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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCGGCGCCGGCGCTCGTCCTGCCGCCACCGCCGCGGCCGCCTGAGCCGATCCCATCCATCCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCCTGgttagcacatcctccttcccatctctctctacccacgctctcactatatcgaatttgcgttaaccctagcttcttctgttctagaaattccttaatacta...

Basic information

species Oryza sativa
transcript LOC_Os08g07960.1
intron # 1
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|88394469|gb|CI605810.1|CI605810
EST:     TCCCATCCATCCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCC--                         --T--GGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCAAACATGAATCC
genomic: TCCCATCCATCCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCCTGgttagcacat ... tgaattgaagGATCAGGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCAAACATGAATCC
EST: gi|33793654|gb|CF322711.1|CF322711
EST:     TCCCATCCATCCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCCTG                         GATCAGGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCAAACATGAATCC
genomic: TCCCATCCATCCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCCTGgttagcacat ... tgaattgaagGATCAGGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCAAACATGAATCC
EST: gi|88451540|gb|CI565593.1|CI565593
EST:     TCCCATCCATCCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCCTG                         GATCAGGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCAAACATGAATCC
genomic: TCCCATCCATCCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCCTGgttagcacat ... tgaattgaagGATCAGGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCAAACATGAATCC
EST: gi|88357567|gb|CI623621.1|CI623621
EST:     TCCCATCCATCCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCCTG                         GATCAGGTAGAAGGAGATGGCGATTCTTGGTCTTGCCCCAAACATGAATCC
genomic: TCCCATCCATCCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCCTGgttagcacat ... tgaattgaagGATCAGGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCAAACATGAATCC
EST: gi|29615879|gb|CB620891.1|CB620891
EST:     TCCCATCCATGCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCC--                         --T--GGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCAAACATGAATCC
genomic: TCCCATCCATCCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCCTGgttagcacat ... tgaattgaagGATCAGGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCAAACATGAATCC
EST: gi|88356897|gb|CI620785.1|CI620785
EST:     TCCCATCCATCCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCCTG                         GATCAGGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCAAACATGAATCC
genomic: TCCCATCCATCCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCCTGgttagcacat ... tgaattgaagGATCAGGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCAAACATGAATCC
EST: gi|88399681|gb|CI583415.1|CI583415
EST:     TCCCATCCATCCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCCTG                         GATCAGGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCAAACATGAATCC
genomic: TCCCATCCATCCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCCTGgttagcacat ... tgaattgaagGATCAGGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCAAACATGAATCC
EST: gi|88314161|gb|CI602493.1|CI602493
EST:     TCCCATCCATCCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCCTG                         GATCAGGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCACACATGAATCC
genomic: TCCCATCCATCCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCCTGgttagcacat ... tgaattgaagGATCAGGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCAAACATGAATCC
EST: gi|33795033|gb|CF323392.1|CF323392
EST:     TCCCATCCATCCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCCTG                         GATCAGGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCAAACATGAATCC
genomic: TCCCATCCATCCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCCTGgttagcacat ... tgaattgaagGATCAGGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCAAACATGAATCC
EST: gi|29681300|gb|CB677575.1|CB677575
EST:     TCCCATCCATCCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCCTG                         GATCAGGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCAAACATGAATCC
genomic: TCCCATCCATCCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCCTGgttagcacat ... tgaattgaagGATCAGGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCAAACATGAATCC
EST: gi|88397869|gb|CI583187.1|CI583187
EST:     TCCCATCCATCCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCCTG                         GATCAGGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCAAACATGAATCC
genomic: TCCCATCCATCCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCCTGgttagcacat ... tgaattgaagGATCAGGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCAAACATGAATCC
EST: gi|88417412|gb|CI579073.1|CI579073
EST:     TCCCATCCATCCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCCTG                         GATCAGGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCAAACATGAATCC
genomic: TCCCATCCATCCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCCTGgttagcacat ... tgaattgaagGATCAGGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCAAACATGAATCC
EST: gi|88394449|gb|CI605790.1|CI605790
EST:     TCCCATCCATCCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCCTG                         GATCAGGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCAAACATGAATCC
genomic: TCCCATCCATCCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCCTGgttagcacat ... tgaattgaagGATCAGGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCAAACATGAATCC
EST: gi|10794894|gb|AU108860.1|AU108860
EST:     TCCCATCCATCCCGCGAGCNAGCGAGCGCTTCCGCCGCATCCTGGTCCTG                         GATCAGGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCAAACATGAATCC
genomic: TCCCATCCATCCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCCTGgttagcacat ... tgaattgaagGATCAGGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCAAACATGAATCC
EST: gi|25799251|gb|CA755212.1|CA755212
EST:     TCCCATCCATCCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCCTG                         GATCAGGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCAAACATGAATCC
genomic: TCCCATCCATCCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCCTGgttagcacat ... tgaattgaagGATCAGGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCAAACATGAATCC
EST: gi|88417428|gb|CI579089.1|CI579089
EST:     TCCCATCCATCCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCCTG                         GATCAGGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCAAACATGAATCC
genomic: TCCCATCCATCCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCCTGgttagcacat ... tgaattgaagGATCAGGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCAAACATGAATCC

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), 56 (downstream exon)
Score: 41

GGCGGCGCCGGCGCTCGTCCTGCCGCCACCGCCGCGGCCGCCTGAGCCGATCCCATCCATCCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCCTGgttagcacat ... tgaattgaagGATCAGGTAGAAGGAGATGGCGACTCTTGGTCTTGCCCCAAACATGAATCCAAACAAGTCATTTGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGCGGCGCCGGCGCTCGTCCTGCCGCCACCGCCGCGGCCGCCTGAGCCGATCCCATCCATCCCGCGAGCGAGCGAGCGCTTCCGCCGCATCCTGGTCCTGgttagcacatcctccttcccatctctctctacccacgctctcactatatcgaatttgcgttaaccctagcttcttctgttctagaaattccttaatacta

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctctctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccacgc