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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCAGAACTGGACATGGCTCAGACAGCAGTACTCGAAGTTGATGCTTCATGGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAGgtcaggctttgcttatttagcttctggttcagtacatccttctcgcatcactcccacgggcactagaactgatatcaggatcggctcaataacttaatga...

Basic information

species Oryza sativa
transcript LOC_Os11g03780.2
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|88727707|gb|CI749509.1|CI749509
EST:     GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAG                         GAAAT-AACCATGCCGGAGCTGGTGGGATATGGGNCGGAGCTTGTCAGTAA
genomic: GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAGgtcaggcttt ... aacatcacagGAAATTAACCATGCCGGAGCTGGTGGGATATGGG-CGGAGCTTGTCAGTAA
EST: gi|88405712|gb|CI609611.1|CI609611
EST:     GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAG                         GAAATTAATCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
genomic: GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAGgtcaggcttt ... aacatcacagGAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
EST: gi|88364204|gb|CI610548.1|CI610548
EST:     GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAG                         GAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
genomic: GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAGgtcaggcttt ... aacatcacagGAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
EST: gi|88695436|gb|CI737474.1|CI737474
EST:     GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAG                         GAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
genomic: GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAGgtcaggcttt ... aacatcacagGAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
EST: gi|88404761|gb|CI583568.1|CI583568
EST:     GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAG                         GAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTG
genomic: GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAGgtcaggcttt ... aacatcacagGAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTG
EST: gi|58671742|gb|CK060428.1|CK060428
EST:     GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAG                         GAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
genomic: GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAGgtcaggcttt ... aacatcacagGAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
EST: gi|88421573|gb|CI618697.1|CI618697
EST:     GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAG                         GAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCA
genomic: GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAGgtcaggcttt ... aacatcacagGAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCA
EST: gi|88692709|gb|CI736284.1|CI736284
EST:     GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAG                         GAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
genomic: GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAGgtcaggcttt ... aacatcacagGAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
EST: gi|58604955|gb|CK032988.1|CK032988
EST:     GGAACCTTTCTCGAAAGATCCCTGACACGCTGGGTGGATTGTCTTTCGAG                         GAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
genomic: GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAGgtcaggcttt ... aacatcacagGAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
EST: gi|88718003|gb|CI741513.1|CI741513
EST:     GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAG                         GAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
genomic: GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAGgtcaggcttt ... aacatcacagGAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
EST: gi|88314645|gb|CI606713.1|CI606713
EST:     GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAG                         GAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
genomic: GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAGgtcaggcttt ... aacatcacagGAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
EST: gi|88731532|gb|CI755145.1|CI755145
EST:     GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAG                         GAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
genomic: GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAGgtcaggcttt ... aacatcacagGAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
EST: gi|88723938|gb|CI745635.1|CI745635
EST:     GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAG                         GAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
genomic: GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAGgtcaggcttt ... aacatcacagGAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
EST: gi|88392471|gb|CI612945.1|CI612945
EST:     GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAG                         GAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
genomic: GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAGgtcaggcttt ... aacatcacagGAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
EST: gi|88372707|gb|CI612635.1|CI612635
EST:     GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAG                         GAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
genomic: GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAGgtcaggcttt ... aacatcacagGAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
EST: gi|88726971|gb|CI750626.1|CI750626
EST:     GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAG                         GAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
genomic: GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAGgtcaggcttt ... aacatcacagGAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
EST: gi|88314494|gb|CI604978.1|CI604978
EST:     GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAG                         GAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
genomic: GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAGgtcaggcttt ... aacatcacagGAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
EST: gi|88695959|gb|CI739534.1|CI739534
EST:     GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAG                         GAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
genomic: GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAGgtcaggcttt ... aacatcacagGAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
EST: gi|88311923|gb|CI577529.1|CI577529
EST:     GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAG                         GAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
genomic: GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAGgtcaggcttt ... aacatcacagGAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
EST: gi|88721230|gb|CI744529.1|CI744529
EST:     GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAG                         GAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
genomic: GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAGgtcaggcttt ... aacatcacagGAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
EST: gi|88719222|gb|CI742732.1|CI742732
EST:     GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAG                         GAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC
genomic: GGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAGgtcaggcttt ... aacatcacagGAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAAC

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: 71 (upstream exon), 55 (downstream exon)
Score: 35

TGCAGAACTGGACATGGCTCAGACAGCAGTACTCGAAGTTGATGCTTCATGGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAGgtcaggcttt ... aacatcacagGAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCAGAACTGGACATGGCTCAGACAGCAGTACTCGAAGTTGATGCTTCATGGAACCTTTCTCGAAAGATCCCTGACACGCTATTTGGATTGTTTTTCGAGgtcaggctttgcttatttagcttctggttcagtacatccttctcgcatcactcccacgggcactagaactgatatcaggatcggctcaataacttaatga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctcccac