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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACCTGGTGACAGAGTTGAGGCTGATGAGCCCATAGCACAGATTGAAACTGATAAGgtacagtcattcaatcactttctgttctgtctgaatagacatgcaatttagcactcatggatagtcttttaaaatgtatcattgcctttctgtattccag

Basic information

species Oryza sativa
transcript LOC_Os04g32330.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g32330.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G079538_T01 (Zea mays), 5'ss of exon 5
AACCTGGTGACAGAGTTGAGGCTGATGAGCCCATAGCACAGATTGAAACTGATAAGgtacagtcattcaatcactttctgttctgtctgaatagacatgcaatttagcactcatggatagtcttttaaaatgtatcattgcctttctgt-attccag
||||||| |||||||| ||||||||||| || ||||| |||||||||||||||||||||  |    |             |||||| |||| |     | || ||   |        | | |  | |  |  |  | || |||| || |   |||||
AACCTGGAGACAGAGTCGAGGCTGATGAACCTATAGCGCAGATTGAAACTGATAAGgtattggtggt-------------ttctgtttgaacattagcgtaacttcatatctgctagtgg-ccataaccacatgacttttccttccttttgctccag

upper sequence: LOC_Os04g32330.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM5G807639_T02 (Zea mays), 5'ss of exon 6
AACCTGGTGACAGAGTTGAGGCTGATGAGCCCATAGCACAGATTGAAACTGATAAGgtacagtcattcaatcactttctgttctgtctgaatagacatgcaatttagcactcatggatagtcttttaaaatgtatcattgcctttctgtattccag
| ||||| |||||||| ||||| ||||| |||||||| ||||||||||||||||||||        |   |  |||      |||| |||| |    || || ||   | |      | | | |   ||    || | |   |   | | ||||||
AGCCTGGAGACAGAGTCGAGGCCGATGAACCCATAGCGCAGATTGAAACTGATAAGgtg-------ttggtggctt------ctgtttgaacatcagtggaactttatatttgctagtggccat---aagcacatgact-tttccttttgttccag

upper sequence: LOC_Os04g32330.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT4G26910.3 (Arabidopsis thaliana), 5'ss of exon 3
AACCTGGTGACAGAGTTGAGGCTGATGAGCCCATAGCACAGATTGAAACTGATAAGgtacagtcattcaatcactttctgttctgtctgaatagacatgcaatttagcactcatggatagtcttttaaaatgtatcattgcctttctgtattccag
|||||||||| |||||  ||||||||||| | || ||||| ||||||||||||||||||     ||| | |   | | |||  | | |  | ||||||     |||    | |       |  ||| |    |||   ||  ||            
AACCTGGTGAGAGAGTCCAGGCTGATGAGGCTATTGCACAAATTGAAACTGATAAGgtatcaatatttattttttctttgtcatttttctaaagacatctgtgttaaattttaaaatctattatttgattcatatttgtggattag----------

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|58590899|gb|CF989207.1|CF989207
EST:     GTGACAGAGTTGAGGCTGATGAGCCCATAGCACAGATTGAAACTGATAAG                         GTTACTATAGA
genomic: GTGACAGAGTTGAGGCTGATGAGCCCATAGCACAGATTGAAACTGATAAGgtacagtcat ... tgtattccagGTTACTATAGA
EST: gi|58676164|gb|CK064851.1|CK064851
EST:     GTGACAGAGTTGAGGCTGATGAGCCCATAGCACAGATTGAAACTGATAAG                         GTTACTATAGATGTTGCTAGTCCGGAAGCTGGTGTTATTGAAAAG
genomic: GTGACAGAGTTGAGGCTGATGAGCCCATAGCACAGATTGAAACTGATAAGgtacagtcat ... tgtattccagGTTACTATAGATGTTGCTAGTCCGGAAGCTGGTGTTATTGAAAAG
EST: gi|33795334|gb|CF323538.1|CF323538
EST:     CAGAGTTGAGGCTGATGAGCCCATAGCACAGATTGAAACTGATAAG                         GTTACTATAGATGTTGCTAGTCCGGAAGCTGGTGTTATTGAAAAG
genomic: CAGAGTTGAGGCTGATGAGCCCATAGCACAGATTGAAACTGATAAGgtacagtcat ... tgtattccagGTTACTATAGATGTTGCTAGTCCGGAAGCTGGTGTTATTGAAAAG
EST: gi|58670038|gb|CK058724.1|CK058724
EST:     GTGACAGAGTTGAGGCTGATGAGCCCATAGCACAGATTGAAACTGATAAG                         GTTACTATAGATGTTGCTAGTCCGGAAGCTGGT
genomic: GTGACAGAGTTGAGGCTGATGAGCCCATAGCACAGATTGAAACTGATAAGgtacagtcat ... tgtattccagGTTACTATAGATGTTGCTAGTCCGGAAGCTGGT
EST: gi|88356597|gb|CI626212.1|CI626212
EST:     GTGACAGAGTTGAGGCTGATGAGCCCATAGCACAGATTGAAACTGATAAG                         GTTACTATAGAT
genomic: GTGACAGAGTTGAGGCTGATGAGCCCATAGCACAGATTGAAACTGATAAGgtacagtcat ... tgtattccagGTTACTATAGAT
EST: gi|218479259|gb|FG949034.1|FG949034
EST:     GTGACAGAGTTGAGGCTGATGAGCCCATAGCACAGATTGAAACTGATAAG                         GTTACTATAGATGTTGCTAGTCCGGAAGCTGGTGTTATTGAAAAG
genomic: GTGACAGAGTTGAGGCTGATGAGCCCATAGCACAGATTGAAACTGATAAGgtacagtcat ... tgtattccagGTTACTATAGATGTTGCTAGTCCGGAAGCTGGTGTTATTGAAAAG
EST: gi|58666465|gb|CK055151.1|CK055151
EST:     GTGACAGAGTTGAGGCTGATGAGCCCATAGCACAGATTGAAACTGATAAG                         GTTACTATAGATGTTGCTAGTCCGGAAGCTGGTGTTATTGAAAAG
genomic: GTGACAGAGTTGAGGCTGATGAGCCCATAGCACAGATTGAAACTGATAAGgtacagtcat ... tgtattccagGTTACTATAGATGTTGCTAGTCCGGAAGCTGGTGTTATTGAAAAG
EST: gi|58592377|gb|CF990685.1|CF990685
EST:     GTGACAGAGTTGAGGCTGATGAGCCCATAGCACAGATTGAAACTGATAAG                         GTTACTATAGATGTTGCTAGTCCGGAAGCTGGTGTTATTGAAAAG
genomic: GTGACAGAGTTGAGGCTGATGAGCCCATAGCACAGATTGAAACTGATAAGgtacagtcat ... tgtattccagGTTACTATAGATGTTGCTAGTCCGGAAGCTGGTGTTATTGAAAAG
EST: gi|218481751|gb|FG959381.1|FG959381
EST:     GTGACAGAGTTGAGGCTGATGAGCCCATATCACAGATTGAAACTGATAAG                         GTTACTATAGATGTTGCTATTCCGGAAGCTGGTGTTATTGAAAAG
genomic: GTGACAGAGTTGAGGCTGATGAGCCCATAGCACAGATTGAAACTGATAAGgtacagtcat ... tgtattccagGTTACTATAGATGTTGCTAGTCCGGAAGCTGGTGTTATTGAAAAG
EST: gi|58668980|gb|CK057666.1|CK057666
EST:     GTGACAGAGTTGAGGCTGATGAGCCCATAGCACAGATTGAAACTGATAAG                         GTTACTATAGATGTTGCTAGTCCGGAAGCTGGTGTTATTGAAAAG
genomic: GTGACAGAGTTGAGGCTGATGAGCCCATAGCACAGATTGAAACTGATAAGgtacagtcat ... tgtattccagGTTACTATAGATGTTGCTAGTCCGGAAGCTGGTGTTATTGAAAAG
EST: gi|58659774|gb|CK048454.1|CK048454
EST:     GTGACAGAGTTGAGGCTGATGAGCCCATAGCACAGATTGAAACTGATAAG                         GTTACTATAGATGTTGCTAGTCCGGAAGCTGGTGTTATTGAAAAG
genomic: GTGACAGAGTTGAGGCTGATGAGCCCATAGCACAGATTGAAACTGATAAGgtacagtcat ... tgtattccagGTTACTATAGATGTTGCTAGTCCGGAAGCTGGTGTTATTGAAAAG
EST: gi|58689671|gb|CK078358.1|CK078358
EST:     GTGACAGAGTTGAGGCTGATGAGCCCATAGCACAGATTGAAACTGATAAG                         GTTACTATAGATGTTGCTAGTCCGGAAGCTGGTGTTATTGAAAAG
genomic: GTGACAGAGTTGAGGCTGATGAGCCCATAGCACAGATTGAAACTGATAAGgtacagtcat ... tgtattccagGTTACTATAGATGTTGCTAGTCCGGAAGCTGGTGTTATTGAAAAG

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: 56 (upstream exon), 45 (downstream exon)
Score: 65

AACCTGGTGACAGAGTTGAGGCTGATGAGCCCATAGCACAGATTGAAACTGATAAGgtacagtcat ... tgtattccagGTTACTATAGATGTTGCTAGTCCGGAAGCTGGTGTTATTGAAAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACCTGGTGACAGAGTTGAGGCTGATGAGCCCATAGCACAGATTGAAACTGATAAGgtacagtcattcaatcactttctgttctgtctgaatagacatgcaatttagcactcatggatagtcttttaaaatgtatcattgcctttctgtattccag

- - - - - - - - - - GCTGAT