST: gi|58662717|gb|CK051403.1|CK051403
EST:     CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAG                         GAGAAGGAGGAGAAGCTTGAAGGC
genomic: CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAGgttagtatga ... tttccaacagGAGAAGGAGGAGAAGCTTGAAGGC
EST: gi|27577531|gb|CB000226.1|CB000226
EST:     CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAG                         GAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
genomic: CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAGgttagtatga ... tttccaacagGAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
EST: gi|25803426|gb|CA759387.1|CA759387
EST:     CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAG                         GAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
genomic: CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAGgttagtatga ... tttccaacagGAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
EST: gi|29660562|gb|CB656837.1|CB656837
EST:     CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAG                         GAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
genomic: CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAGgttagtatga ... tttccaacagGAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
EST: gi|29625918|gb|CB630929.1|CB630929
EST:     CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAG                         GAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
genomic: CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAGgttagtatga ... tttccaacagGAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
EST: gi|88202553|gb|CI200908.1|CI200908
EST:     AGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAG                         GAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
genomic: AGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAGgttagtatga ... tttccaacagGAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
EST: gi|29669130|gb|CB665405.1|CB665405
EST:     CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAG                         GAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
genomic: CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAGgttagtatga ... tttccaacagGAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
EST: gi|27578357|gb|CB001052.1|CB001052
EST:     CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAG                         GAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
genomic: CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAGgttagtatga ... tttccaacagGAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
EST: gi|29655865|gb|CB652140.1|CB652140
EST:     CAAAATCCAAGAAAGACTGGGATAACCTGGAAGCTGAAGTTAAAAAGGAG                         GAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
genomic: CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAGgttagtatga ... tttccaacagGAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
EST: gi|11565208|gb|AU165844.1|AU165844
EST:     AAATCCCAAGAAAGACTGGGATAAACTGGGAAGCTGAAGTTAAAAAGGAG                         GAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACCAAATTTTTCCG
genomic: AAAT-CCAAGAAAGACTGGGATAAACT-GGAAGCTGAAGTTAAAAAGGAGgttagtatga ... tttccaacagGAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAA-CAAATTTTTCCG
EST: gi|4714313|gb|AU058280.1|AU058280
EST:     AAATCCAAGAAAGACTGGGATAAACTGGGAAGCTGGAAGTTAAAAAGGAG                         GNAGAAGGAGGAGAAGCTTGAAGGCG-TGCTGCATTGGACCAATTTT
genomic: AAATCCAAGAAAGACTGGGATAAACTGG-AAGCTG-AAGTTAAAAAGGAGgttagtatga ... tttccaacagG-AGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTT
EST: gi|33686913|gb|CF315152.1|CF315152
EST:     CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAG                         GAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAANTTTTCCGT
genomic: CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAGgttagtatga ... tttccaacagGAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
EST: gi|88271546|gb|CI387599.1|CI387599
EST:     GACTGGGATAAACT-GAAGCTGAAGTTAAAAAGGAG                         GAGAA-GAGGAGAAGCTTGAAGCCGATGCTCCATTGAACAAATTTTTCCGT
genomic: GACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAGgttagtatga ... tttccaacagGAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
EST: gi|86866170|gb|CI336858.1|CI336858
EST:     GGATAAACTGGAAGCTGAAGTTAAAAAGGAG                         GAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
genomic: GGATAAACTGGAAGCTGAAGTTAAAAAGGAGgttagtatga ... tttccaacagGAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
EST: gi|88997216|gb|CI389882.1|CI389882
EST:     GCTGAAGTTAAAAAGGAG                         GAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
genomic: GCTGAAGTTAAAAAGGAGgttagtatga ... tttccaacagGAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
EST: gi|23512886|gb|BU672887.1|BU672887
EST:     CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAG                         GAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACCAATTTTTCCGT
genomic: CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAGgttagtatga ... tttccaacagGAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
EST: gi|88843613|gb|CI372513.1|CI372513
EST:     ACTGGAAGCTGAAGTTAAAAAGGAG                         GAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
genomic: ACTGGAAGCTGAAGTTAAAAAGGAGgttagtatga ... tttccaacagGAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
EST: gi|157651612|gb|EX451246.1|EX451246
EST:     CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAG                         GAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
genomic: CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAGgttagtatga ... tttccaacagGAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
EST: gi|29658977|gb|CB655252.1|CB655252
EST:     CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAG                         GAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
genomic: CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAGgttagtatga ... tttccaacagGAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
EST: gi|86529243|gb|CI169449.1|CI169449
EST:     CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAG                         GAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
genomic: CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAGgttagtatga ... tttccaacagGAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
EST: gi|88980948|gb|CI021075.1|CI021075
EST:     CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAG                         GAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
genomic: CAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAGgttagtatga ... tttccaacagGAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
EST: gi|86843508|gb|CI339570.1|CI339570
EST:     GGAAGCTGAAGTTAAAAAGGAG                         GAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
genomic: GGAAGCTGAAGTTAAAAAGGAGgttagtatga ... tttccaacagGAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
EST: gi|88271207|gb|CI387260.1|CI387260
EST:     GATAAACTGGAAGCTGAAGTTAAAAAGGAG                         GAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT
genomic: GATAAACTGGAAGCTGAAGTTAAAAAGGAGgttagtatga ... tttccaacagGAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGT

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: 73 (upstream exon), 72 (downstream exon)
Score: 133

CTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAGgttagtatga ... tttccaacagGAGAAGGAGGAGAAGCTTGAAGGCGATGCTGCATTGAACAAATTTTTCCGTGACATCTACAGTGATGCTGATGAAGACATGCGACGAGCAATGATGAAAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGAATCGGCCCAGAGGCCATCATATCCTTCCTCAAAATCCAAGAAAGACTGGGATAAACTGGAAGCTGAAGTTAAAAAGGAGgttagtatgatgcacatggttcaacgtttcactgcctgtggacattccttgaactctggtaattattgaattgccatgactttgaatttccaacag

- - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG