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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGACTCCAATGGTATATCTCAACAACATCGTCAAGGGATGTGTTGCCAATGTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAGgtacacattcgccgccctctctcctttcctttcctttccttgccttgctggactcaccttatacccccaatttcttttcag

Basic information

species Oryza sativa
transcript LOC_Os01g74650.1
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|88400288|gb|CI590978.1|CI590978
EST:     GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAG                         GATAGGATACAGTATGATTTCTGA
genomic: GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAGgtacacattc ... ttcttttcagGATAGGATACAGTATGATTTCTGA
EST: gi|88300958|gb|CI592138.1|CI592138
EST:     GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAG                         GATAGGATACAGTA
genomic: GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAGgtacacattc ... ttcttttcagGATAGGATACAGTA
EST: gi|88430337|gb|CI567356.1|CI567356
EST:     GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAG                         GATAGGATACAGTATGATTTCTGATGCGGAAGAGAAAGGCTTGATA
genomic: GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAGgtacacattc ... ttcttttcagGATAGGATACAGTATGATTTCTGATGCGGAAGAGAAAGGCTTGATA
EST: gi|88406356|gb|CI596483.1|CI596483
EST:     GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCA-GGACAG                         GATAGGATACAGTATGATTTCT
genomic: GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAGgtacacattc ... ttcttttcagGATAGGATACAGTATGATTTCT
EST: gi|88425870|gb|CI571770.1|CI571770
EST:     GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAG                         GATAGGATACAGTATGATTTCT
genomic: GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAGgtacacattc ... ttcttttcagGATAGGATACAGTATGATTTCT
EST: gi|88324363|gb|CI566176.1|CI566176
EST:     GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAG                         GATAGGATA-AGTATGATTTCTGATGCGGAAGAGAAAGGCTTGATAACTCC
genomic: GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAGgtacacattc ... ttcttttcagGATAGGATACAGTATGATTTCTGATGCGGAAGAGAAAGGCTTGATAACTCC
EST: gi|86829529|gb|CI286728.1|CI286728
EST:     GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAG                         GATAGGATACAGTATGATTTCTGATGCGGAAGAGAAAGGCTTGATAACTCC
genomic: GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAGgtacacattc ... ttcttttcagGATAGGATACAGTATGATTTCTGATGCGGAAGAGAAAGGCTTGATAACTCC
EST: gi|88410128|gb|CI573367.1|CI573367
EST:     GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAG                         GATAGGATACAGT
genomic: GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAGgtacacattc ... ttcttttcagGATAGGATACAGT
EST: gi|58608600|gb|CK036633.1|CK036633
EST:     GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAG                         GATAGGATACAGTATGATTTCTGATGCGGAAGAGAAAGGCTTGATAACTCC
genomic: GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAGgtacacattc ... ttcttttcagGATAGGATACAGTATGATTTCTGATGCGGAAGAGAAAGGCTTGATAACTCC
EST: gi|88385698|gb|CI566560.1|CI566560
EST:     GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAG                         GATAGGATACAGTATGATTTCTGATGCGGAAGAGAAAGGCTTGATAACTCC
genomic: GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAGgtacacattc ... ttcttttcagGATAGGATACAGTATGATTTCTGATGCGGAAGAGAAAGGCTTGATAACTCC
EST: gi|88424191|gb|CI581746.1|CI581746
EST:     GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAG                         GATAGGATACAGTATGATTT
genomic: GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAGgtacacattc ... ttcttttcagGATAGGATACAGTATGATTT
EST: gi|13806171|gb|AU181396.1|AU181396
EST:     GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAG                         GATAGGATACAGTTTGATTTCTGATGCGGAAGAGAAAGGCTTG
genomic: GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAGgtacacattc ... ttcttttcagGATAGGATACAGTATGATTTCTGATGCGGAAGAGAAAGGCTTG
EST: gi|88389409|gb|CI600578.1|CI600578
EST:     GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAG                         GATAGGATACAGTATGATTTCTGATG
genomic: GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAGgtacacattc ... ttcttttcagGATAGGATACAGTATGATTTCTGATG
EST: gi|88430584|gb|CI569607.1|CI569607
EST:     GTCGCTGCTCAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAG                         GATAGGATACCGTATGATTTCTGATGCGGCAGACAACGGCTTGATACCTCC
genomic: GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAGgtacacattc ... ttcttttcagGATAGGATACAGTATGATTTCTGATGCGGAAGAGAAAGGCTTGATAACTCC
EST: gi|33678770|gb|CF307009.1|CF307009
EST:     GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAG                         GATAGGATACAGTATGATTTCTGATGCGGAAGAGAAAGGCTTGATAACTCC
genomic: GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAGgtacacattc ... ttcttttcagGATAGGATACAGTATGATTTCTGATGCGGAAGAGAAAGGCTTGATAACTCC
EST: gi|88431199|gb|CI574370.1|CI574370
EST:     GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAG                         GATAGGATACAGTATGATTTCTGA
genomic: GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAGgtacacattc ... ttcttttcagGATAGGATACAGTATGATTTCTGA
EST: gi|88430623|gb|CI569646.1|CI569646
EST:     GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAG                         GATAGGATACAGTATGATTTCTGATGCGGAAGAGAGAGGGTTGATAACTCC
genomic: GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAGgtacacattc ... ttcttttcagGATAGGATACAGTATGATTTCTGATGCGGAAGAGAAAGGCTTGATAACTCC
EST: gi|88403644|gb|CI575528.1|CI575528
EST:     GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCA-GGACAG                         GATAGGATA-AGTATGATTTCTGATGCGGAAGAGAAAGGCTTGATAACTC-
genomic: GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAGgtacacattc ... ttcttttcagGATAGGATACAGTATGATTTCTGATGCGGAAGAGAAAGGCTTGATAACTCC
EST: gi|88411818|gb|CI571310.1|CI571310
EST:     GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAG                         GATAGGATACAGTATGATTTCTGATGCGGAAGAGAA
genomic: GTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAGgtacacattc ... ttcttttcagGATAGGATACAGTATGATTTCTGATGCGGAAGAGAA

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: 73 (upstream exon), 60 (downstream exon)
Score: 88

AGACTCCAATGGTATATCTCAACAACATCGTCAAGGGATGTGTTGCCAATGTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAGgtacacattc ... ttcttttcagGATAGGATACAGTATGATTTCTGATGCGGAAGAGAAAGGCTTGATAACTCCTGGAAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGACTCCAATGGTATATCTCAACAACATCGTCAAGGGATGTGTTGCCAATGTCGCTGCTAAGCTCGAGATTATGGAGCCCTGTTGCAGTGTCAAGGACAGgtacacattcgccgccctctctcctttcctttcctttccttgccttgctggactcaccttatacccccaatttcttttcag

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