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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttattttgtccatttatactagtatacatacttgcagccacatattcatccatccttgtgctaatgaatatctgtgcatgcactactttctttatctaatattttgcactgtgtgtttcatgctgttgcagCCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACATCCAAGATTTAAGAGGAAATATGATGACCTGTTCATTGAGCGCACAATCT

Basic information

species Oryza sativa
transcript LOC_Os04g46390.3
intron # 6
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|29644137|gb|CB649144.1|CB649144
EST:     GAATGCAACATGGCCAAAAAATTGTATTCCAAGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACAT
genomic: GAATGCAACATGGCCAAAAAATTGTATTCCAAGGTGAAGCTGATGAAGCTgtaagtttat ... gctgttgcagCCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACAT
EST: gi|218494336|gb|FG947221.1|FG947221
EST:     GAATGCAACATGGCCAAAAAATTGTATTCCAAGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACAT
genomic: GAATGCAACATGGCCAAAAAATTGTATTCCAAGGTGAAGCTGATGAAGCTgtaagtttat ... gctgttgcagCCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACAT
EST: gi|8858764|gb|AU096082.1|AU096082
EST:     GAATGCAACATGGCCAAAAAATTGTATTCCAAGGTGAAGCTGATGAAGCT                         CCT-ATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACAT
genomic: GAATGCAACATGGCCAAAAAATTGTATTCCAAGGTGAAGCTGATGAAGCTgtaagtttat ... gctgttgcagCCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACAT
EST: gi|29678522|gb|CB674797.1|CB674797
EST:     GAATGCAACATGGCCAAAAAATTGTATTCCAAGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACAT
genomic: GAATGCAACATGGCCAAAAAATTGTATTCCAAGGTGAAGCTGATGAAGCTgtaagtttat ... gctgttgcagCCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACAT
EST: gi|25798325|gb|CA754286.1|CA754286
EST:     GAATGCAACATGGCCAAAAAATTGTATTCCAAGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGATATAGTATNTATCTTGCAAGTTAAGGTACAT
genomic: GAATGCAACATGGCCAAAAAATTGTATTCCAAGGTGAAGCTGATGAAGCTgtaagtttat ... gctgttgcagCCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACAT
EST: gi|29644138|gb|CB649145.1|CB649145
EST:     AAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACAT
genomic: AAGCTGATGAAGCTgtaagtttat ... gctgttgcagCCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACAT
EST: gi|29643237|gb|CB648244.1|CB648244
EST:     AAAATTGTATTCCAAGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACAT
genomic: AAAATTGTATTCCAAGGTGAAGCTGATGAAGCTgtaagtttat ... gctgttgcagCCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACAT
EST: gi|29663532|gb|CB659807.1|CB659807
EST:     GAATGCAACATGGCCAAAAAATTGTATTCCAAGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACAT
genomic: GAATGCAACATGGCCAAAAAATTGTATTCCAAGGTGAAGCTGATGAAGCTgtaagtttat ... gctgttgcagCCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACAT
EST: gi|27577316|gb|CB000011.1|CB000011
EST:     GAATGCAACATGGCCAAAAAATTGTATTCCAAGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACAT
genomic: GAATGCAACATGGCCAAAAAATTGTATTCCAAGGTGAAGCTGATGAAGCTgtaagtttat ... gctgttgcagCCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACAT
EST: gi|29645124|gb|CB650131.1|CB650131
EST:     GAATGCAACATGGCCAAAAAATTGTATTCCAAGGTGAAGCTGATGAAGCT                         CCTGATACAGTGA
genomic: GAATGCAACATGGCCAAAAAATTGTATTCCAAGGTGAAGCTGATGAAGCTgtaagtttat ... gctgttgcagCCTGATACAGTGA
EST: gi|29668765|gb|CB665040.1|CB665040
EST:     GCTGATGAAGCT                         CCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACAT
genomic: GCTGATGAAGCTgtaagtttat ... gctgttgcagCCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACAT
EST: gi|29685950|gb|CB682225.1|CB682225
EST:     GAATGCAACATGGCCAAAAAATTGTATTCCAAGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACAT
genomic: GAATGCAACATGGCCAAAAAATTGTATTCCAAGGTGAAGCTGATGAAGCTgtaagtttat ... gctgttgcagCCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACAT
EST: gi|29678573|gb|CB674848.1|CB674848
EST:     GAATGCAACATGGCCAAAAAATTGTATTCCAAGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACAT
genomic: GAATGCAACATGGCCAAAAAATTGTATTCCAAGGTGAAGCTGATGAAGCTgtaagtttat ... gctgttgcagCCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACAT
EST: gi|29643292|gb|CB648299.1|CB648299
EST:     GAATGCAACATGGCCAAAAAATTGTATTCCAAGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACAT
genomic: GAATGCAACATGGCCAAAAAATTGTATTCCAAGGTGAAGCTGATGAAGCTgtaagtttat ... gctgttgcagCCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACAT
EST: gi|29683515|gb|CB679790.1|CB679790
EST:     GAATGCAACATGGCCAAAAAATTGTATTCCAAGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACAT
genomic: GAATGCAACATGGCCAAAAAATTGTATTCCAAGGTGAAGCTGATGAAGCTgtaagtttat ... gctgttgcagCCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACAT
EST: gi|29670818|gb|CB667093.1|CB667093
EST:     CAAAAAATTGTATTCCAAGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACAT
genomic: CAAAAAATTGTATTCCAAGGTGAAGCTGATGAAGCTgtaagtttat ... gctgttgcagCCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACAT
EST: gi|700654|gb|D46945.1|D46945
EST:     GAATGCAACATGGCCAAAAAATTGTATTCCAAGGTGAAGCTGATGAAGCT                         CCT-ATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACAT
genomic: GAATGCAACATGGCCAAAAAATTGTATTCCAAGGTGAAGCTGATGAAGCTgtaagtttat ... gctgttgcagCCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACAT
EST: gi|29670817|gb|CB667092.1|CB667092
EST:     GAATGCAACATGGCCAAAAAATTGTATTCCAAGGTGAAGCTGATGAAGCT                         CCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACAT
genomic: GAATGCAACATGGCCAAAAAATTGTATTCCAAGGTGAAGCTGATGAAGCTgtaagtttat ... gctgttgcagCCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACAT

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: 74 (upstream exon), 75 (downstream exon)
Score: 176

TAGCAAAGTTATTCAGGAGAAAAAGGTGCTTGAGGTTCATATTGAGAAGGGAATGCAACATGGCCAAAAAATTGTATTCCAAGGTGAAGCTGATGAAGCTgtaagtttat ... gctgttgcagCCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACATCCAAGATTTAAGAGGAAATATGATGACCTGTTCATTGAGCGCACAATCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgcactactttctttatctaatattttgcactgtgtgtttcatgctgttgcagCCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACATCCAAGATTTAAGAGGAAATATGATGACCTGTTCATTGAGCGCACAATCT
                 atctaat  putative branch site (score: 176)
       tactttctttatctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttattttgtccatttatactagtatacatacttgcagccacatattcatccatccttgtgctaatgaatatctgtgcatgcactactttctttatctaatattttgcactgtgtgtttcatgctgttgcagCCTGATACAGTGACAGGAGATATAGTATTTATCTTGCAAGTTAAGGTACATCCAAGATTTAAGAGGAAATATGATGACCTGTTCATTGAGCGCACAATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA