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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattcttcaactactaccatgtttcgctgccatgatctatctttttttaggggatatctcctaatattaatttgggaggctttgtgcag

Basic information

species Oryza sativa
transcript LOC_Os07g43470.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g43470.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G158021_T01 (Zea mays), 5'ss of exon 9
TGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattcttcaactactaccatgtttcgctgccatgatctatctttttttaggggatat-ctcctaatattaatttgggaggcttt-gtgcag
 ||  |||| |||||||| || ||||| ||||||||||||||||||||||||||| ||||   |  || |  |  ||||| |  ||  |    |   |  |   | || | ||   ||||   | | ||||     ||||| ||||||
CGCTCTGGTATGGGGTTCCAGTGTGAAACATAAGCCTCAGAGAGTTGGCAAGgtatgcat---tagaccagcatgatgttacattgttacacacc--cactgggtgggtgttaggttccttgcactgatttattgtgctttcgtgcag
















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|88831549|gb|CI369231.1|CI369231
EST:     CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG                         GAACATGAGCTTGAGGATGAGGACCTTGTCCAGATCATCAAGAAAGTTTAG
genomic: CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
EST: gi|86412717|gb|CI067122.1|CI067122
EST:     TTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG                         GAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
genomic: TTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
EST: gi|88845150|gb|CI084075.1|CI084075
EST:     CATTGGTGTGGAGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCTAG                         GAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
genomic: CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
EST: gi|86498576|gb|CI141209.1|CI141209
EST:     CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG                         GAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAANGAAAGTTAT
genomic: CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAA-GAAAGTT-T
EST: gi|86887194|gb|CI326009.1|CI326009
EST:     CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG                         GAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
genomic: CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
EST: gi|88831194|gb|CI082004.1|CI082004
EST:     CATTGGTGTGGAGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTNGGCTAG                         GAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
genomic: CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
EST: gi|86887208|gb|CI326023.1|CI326023
EST:     CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG                         GAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
genomic: CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
EST: gi|86852710|gb|CI321830.1|CI321830
EST:     AGTTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG                         GAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
genomic: A-TTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
EST: gi|88381165|gb|CI525935.1|CI525935
EST:     CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG                         GAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
genomic: CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
EST: gi|88294527|gb|CI530067.1|CI530067
EST:     CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG                         GAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
genomic: CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
EST: gi|88488132|gb|CI425403.1|CI425403
EST:     CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG                         GAACATGAGCTTGAGGATGAGGACNTTGTCCAGATCATCAAGAAAGTTTAG
genomic: CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
EST: gi|13807087|gb|AU181805.1|AU181805
EST:     CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG                         GAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
genomic: CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
EST: gi|88250102|gb|CI249951.1|CI249951
EST:     CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG                         GAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
genomic: CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
EST: gi|88840330|gb|CI079784.1|CI079784
EST:     CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG                         GAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
genomic: CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
EST: gi|88246122|gb|CI245971.1|CI245971
EST:     CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG                         GAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
genomic: CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
EST: gi|86428361|gb|CI075042.1|CI075042
EST:     CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG                         GAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTNAG
genomic: CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
EST: gi|86488429|gb|CI131062.1|CI131062
EST:     CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG                         GAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
genomic: CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
EST: gi|5003286|gb|AU068435.1|AU068435
EST:     CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG                         GAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
genomic: CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
EST: gi|88842869|gb|CI371769.1|CI371769
EST:     CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG                         GAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
genomic: CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
EST: gi|88250137|gb|CI249986.1|CI249986
EST:     CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG                         GAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
genomic: CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
EST: gi|12622128|gb|AU172341.1|AU172341
EST:     CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG                         GAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
genomic: CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
EST: gi|88445591|gb|CI544350.1|CI544350
EST:     AGAGTTGGCAAG                         GAACATGAGCTTGAGGATGA-GACGTTGNTCCAGATCATCAAGAAANTTTA
genomic: AGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTG-TCCAGATCATCAAGAAAGTTTA
EST: gi|86858867|gb|CI275094.1|CI275094
EST:     CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG                         GAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
genomic: CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
EST: gi|88830896|gb|CI079330.1|CI079330
EST:     CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG                         GAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
genomic: CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
EST: gi|88845195|gb|CI084120.1|CI084120
EST:     CATTGGTGTGGAGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTNGGCTAG                         GAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTNAG
genomic: CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
EST: gi|86487602|gb|CI130235.1|CI130235
EST:     CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG                         GAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
genomic: CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
EST: gi|88245533|gb|CI245382.1|CI245382
EST:     CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG                         GAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
genomic: CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
EST: gi|86525484|gb|CI165690.1|CI165690
EST:     CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG                         GAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
genomic: CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
EST: gi|88830576|gb|CI078020.1|CI078020
EST:     CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG                         GAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTNAG
genomic: CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
EST: gi|86887193|gb|CI326008.1|CI326008
EST:     CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG                         GAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
genomic: CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
EST: gi|86823697|gb|CI258751.1|CI258751
EST:     CATTGGTGTGGGGTTCTAGCGCGAAGCATAAGCCTCAGAGAGTTGGCAAG                         GAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
genomic: CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
EST: gi|88228618|gb|CI228098.1|CI228098
EST:     CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG                         GAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
genomic: CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
EST: gi|86887118|gb|CI325933.1|CI325933
EST:     CATT-GTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAG                         GAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG
genomic: CATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAG

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: 54 (upstream exon), 70 (downstream exon)
Score: 32

TGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattc ... ctttgtgcagGAACATGAGCTTGAGGATGAGGACGTTGTCCAGATCATCAAGAAAGTTTAGGTATATTGTAGTGGTCACGTTCTGCAAACCTGGAAGGAGGTATGAGCTA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCATTGGTGTGGGGTTCTAGCGTGAAGCATAAGCCTCAGAGAGTTGGCAAGgtaggcattcttcaactactaccatgtttcgctgccatgatctatctttttttaggggatatctcctaatattaatttgggaggctttgtgcag

- - - - - - - - - - -  TGAAGC