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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTATgtcagtccgccctcccttctcttctcttgttctttttatttccccttctttctgttacttattattaagggcgatttgaatactaatctgcttccttggctgcag

Basic information

species Oryza sativa
transcript LOC_Os01g01700.1
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|87010441|gb|CI283516.1|CI283516
EST:     TATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTAT                         GCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
genomic: TATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTATgtcagtccgc ... ttggctgcagGCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
EST: gi|87028533|gb|CI265932.1|CI265932
EST:     TATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTAT                         GCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
genomic: TATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTATgtcagtccgc ... ttggctgcagGCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
EST: gi|86597337|gb|CI280474.1|CI280474
EST:     CTGCGCCATCTGCCGCAACCACATCATGGATCTAT                         GCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
genomic: CTGCGCCATCTGCCGCAACCACATCATGGATCTATgtcagtccgc ... ttggctgcagGCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
EST: gi|88486358|gb|CI423629.1|CI423629
EST:     CCATCTGCCGCAACCACATCATGGATCTAT                         GCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
genomic: CCATCTGCCGCAACCACATCATGGATCTATgtcagtccgc ... ttggctgcagGCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
EST: gi|86530369|gb|CI170575.1|CI170575
EST:     CATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTAT                         GCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
genomic: TATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTATgtcagtccgc ... ttggctgcagGCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
EST: gi|86525235|gb|CI165441.1|CI165441
EST:     CGCCATCTGCCGCAACCACATCATGGATCTAT                         GCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
genomic: CGCCATCTGCCGCAACCACATCATGGATCTATgtcagtccgc ... ttggctgcagGCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
EST: gi|9865650|gb|AU101400.1|AU101400
EST:     TATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTAT                         GCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
genomic: TATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTATgtcagtccgc ... ttggctgcagGCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
EST: gi|89170244|gb|CI039521.1|CI039521
EST:     TATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTAT                         GCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
genomic: TATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTATgtcagtccgc ... ttggctgcagGCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
EST: gi|88239603|gb|CI240080.1|CI240080
EST:     TATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTAT                         GCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
genomic: TATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTATgtcagtccgc ... ttggctgcagGCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
EST: gi|89165245|gb|CI255302.1|CI255302
EST:     TATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTAT                         GCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
genomic: TATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTATgtcagtccgc ... ttggctgcagGCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
EST: gi|88264264|gb|CI368038.1|CI368038
EST:     ACATCATGGATCTAT                         GCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
genomic: ACATCATGGATCTATgtcagtccgc ... ttggctgcagGCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
EST: gi|88979016|gb|CI025534.1|CI025534
EST:     TCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTAT                         GCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
genomic: TCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTATgtcagtccgc ... ttggctgcagGCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
EST: gi|86419648|gb|CI054449.1|CI054449
EST:     ACTGCGCCATCTGCCGCAACCACATCATGGATCTAT                         GCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
genomic: ACTGCGCCATCTGCCGCAACCACATCATGGATCTATgtcagtccgc ... ttggctgcagGCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
EST: gi|88559135|gb|CI489688.1|CI489688
EST:     CAACTGCGCCATCTGCCNCAACCACATCATGGATCTAT                         GCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
genomic: CAACTGCGCCATCTGCCGCAACCACATCATGGATCTATgtcagtccgc ... ttggctgcagGCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
EST: gi|88214117|gb|CI213966.1|CI213966
EST:     GATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTAT                         GCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
genomic: TATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTATgtcagtccgc ... ttggctgcagGCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
EST: gi|86854819|gb|CI260887.1|CI260887
EST:     TATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTAT                         GCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
genomic: TATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTATgtcagtccgc ... ttggctgcagGCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
EST: gi|88844742|gb|CI021317.1|CI021317
EST:     TATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTAT                         GCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
genomic: TATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTATgtcagtccgc ... ttggctgcagGCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
EST: gi|700261|gb|D46552.1|D46552
EST:     TATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTAT                         GCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTNAGGAGTGCACTG
genomic: TATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTATgtcagtccgc ... ttggctgcagGCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
EST: gi|88208384|gb|CI208233.1|CI208233
EST:     TATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTAT                         GCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
genomic: TATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTATgtcagtccgc ... ttggctgcagGCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
EST: gi|88506675|gb|CI434181.1|CI434181
EST:     CGCCATCTGCCGCAACCACATCATGGATCTAT                         GCATCGAGTGCCA-GCGAAGCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
genomic: CGCCATCTGCCGCAACCACATCATGGATCTATgtcagtccgc ... ttggctgcagGCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
EST: gi|88279001|gb|CI400001.1|CI400001
EST:     CAACCACATCATGGATCTAT                         GCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
genomic: CAACCACATCATGGATCTATgtcagtccgc ... ttggctgcagGCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
EST: gi|89170150|gb|CI039427.1|CI039427
EST:     TATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTAT                         GCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
genomic: TATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTATgtcagtccgc ... ttggctgcagGCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
EST: gi|86523241|gb|CI163447.1|CI163447
EST:     TATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTAT                         GCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
genomic: TATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTATgtcagtccgc ... ttggctgcagGCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
EST: gi|88202160|gb|CI202515.1|CI202515
EST:     TATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTAT                         GCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
genomic: TATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTATgtcagtccgc ... ttggctgcagGCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
EST: gi|86253813|gb|CI058540.1|CI058540
EST:     NATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTAT                         GCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
genomic: TATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTATgtcagtccgc ... ttggctgcagGCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
EST: gi|86413387|gb|CI067792.1|CI067792
EST:     AATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTAT                         GCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
genomic: TATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTATgtcagtccgc ... ttggctgcagGCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
EST: gi|58599948|gb|CK010476.1|CK010476
EST:     TATCGTCGTCGACCACTGCGCCATCTGCCGCAACCACATCATGGATCTAT                         GCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
genomic: TATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTATgtcagtccgc ... ttggctgcagGCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
EST: gi|86434462|gb|CI094805.1|CI094805
EST:     NATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTAT                         GCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
genomic: TATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTATgtcagtccgc ... ttggctgcagGCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
EST: gi|86828745|gb|CI280591.1|CI280591
EST:     CAACCACATCATGGATCTAT                         GCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
genomic: CAACCACATCATGGATCTATgtcagtccgc ... ttggctgcagGCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
EST: gi|86533593|gb|CI173799.1|CI173799
EST:     CATGGATCTAT                         GCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG
genomic: CATGGATCTATgtcagtccgc ... ttggctgcagGCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTG

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: 51 (upstream exon), 72 (downstream exon)
Score: 28

ATATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTATgtcagtccgc ... ttggctgcagGCATCGAGTGCCAGGCGAACCAGGCCAGCGCCACCAGTGAGGAGTGCACTGTCGCTTGGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATATCGTCGTCGACAACTGCGCCATCTGCCGCAACCACATCATGGATCTATgtcagtccgccctcccttctcttctcttgttctttttatttccccttctttctgttacttattattaagggcgatttgaatactaatctgcttccttggctgcag

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