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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCTTCATCAAGTAGTTCTGGAATGGAATCCAGGGACGATGATCTTGATGCTGACTTCTCTCAgtaagtccgataatgtgtccttcagtgcaggttgaatcttcactccatcatgtacttattttttttgttttgtgctatgaattccag

Basic information

species Oryza sativa
transcript LOC_Os01g05420.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g05420.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G085254_T03 (Zea mays), 5'ss of exon 7
GCCTTCATCAAGTAGTTCTGGAATGGAATCCAGGGACGATGATCTTGATGCTGACTTCTCTCAgtaagtccgata-----atgtgtccttcagtgcaggt-tgaatcttcactccatcatgtacttattttt--tttgttttgtgctatgaattccag--------
 |||||||| ||||| ||||||||||||||||| || |||||||||||||||||||| || ||||||||     |      | || | ||   ||||  | ||  | ||  | ||||    | || ||| ||  |||  | | |  |||  || |           
ACCTTCATCGAGTAGCTCTGGAATGGAATCCAGAGATGATGATCTTGATGCTGACTTTTCACAgtaagtttatcatatttgtttggcattggatgcacatgtgcttgttatcaccatttcctcctaattgttagtttaatctattttatttatgctttgtatttag

upper sequence: LOC_Os01g05420.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G100881_T02 (Zea mays), 5'ss of exon 8
-------------------------------------GCCTTCATCAAGTAGTTCTGGAATGGAATCCAGGGACGATGATCTTGATGCTGACTTCTCTCAgtaagtccgataatgtgtccttcagtgcaggttga-atcttcactccatcatgtacttattttttttgttttgtgctatgaattccag
                                          |||||||||| ||||||||||||||||| || |||||| ||||||||||||| || |||||||| |  ||     |  ||   |||| |||   | | |      ||  |    ||| | | |||  ||| |||| || |||    
GTGTACTTTGTGTTCTTATTGGTTATCCTCTGTCATGAAGACCATCAAGTAGCTCTGGAATGGAATCCAGAGATGATGATGTTGATGCTGACTTTTCACAgtaagttcatta-----tatttggatgcatgttttcaacattttctaattgttagtttaatatgttttatttatgctttgtatttag-

upper sequence: LOC_Os01g05420.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G085254_T02 (Zea mays), 5'ss of exon 8
-------------------------------------GCCTTCATCAAGTAGTTCTGGAATGGAATCCAGGGACGATGATCTTGATGCTGACTTCTCTCAgtaagtccgata-----atgtgtccttcagtgcaggt-tgaatcttcactccatcatgtacttattttt--tttgttttgtgctatgaattccag--------
                                      |||||||| ||||| ||||||||||||||||| || |||||||||||||||||||| || ||||||||     |      | || | ||   ||||  | ||  | ||  | ||||    | || ||| ||  |||  | | |  |||  || |           
TCTTATTGGTTAACCTTTGTGTCATACTGTCATGAAGACCTTCATCGAGTAGCTCTGGAATGGAATCCAGAGATGATGATCTTGATGCTGACTTTTCACAgtaagtttatcatatttgtttggcattggatgcacatgtgcttgttatcaccatttcctcctaattgttagtttaatctattttatttatgctttgtatttag

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|29665318|gb|CB661593.1|CB661593
EST:     AGTTCTGGAATGGAATCCAGGGACGATGATCTTGATGCTGACTTCTCTCA                         GCGCAAGTCTGGGCAAGGTGGTGCAAGGCAGCATGCTTCTAGGCCAGAAGC
genomic: AGTTCTGGAATGGAATCCAGGGACGATGATCTTGATGCTGACTTCTCTCAgtaagtccga ... tgaattccagGCGCAAGTCTGGGCAAGGTGGTGCAAGGCAGCATGCTTCTAGGCCAGAAGC
EST: gi|29662253|gb|CB658528.1|CB658528
EST:     AGTTCTGGAATGGAATCCAGGGACGATGATCTTGATGCTGACTTCTCTCA                         GCGCAAGTCTGGGCAAGGTGGTGCAAGGCAGCATGCTTCTAGGCCAGAAGC
genomic: AGTTCTGGAATGGAATCCAGGGACGATGATCTTGATGCTGACTTCTCTCAgtaagtccga ... tgaattccagGCGCAAGTCTGGGCAAGGTGGTGCAAGGCAGCATGCTTCTAGGCCAGAAGC
EST: gi|29670427|gb|CB666702.1|CB666702
EST:     AGTTCTGGAATGGAATCCAGGGACGATGATCTTGATGCTGACTTCTCTCA                         GCGCAAGTCTGGGCAAGGTGGTGCAAGGCAGCATGCTTCTAGGCCAGAAGC
genomic: AGTTCTGGAATGGAATCCAGGGACGATGATCTTGATGCTGACTTCTCTCAgtaagtccga ... tgaattccagGCGCAAGTCTGGGCAAGGTGGTGCAAGGCAGCATGCTTCTAGGCCAGAAGC
EST: gi|29679612|gb|CB675887.1|CB675887
EST:     AGTTCTGGAATGGAATCCAGGGACGATGATCTTGATGCTGACTTCTCTCA                         GCGCAAGTCTGGGCAAGGTGGTGCAAGGCAGCATGCTTCTAGGCCAGAAGC
genomic: AGTTCTGGAATGGAATCCAGGGACGATGATCTTGATGCTGACTTCTCTCAgtaagtccga ... tgaattccagGCGCAAGTCTGGGCAAGGTGGTGCAAGGCAGCATGCTTCTAGGCCAGAAGC
EST: gi|29670426|gb|CB666701.1|CB666701
EST:     AGTTCTGGAATGGAATCCAGGGACGATGATCTTGATGCTGACTTCTCTCA                         GCGCAAGTCTGGG
genomic: AGTTCTGGAATGGAATCCAGGGACGATGATCTTGATGCTGACTTCTCTCAgtaagtccga ... tgaattccagGCGCAAGTCTGGG
EST: gi|66923574|gb|CX110422.1|CX110422
EST:     AGTTCTGGAATGGAATCCAGGGACGATGATCTTGATGCTGACTTCTCTCA                         GCGCAAGTCTGGGCAAGGTGGTGCAAGGCAGCATGCTTCTAGGCCAGAAGC
genomic: AGTTCTGGAATGGAATCCAGGGACGATGATCTTGATGCTGACTTCTCTCAgtaagtccga ... tgaattccagGCGCAAGTCTGGGCAAGGTGGTGCAAGGCAGCATGCTTCTAGGCCAGAAGC
EST: gi|218504271|gb|FG960657.1|FG960657
EST:     AGTTCTGGAATGGAATCCAGGGACGATGATCTTGATGCTGACTTCTCTCA                         GCGCAAGTCTGGGCAAGGTGGTGCAAGGCAGCATGCTTCTAGGCCAGAAGC
genomic: AGTTCTGGAATGGAATCCAGGGACGATGATCTTGATGCTGACTTCTCTCAgtaagtccga ... tgaattccagGCGCAAGTCTGGGCAAGGTGGTGCAAGGCAGCATGCTTCTAGGCCAGAAGC
EST: gi|2797946|gb|AA751240.1|AA751240
EST:     AGTTCTGGAATGGAATCCAGGGACGATGATCTTGATGCTGACTTCTCTCA                         GCGCAAGTCTGGGCAAGGTGGTGCAAGGCAGCATGCTTCTAGGCCAGAAGC
genomic: AGTTCTGGAATGGAATCCAGGGACGATGATCTTGATGCTGACTTCTCTCAgtaagtccga ... tgaattccagGCGCAAGTCTGGGCAAGGTGGTGCAAGGCAGCATGCTTCTAGGCCAGAAGC
EST: gi|29665319|gb|CB661594.1|CB661594
EST:     AGTTCTGGAATGGAATCCAGGGACGATGATCTTGATGCTGACTTCTCTCA                         GCGCAAGTCTGGGCAAGGTGGTGCAAGGCAGCATGCTTCTAGGCCAGAAGC
genomic: AGTTCTGGAATGGAATCCAGGGACGATGATCTTGATGCTGACTTCTCTCAgtaagtccga ... tgaattccagGCGCAAGTCTGGGCAAGGTGGTGCAAGGCAGCATGCTTCTAGGCCAGAAGC
EST: gi|27577848|gb|CB000543.1|CB000543
EST:     AGTTCTGGAATGGAATCCAGGGACGATGATCTTGATGCTGACTTCTCTCA                         GCGCAAGTCTGGGCAAGGTGGTGCAAGGCAGCATGCTTCTAGGCCAGAAGC
genomic: AGTTCTGGAATGGAATCCAGGGACGATGATCTTGATGCTGACTTCTCTCAgtaagtccga ... tgaattccagGCGCAAGTCTGGGCAAGGTGGTGCAAGGCAGCATGCTTCTAGGCCAGAAGC

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: 63 (upstream exon), 44 (downstream exon)
Score: 45

GCCTTCATCAAGTAGTTCTGGAATGGAATCCAGGGACGATGATCTTGATGCTGACTTCTCTCAgtaagtccga ... tgaattccagGCGCAAGTCTGGGCAAGGTGGTGCAAGGCAGCATGCTTCTAGGCCAGAAGCATCACCCTTGGACTTTGTTATTCGCCCGCAGTCCAAAATTGATCCCGAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCTTCATCAAGTAGTTCTGGAATGGAATCCAGGGACGATGATCTTGATGCTGACTTCTCTCAgtaagtccgataatgtgtccttcagtgcaggttgaatcttcactccatcatgtacttattttttttgttttgtgctatgaattccag

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