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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtttcttcatcttgttccataaattttgaagagccaccaaattttctaaccctgttctgtgataatgcagATACTGTGGAACATGATGAGCTGTAGTCCTGTAGAGGATAGACAGGTGTATATGCGACATGTCGTAAGGCAGATAATTTTGCAGTTTATTTGTTCCATAC

Basic information

species Oryza sativa
transcript LOC_Os02g35700.2
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|88541810|gb|CI471103.1|CI471103
EST:     TCTGCAGCCAGAGAAATTTCATTTTTCTTTGGAGATGTTAGATCTG                         ATACTGTGGAACATGATGAGCTGTAGTCCTGTAGAGGATAGACAGGTGTAT
genomic: TCTGCAGCCAGAGAAATTTCATTTTTCTTTGGAGATGTTAGATCTGgttggtttct ... gataatgcagATACTGTGGAACATGATGAGCTGTAGTCCTGTAGAGGATAGACAGGTGTAT
EST: gi|88546587|gb|CI476239.1|CI476239
EST:     CCAGAGAAATTTCATTTTTCTTTGGAGATGTTAGATCTG                         ATACTGTGGAACATGATGAGCTGTAGTCCTGTAGAGGATAGACAGGTGTAT
genomic: CCAGAGAAATTTCATTTTTCTTTGGAGATGTTAGATCTGgttggtttct ... gataatgcagATACTGTGGAACATGATGAGCTGTAGTCCTGTAGAGGATAGACAGGTGTAT
EST: gi|86415016|gb|CI069419.1|CI069419
EST:     ACAATCTGCAGCCAGAGAAATTTCATTTTTCTTNGGAGATGTTAGATCTG                         ATACTGTGGAACATGATGAGCTGTAGTCCTGTAGAGGATAGACAGGTGTAT
genomic: ACAATCTGCAGCCAGAGAAATTTCATTTTTCTTTGGAGATGTTAGATCTGgttggtttct ... gataatgcagATACTGTGGAACATGATGAGCTGTAGTCCTGTAGAGGATAGACAGGTGTAT
EST: gi|88545410|gb|CI474971.1|CI474971
EST:     CATTTTTCTTTGGAGATGTTAGATCTG                         ATACTGTGGAACATGATGAGCTGTAGTCCTGTAGAGGATAGACAGGTGTAT
genomic: CATTTTTCTTTGGAGATGTTAGATCTGgttggtttct ... gataatgcagATACTGTGGAACATGATGAGCTGTAGTCCTGTAGAGGATAGACAGGTGTAT
EST: gi|15852143|gb|BI804939.1|BI804939
EST:     ACAATCTGCAGCCAGAGAAATTTCATTTTTCTTTGGAGATGTTAGATCTG                         ATACTGTGGAACATGATGAGCTGTAGTCCTGTAGAGGATAGACAGGTGTAT
genomic: ACAATCTGCAGCCAGAGAAATTTCATTTTTCTTTGGAGATGTTAGATCTGgttggtttct ... gataatgcagATACTGTGGAACATGATGAGCTGTAGTCCTGTAGAGGATAGACAGGTGTAT
EST: gi|88551382|gb|CI481435.1|CI481435
EST:     AGAGAAATTTCATTTTTCTTTGGAGATGTTAGATCTG                         ATACTGTGGAACATGATGAGCTGTAGTCCTGTAGAGGATAGACAGGTGTAT
genomic: AGAGAAATTTCATTTTTCTTTGGAGATGTTAGATCTGgttggtttct ... gataatgcagATACTGTGGAACATGATGAGCTGTAGTCCTGTAGAGGATAGACAGGTGTAT

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: 68 (upstream exon), 61 (downstream exon)
Score: 14

ATGTGTGGAGTGGACTCAGAGAAAAACTGTGTGCATGGTTCAGATTCACCACAATCTGCAGCCAGAGAAATTTCATTTTTCTTTGGAGATGTTAGATCTGgttggtttct ... gataatgcagATACTGTGGAACATGATGAGCTGTAGTCCTGTAGAGGATAGACAGGTGTATATGCGACATGTCGTAAGGCAGATAATTTTGCAGTTTATTTGTTCCATAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccataaattttgaagagccaccaaattttctaaccctgttctgtgataatgcagATACTGTGGAACATGATGAGCTGTAGTCCTGTAGAGGATAGACAGGTGTATATGCGACATGTCGTAAGGCAGATAATTTTGCAGTTTATTTGTTCCATAC
                            ttctaac  putative branch site (score: 14)
                       aaattttctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtttcttcatcttgttccataaattttgaagagccaccaaattttctaaccctgttctgtgataatgcagATACTGTGGAACATGATGAGCTGTAGTCCTGTAGAGGATAGACAGGTGTATATGCGACATGTCGTAAGGCAGATAATTTTGCAGTTTATTTGTTCCATAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT