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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCAgtatgatctcaatatttctctcaagaccacattcacataatgtacagtattgattttcctagtatttagtgtgctcattgatttgttttctatcag

Basic information

species Oryza sativa
transcript LOC_Os08g07960.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g07960.2 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G058498_T01 (Zea mays), 5'ss of exon 4
GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCAgtatgatctcaatatttctctcaagaccacatt-cacataat-gtacagta--ttgattttccta------gtatttagtgtgctcattgatttgttttctatcag
||| |||||||||||||||||||||| |  ||||| |||||||| || || || ||||| ||||| ||||||||| | | |||      | |    | |  |  | || |  | |||  |||  || | |       |||| | || | ||||||||||||||| || | ||
GTGAGGTGCTGGGAGATTGTTGGTGGTAACAGTCAGCCAAAGGCGTCCATTTCTCATGATCAGCCGgtatgatcttagtgttttctgggatatgttaatatatttgattgggcggtagattgtcttccatgtagtttgtatctggtatcctcattgatttgtttccttttag
















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|88394469|gb|CI605810.1|CI605810
EST:     TTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCA                         GTCCTCTGTTCAGCTTGGAAGGATGATGGAACTACTGTGTTCTCTGGAGGC
genomic: TTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCAgtatgatctc ... tttctatcagGTCCTCTGTTCAGCTTGGAAGGATGATGGAACTACTGTGTTCTCTGGAGGC
EST: gi|33793654|gb|CF322711.1|CF322711
EST:     TTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCA                         GTCCTCTGTTCAGCTTGGAAGGATGATGGAACTACTGTGTTCTCTGGAGGC
genomic: TTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCAgtatgatctc ... tttctatcagGTCCTCTGTTCAGCTTGGAAGGATGATGGAACTACTGTGTTCTCTGGAGGC
EST: gi|88451540|gb|CI565593.1|CI565593
EST:     TTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCA                         GGTCCTCTGTTCAGCTTGGAAGGATGATGGAACTACTGTGTTCTCTGGAGG
genomic: TTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCAgtatgatctc ... tttctatcagG-TCCTCTGTTCAGCTTGGAAGGATGATGGAACTACTGTGTTCTCTGGAGG
EST: gi|29615879|gb|CB620891.1|CB620891
EST:     TTGTTGGGGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCA                         GTCCTCTGTTCAGCTTGGAAGGATGATGGAACTACTGTGTTCTCTGGAGGC
genomic: TTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCAgtatgatctc ... tttctatcagGTCCTCTGTTCAGCTTGGAAGGATGATGGAACTACTGTGTTCTCTGGAGGC
EST: gi|88356897|gb|CI620785.1|CI620785
EST:     TTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCA                         GTCCTCTGTTCAGCTTGGAAGGATGATGGAACTACTGTGTTCTCTGGGGGC
genomic: TTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCAgtatgatctc ... tttctatcagGTCCTCTGTTCAGCTTGGAAGGATGATGGAACTACTGTGTTCTCTGGAGGC
EST: gi|88399681|gb|CI583415.1|CI583415
EST:     TTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCA                         GTCCTCTGTTCAGCTTGGAAGGATGA
genomic: TTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCAgtatgatctc ... tttctatcagGTCCTCTGTTCAGCTTGGAAGGATGA
EST: gi|33795033|gb|CF323392.1|CF323392
EST:     TTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCA                         GTCCTCTGTTCAGCTTGGAAGGATGATGGAACTACTGTGTTCTCTGGAGGC
genomic: TTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCAgtatgatctc ... tttctatcagGTCCTCTGTTCAGCTTGGAAGGATGATGGAACTACTGTGTTCTCTGGAGGC
EST: gi|29681300|gb|CB677575.1|CB677575
EST:     TTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCA                         GTCCTCTGTTCAGCTTGGAAGGATGATGGAACTACTGTGTTCTCTGGAGGC
genomic: TTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCAgtatgatctc ... tttctatcagGTCCTCTGTTCAGCTTGGAAGGATGATGGAACTACTGTGTTCTCTGGAGGC
EST: gi|88417412|gb|CI579073.1|CI579073
EST:     TTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCA                         GTCCTCTGTTC
genomic: TTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCAgtatgatctc ... tttctatcagGTCCTCTGTTC
EST: gi|218492102|gb|FG950663.1|FG950663
EST:     TTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCA                         GTTCTCTGTTCAGCTTGGAAGGATGATGGAACTACTGTGTTCTCTGGAGGC
genomic: TTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCAgtatgatctc ... tttctatcagGTCCTCTGTTCAGCTTGGAAGGATGATGGAACTACTGTGTTCTCTGGAGGC
EST: gi|88394449|gb|CI605790.1|CI605790
EST:     TTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCA                         GTCCTCTGTTCAGCTTGGAAGGATGATGGAACTAC
genomic: TTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCAgtatgatctc ... tttctatcagGTCCTCTGTTCAGCTTGGAAGGATGATGGAACTAC
EST: gi|58598341|gb|CK008869.1|CK008869
EST:     TTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCA                         GTCCTCTGTTCAGCTTGGAAGGATGATGGAACTACTGTGTTCTCTGGAGGC
genomic: TTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCAgtatgatctc ... tttctatcagGTCCTCTGTTCAGCTTGGAAGGATGATGGAACTACTGTGTTCTCTGGAGGC
EST: gi|10794894|gb|AU108860.1|AU108860
EST:     TTGTTGGTGGGAGTAGTCAACCAAAGGCANCTATATCGCATGACCAGCCA                         GTCCTCTGTTCAGCTTGGAAGGATGATGGAACTACTGTGTTCTCTGGAGGC
genomic: TTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCAgtatgatctc ... tttctatcagGTCCTCTGTTCAGCTTGGAAGGATGATGGAACTACTGTGTTCTCTGGAGGC
EST: gi|25799251|gb|CA755212.1|CA755212
EST:     TTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCA                         GTCCTCTGTTCAGCTTGGAAGGATGATGGAACTACTGTGTTCTCTGGAGGC
genomic: TTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCAgtatgatctc ... tttctatcagGTCCTCTGTTCAGCTTGGAAGGATGATGGAACTACTGTGTTCTCTGGAGGC

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: 65 (upstream exon), 61 (downstream exon)
Score: 37

GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCAgtatgatctc ... tttctatcagGTCCTCTGTTCAGCTTGGAAGGATGATGGAACTACTGTGTTCTCTGGAGGCTGTGATAAACAAGTAAAAATGTGGCCTCTGTTGTCTGGTGGGCAGGCTC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCGGTGCTGGGAGATTGTTGGTGGGAGTAGTCAACCAAAGGCATCTATATCGCATGACCAGCCAgtatgatctcaatatttctctcaagaccacattcacataatgtacagtattgattttcctagtatttagtgtgctcattgatttgttttctatcag

- - - - - - - - - - TGGTGG