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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttcgacatcttcatgaaattgtatttgtttttcctgtcccctatgaagttcaatcatcaattttgcacatatttatgcctttgttgtatattgctacagATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT

Basic information

species Oryza sativa
transcript LOC_Os04g40874.1
intron # 3
splice site 3'
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|88421242|gb|CI569087.1|CI569087
EST:     TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGG                         ATACCTCAAAGGAGCCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
genomic: TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGGgtatggtttc ... attgctacagATACCTCAAAGGAGCC-TCAGAAGAACATCTCTCAGACTTTTTGCAACAT
EST: gi|29663317|gb|CB659592.1|CB659592
EST:     TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGG                         ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
genomic: TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGGgtatggtttc ... attgctacagATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
EST: gi|88313812|gb|CI597443.1|CI597443
EST:     TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGG                         ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
genomic: TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGGgtatggtttc ... attgctacagATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
EST: gi|88449978|gb|CI572109.1|CI572109
EST:     TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGG                         ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
genomic: TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGGgtatggtttc ... attgctacagATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
EST: gi|58654814|gb|CK043494.1|CK043494
EST:     TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGG                         ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
genomic: TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGGgtatggtttc ... attgctacagATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
EST: gi|88719764|gb|CI743274.1|CI743274
EST:     TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGG                         ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
genomic: TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGGgtatggtttc ... attgctacagATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
EST: gi|88421660|gb|CI616985.1|CI616985
EST:     TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGG                         ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTG
genomic: TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGGgtatggtttc ... attgctacagATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTG
EST: gi|58611861|gb|CK039573.1|CK039573
EST:     TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGG                         ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
genomic: TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGGgtatggtttc ... attgctacagATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
EST: gi|88388045|gb|CI590321.1|CI590321
EST:     TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGG                         ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
genomic: TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGGgtatggtttc ... attgctacagATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
EST: gi|88305522|gb|CI630684.1|CI630684
EST:     TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGG                         ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGA
genomic: TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGGgtatggtttc ... attgctacagATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGA
EST: gi|88407965|gb|CI588994.1|CI588994
EST:     TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGG                         ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
genomic: TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGGgtatggtttc ... attgctacagATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
EST: gi|88430411|gb|CI567430.1|CI567430
EST:     TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGG                         ATACC-CAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
genomic: TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGGgtatggtttc ... attgctacagATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
EST: gi|88403389|gb|CI573112.1|CI573112
EST:     TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGG                         ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACATAT
genomic: TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGGgtatggtttc ... attgctacagATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACATAT
EST: gi|88409948|gb|CI571205.1|CI571205
EST:     TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGG                         ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
genomic: TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGGgtatggtttc ... attgctacagATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
EST: gi|29634314|gb|CB639323.1|CB639323
EST:     TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGG                         ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
genomic: TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGGgtatggtttc ... attgctacagATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
EST: gi|29614696|gb|CB619709.1|CB619709
EST:     TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGG                         ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
genomic: TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGGgtatggtttc ... attgctacagATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
EST: gi|88396043|gb|CI595591.1|CI595591
EST:     TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGG                         ATAC-TCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGGAACAT
genomic: TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGGgtatggtttc ... attgctacagATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
EST: gi|88421686|gb|CI569067.1|CI569067
EST:     ATGCGAGATCAAACCCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGG                         ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
genomic: ATGCGAGATCAAACC-TTTCTGATGATGGGTTAAGGGAACGCATTCGTGGgtatggtttc ... attgctacagATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
EST: gi|58608815|gb|CK036848.1|CK036848
EST:     ATGCGAGATCAAACCTTTCTGATGATGGGTTGAAGGGAACGCATTCGTGG                         ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
genomic: ATGCGAGATCAAACCTTTCTGATGATGGGTT-AAGGGAACGCATTCGTGGgtatggtttc ... attgctacagATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
EST: gi|88300652|gb|CI587456.1|CI587456
EST:     TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGG                         ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACATAT
genomic: TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGGgtatggtttc ... attgctacagATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACATAT
EST: gi|58670061|gb|CK058747.1|CK058747
EST:     TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGG                         ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
genomic: TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGGgtatggtttc ... attgctacagATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
EST: gi|29680803|gb|CB677078.1|CB677078
EST:     TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGG                         ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
genomic: TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGGgtatggtttc ... attgctacagATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
EST: gi|29635386|gb|CB640395.1|CB640395
EST:     TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGG                         ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
genomic: TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGGgtatggtttc ... attgctacagATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
EST: gi|88363865|gb|CI607175.1|CI607175
EST:     TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGG                         ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAAAAT
genomic: TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGGgtatggtttc ... attgctacagATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
EST: gi|163920079|gb|EG712021.1|EG712021
EST:     TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGG                         ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
genomic: TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGGgtatggtttc ... attgctacagATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
EST: gi|117243651|gb|CT843162.1|CT843162
EST:     TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGG                         ATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
genomic: TATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGGgtatggtttc ... attgctacagATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT

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: 70 (upstream exon), 49 (downstream exon)
Score: 58

GGATTTATACAATCAGGTGAAGTGCATATATTTGGGTATGCGAGATCAAACCTTTCTGATGATGGGTTAAGGGAACGCATTCGTGGgtatggtttc ... attgctacagATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagttcaatcatcaattttgcacatatttatgcctttgttgtatattgctacagATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT
                      acatatttat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgacatcttcatgaaattgtatttgtttttcctgtcccctatgaagttcaatcatcaattttgcacatatttatgcctttgttgtatattgctacagATACCTCAAAGGAGCCTCAGAAGAACATCTCTCAGACTTTTTGCAACAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - -cttcatg
- - - - - - - - - - - - - - - - - ctgtccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttttgca