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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACGgtaagcacttacatgaacgagtgaatgatccacgaaaaatcagtggattgtgtttattttatatgcgtgttttataaggctggacttgctcgtggatgtaacag

Basic information

species Oryza sativa
transcript LOC_Os01g09000.1
intron # 2
splice site 5'
intron type U2

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|7332447|gb|AU085793.1|AU085793
EST:     GCTGGTATAAGTGGATGTGATAAAGCCGGTTGGGAACCTCCTGTACACG                         GTTNCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCCTGTACTCATT
genomic: GCTGGTATAAGTGGATGTGAT-AAGACGGTTGGGAACCTCCTGTACACGgtaagcactt ... gatgtaacagGTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCCTGTACTCATT
EST: gi|88356468|gb|CI624888.1|CI624888
EST:     GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG                         GTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCCCTGTACTCAT
genomic: GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACGgtaagcactt ... gatgtaacagGTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCC-TGTACTCAT
EST: gi|89161518|gb|CI099490.1|CI099490
EST:     GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG                         GTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCCTGTACTCATT
genomic: GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACGgtaagcactt ... gatgtaacagGTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCCTGTACTCATT
EST: gi|88994745|gb|CI036326.1|CI036326
EST:     GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG                         GTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCCTGTACTCATT
genomic: GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACGgtaagcactt ... gatgtaacagGTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCCTGTACTCATT
EST: gi|570024|gb|D40873.1|D40873
EST:     GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG                         GTTGCCACTAAATACCCAACCAATGCGCTT
genomic: GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACGgtaagcactt ... gatgtaacagGTTGCCACTAAATACCCAACCAATGCGCTT
EST: gi|58672280|gb|CK060966.1|CK060966
EST:     GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG                         GTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCCTGTACTCATT
genomic: GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACGgtaagcactt ... gatgtaacagGTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCCTGTACTCATT
EST: gi|88311944|gb|CI577550.1|CI577550
EST:     GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG                         GTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCCTGTACTCATT
genomic: GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACGgtaagcactt ... gatgtaacagGTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCCTGTACTCATT
EST: gi|88351919|gb|CI625919.1|CI625919
EST:     GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG                         GTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCCTGTACTCATT
genomic: GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACGgtaagcactt ... gatgtaacagGTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCCTGTACTCATT
EST: gi|86889728|gb|CI299926.1|CI299926
EST:     GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG                         GTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCCTGTACTCATT
genomic: GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACGgtaagcactt ... gatgtaacagGTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCCTGTACTCATT
EST: gi|86826937|gb|CI268818.1|CI268818
EST:     GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG                         GTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCCTGTACTCATT
genomic: GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACGgtaagcactt ... gatgtaacagGTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCCTGTACTCATT
EST: gi|88454226|gb|CI567831.1|CI567831
EST:     GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG                         GTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTC-TGTA-TCATT
genomic: GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACGgtaagcactt ... gatgtaacagGTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCCTGTACTCATT
EST: gi|88294826|gb|CI604698.1|CI604698
EST:     GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG                         GTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCCTGTACTCATT
genomic: GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACGgtaagcactt ... gatgtaacagGTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCCTGTACTCATT
EST: gi|58663041|gb|CK051727.1|CK051727
EST:     GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG                         GTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCCTGTACTCATT
genomic: GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACGgtaagcactt ... gatgtaacagGTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCCTGTACTCATT
EST: gi|58691015|gb|CK079702.1|CK079702
EST:     AGACGGTTGGGAACCTCCTGTACACG                         GTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCCTGTACTCATT
genomic: AGACGGTTGGGAACCTCCTGTACACGgtaagcactt ... gatgtaacagGTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCCTGTACTCATT
EST: gi|88903715|gb|CI089253.1|CI089253
EST:     GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG                         GTTGCCACTAAATACCCAACCAATGCGCTTGTCTATCGTCCTGTACTCATT
genomic: GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACGgtaagcactt ... gatgtaacagGTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCCTGTACTCATT
EST: gi|88346641|gb|CI623098.1|CI623098
EST:     GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG                         GTTGCCACTAAATACCCAACCAATGCGCTTGTTCATCGTCCTGT
genomic: GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACGgtaagcactt ... gatgtaacagGTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCCTGT
EST: gi|66921782|gb|CX108630.1|CX108630
EST:     GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG                         GTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCCTGTACTCATT
genomic: GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACGgtaagcactt ... gatgtaacagGTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCCTGTACTCATT
EST: gi|58671495|gb|CK060181.1|CK060181
EST:     GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACG                         GTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCCTGTACTCATT
genomic: GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACGgtaagcactt ... gatgtaacagGTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCCTGTACTCATT

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: 75 (upstream exon), 75 (downstream exon)
Score: 46

GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACGgtaagcactt ... gatgtaacagGTTGCCACTAAATACCCAACCAATGCGCTTGTCCATCGTCCTGTACTCATTGACTATATTGTGTCAACGAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGGTATAAGTGGATGTGATAAGACGGTTGGGAACCTCCTGTACACGgtaagcacttacatgaacgagtgaatgatccacgaaaaatcagtggattgtgtttattttatatgcgtgttttataaggctggacttgctcgtggatgtaacag

- - - -  AGTGGA