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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttttctcttaattcgccttaaccttctctagatccgaccctgactagcagcagcagtttgtttccaagaaattaaaaaaaatattttgctggttgcagTTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTGGCCGTGTCTCCTCCACAGGAAGGAAGGCACCGGGGATCTAGAGGAGGCC

Basic information

species Oryza sativa
transcript LOC_Os02g21250.1
intron # 1
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|24208139|gb|AU225166.1|AU225166
EST:     GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTG                         TTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
genomic: GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTGgtgagcatcc ... ctggttgcagTTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
EST: gi|88302037|gb|CI667883.1|CI667883
EST:     GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTG                         TTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
genomic: GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTGgtgagcatcc ... ctggttgcagTTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
EST: gi|88355724|gb|CI629008.1|CI629008
EST:     GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTG                         TTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
genomic: GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTGgtgagcatcc ... ctggttgcagTTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
EST: gi|88355715|gb|CI628999.1|CI628999
EST:     GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTG                         TTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
genomic: GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTGgtgagcatcc ... ctggttgcagTTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
EST: gi|88724896|gb|CI748155.1|CI748155
EST:     GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTG                         TTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
genomic: GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTGgtgagcatcc ... ctggttgcagTTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
EST: gi|163926048|gb|EG712328.1|EG712328
EST:     GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTG                         TTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
genomic: GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTGgtgagcatcc ... ctggttgcagTTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
EST: gi|88576575|gb|CI670720.1|CI670720
EST:     GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTG                         TTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
genomic: GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTGgtgagcatcc ... ctggttgcagTTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
EST: gi|88353711|gb|CI633102.1|CI633102
EST:     GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCGG                         TTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
genomic: GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTGgtgagcatcc ... ctggttgcagTTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
EST: gi|88571060|gb|CI662433.1|CI662433
EST:     GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTG                         TTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
genomic: GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTGgtgagcatcc ... ctggttgcagTTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
EST: gi|218496929|gb|FG959091.1|FG959091
EST:     GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTG                         TTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
genomic: GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTGgtgagcatcc ... ctggttgcagTTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
EST: gi|88719291|gb|CI742801.1|CI742801
EST:     GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTG                         TTTTGAGCCTGCATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
genomic: GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTGgtgagcatcc ... ctggttgcagTTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
EST: gi|163928617|gb|EG711178.1|EG711178
EST:     GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTG                         TTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTGCTGCTTTCGGTG
genomic: GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTGgtgagcatcc ... ctggttgcagTTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
EST: gi|88414612|gb|CI698719.1|CI698719
EST:     GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTG                         TTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
genomic: GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTGgtgagcatcc ... ctggttgcagTTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
EST: gi|88346751|gb|CI657302.1|CI657302
EST:     GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCGG                         TTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
genomic: GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTGgtgagcatcc ... ctggttgcagTTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
EST: gi|88345106|gb|CI628360.1|CI628360
EST:     GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTG                         TTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
genomic: GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTGgtgagcatcc ... ctggttgcagTTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
EST: gi|88572505|gb|CI664076.1|CI664076
EST:     GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTG                         TTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
genomic: GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTGgtgagcatcc ... ctggttgcagTTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
EST: gi|88325937|gb|CI649788.1|CI649788
EST:     GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTG                         TTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
genomic: GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTGgtgagcatcc ... ctggttgcagTTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
EST: gi|117248583|gb|CT862782.1|CT862782
EST:     GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTG                         TTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
genomic: GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTGgtgagcatcc ... ctggttgcagTTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
EST: gi|87012336|gb|CI293386.1|CI293386
EST:     GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTG                         TTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
genomic: GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTGgtgagcatcc ... ctggttgcagTTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
EST: gi|88327839|gb|CI648236.1|CI648236
EST:     GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTG                         TTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG
genomic: GGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTGgtgagcatcc ... ctggttgcagTTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTG

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), 68 (downstream exon)
Score: 11

CTCGCGACTCGCGAGCAGAGCAGGGTTGGTAGGGGCGCCCATCTCCATCCGGCGAGCAGAGCAGAGCGGAGGAGGTGCGCCATCGTCCCGCTGCATCCTGgtgagcatcc ... ctggttgcagTTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTGGCCGTGTCTCCTCCACAGGAAGGAAGGCACCGGGGATCTAGAGGAGGCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctagcagcagcagtttgtttccaagaaattaaaaaaaatattttgctggttgcagTTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTGGCCGTGTCTCCTCCACAGGAAGGAAGGCACCGGGGATCTAGAGGAGGCC
                                        ttttgct  CT-rich tract
             tttgtttccaagaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttttctcttaattcgccttaaccttctctagatccgaccctgactagcagcagcagtttgtttccaagaaattaaaaaaaatattttgctggttgcagTTTTGAGCCTGGATCTTGCCAAACAAGTGGTTGATCTTACTGCTTTCGGTGGCCGTGTCTCCTCCACAGGAAGGAAGGCACCGGGGATCTAGAGGAGGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - cctgact
- - - - - - - - - - - - - - - - - - - - - - - - -cagcagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa