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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACGTATCCACAAACCAAAGCCCCCCTTTAAAATCCGACACAAGAAACAGATCCAACCAATTCGCTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAGgtacggtgctcacttctctctcttctcctttcctttttttttggttgtttttagcggtggattttgggctccacgcgcgtcgcggggcggcaatcgcgtc...

Basic information

species Oryza sativa
transcript LOC_Os02g56850.1
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|88366537|gb|CI612361.1|CI612361
EST:     TCCAACCAATTCGCTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAG                         GGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
genomic: TCCAACCAATTCGCTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAGgtacggtgct ... tgcgcgttagGGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
EST: gi|88314032|gb|CI600034.1|CI600034
EST:     AATTCGCTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAG                         GGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
genomic: AATTCGCTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAGgtacggtgct ... tgcgcgttagGGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
EST: gi|29670415|gb|CB666690.1|CB666690
EST:     TCCAACCAATTCGCTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAG                         GGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
genomic: TCCAACCAATTCGCTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAGgtacggtgct ... tgcgcgttagGGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
EST: gi|88417483|gb|CI579144.1|CI579144
EST:     TCCAACCAATTCGCTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAG                         GGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
genomic: TCCAACCAATTCGCTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAGgtacggtgct ... tgcgcgttagGGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
EST: gi|88760896|gb|CI770452.1|CI770452
EST:     ATTCACTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAG                         GGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
genomic: ATTCGCTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAGgtacggtgct ... tgcgcgttagGGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
EST: gi|88352021|gb|CI626021.1|CI626021
EST:     AATTCGCTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAG                         GGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
genomic: AATTCGCTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAGgtacggtgct ... tgcgcgttagGGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
EST: gi|88337120|gb|CI628206.1|CI628206
EST:     AATTCGCTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAG                         GGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
genomic: AATTCGCTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAGgtacggtgct ... tgcgcgttagGGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
EST: gi|88430778|gb|CI596892.1|CI596892
EST:     CCAACCAATTCGCTCGCTTAAGCCTGCCGGCAAATCAACCCAACCCCAAG                         GGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
genomic: CCAACCAATTCGCTCGCTTAAGCC-GCCGGCAAATCAACCCAACCCCAAGgtacggtgct ... tgcgcgttagGGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
EST: gi|2443112|gb|C74883.1|C74883
EST:     AGCCGCCGGCAAATCAACCCAACCCCAAG                         GGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
genomic: AGCCGCCGGCAAATCAACCCAACCCCAAGgtacggtgct ... tgcgcgttagGGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
EST: gi|33658225|gb|CF280839.1|CF280839
EST:     TCCAACCAATTCGCTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAG                         GGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
genomic: TCCAACCAATTCGCTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAGgtacggtgct ... tgcgcgttagGGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
EST: gi|38469842|gb|CF953973.1|CF953973
EST:     TCCAACCAATTCGCTCGCTTAAGCCGCCGGCAAATCAACCCAGCCCCAAG                         GGTTTTTCGTGTGGTGTTGAGTGATCCATGGCTAGGAAGATGCTCAAGGAC
genomic: TCCAACCAATTCGCTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAGgtacggtgct ... tgcgcgttagGGTTTTTCGTGTGGTGTTGAG-GATCCATGGCTAGGAAGATGCTCAAGGAC
EST: gi|88760244|gb|CI769800.1|CI769800
EST:     ATTCACTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAG                         GGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
genomic: ATTCGCTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAGgtacggtgct ... tgcgcgttagGGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
EST: gi|426418|gb|D22281.1|D22281
EST:     AAGCCGCCGGCAAATCAACCCAACCCCAAG                         GGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
genomic: AAGCCGCCGGCAAATCAACCCAACCCCAAGgtacggtgct ... tgcgcgttagGGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
EST: gi|88396564|gb|CI601047.1|CI601047
EST:     AATTCGCTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAG                         GGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
genomic: AATTCGCTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAGgtacggtgct ... tgcgcgttagGGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
EST: gi|29680732|gb|CB677007.1|CB677007
EST:     TCCAACCAATTCGCTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAG                         GGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
genomic: TCCAACCAATTCGCTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAGgtacggtgct ... tgcgcgttagGGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
EST: gi|25802825|gb|CA758786.1|CA758786
EST:     CGCCGGCAAATCAACCCAACCCCAAG                         GGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
genomic: CGCCGGCAAATCAACCCAACCCCAAGgtacggtgct ... tgcgcgttagGGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
EST: gi|29675048|gb|CB671323.1|CB671323
EST:     CGCTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAG                         GGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
genomic: CGCTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAGgtacggtgct ... tgcgcgttagGGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
EST: gi|88726529|gb|CI750184.1|CI750184
EST:     TCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAG                         GGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
genomic: TCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAGgtacggtgct ... tgcgcgttagGGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
EST: gi|88389287|gb|CI598085.1|CI598085
EST:     AATTCGCTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAG                         GGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
genomic: AATTCGCTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAGgtacggtgct ... tgcgcgttagGGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
EST: gi|88417209|gb|CI576283.1|CI576283
EST:     TCGCTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAG                         GGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
genomic: TCGCTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAGgtacggtgct ... tgcgcgttagGGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
EST: gi|88744812|gb|CI768172.1|CI768172
EST:     AATTCGCTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAG                         GGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG
genomic: AATTCGCTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAGgtacggtgct ... tgcgcgttagGGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACG

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: 60 (upstream exon), 72 (downstream exon)
Score: 72

ACGTATCCACAAACCAAAGCCCCCCTTTAAAATCCGACACAAGAAACAGATCCAACCAATTCGCTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAGgtacggtgct ... tgcgcgttagGGTTTTTCGTGTGGTGTTGAGGATCCATGGCTAGGAAGATGCTCAAGGACGAGGAGGTGGAGGTGGCCGTCACCGACGGCGGGAGCTACGACTACGACCT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACGTATCCACAAACCAAAGCCCCCCTTTAAAATCCGACACAAGAAACAGATCCAACCAATTCGCTCGCTTAAGCCGCCGGCAAATCAACCCAACCCCAAGgtacggtgctcacttctctctcttctcctttcctttttttttggttgtttttagcggtggattttgggctccacgcgcgtcgcggggcggcaatcgcgtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcggtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccacgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggcggca