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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttattccagtgcatagctcttgcatcttattctgtgaattaccatgtactatctgaagttgtgaattgatctgcatagagtgtttgcctttattttatagATGCCTTCTTGGAGACCCTCACAAGTCACAACCAGTTCAACTGAAGTGGGCGACTTTCATAATGCATCTGATTCTGAACACTGGGGTTGCATTTAGTTAC

Basic information

species Oryza sativa
transcript LOC_Os02g01710.2
intron # 7
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|86497902|gb|CI140535.1|CI140535
EST:     GGACCATTGATGCATTGCTGACTGCTGAGCTCTGCGTTGGGTTTTATAAT                         ATGCCTTCTTGGAGACCCTCACAAGTCACAACCAGTTCAACTGAAGTGGGC
genomic: GGACCATTGATGCATTGCTGACTGCTGAGCTCTGCGTTGGGTTTTATAATgtatgtatgg ... tattttatagATGCCTTCTTGGAGACCCTCACAAGTCACAACCAGTTCAACTGAAGTGGGC
EST: gi|88558912|gb|CI489444.1|CI489444
EST:     GGACCATTGATGCATTGCTGACTGCTGAGCTCTGCGTTGGGTTTTATAAT                         ATGCCTTCTTGGAGACCCTCACAAGTCACAACCAGTTCAACTGAAGTGGGC
genomic: GGACCATTGATGCATTGCTGACTGCTGAGCTCTGCGTTGGGTTTTATAATgtatgtatgg ... tattttatagATGCCTTCTTGGAGACCCTCACAAGTCACAACCAGTTCAACTGAAGTGGGC
EST: gi|86498521|gb|CI141154.1|CI141154
EST:     GGACCATTGATGCATTGCTGACTGCTGAGCTCTGCGTTGGGTTTTATAAT                         ATGCCTTCTTGGAGACCCTCACAAGTCACAACCAGTTCAACTGAAGTGGGC
genomic: GGACCATTGATGCATTGCTGACTGCTGAGCTCTGCGTTGGGTTTTATAATgtatgtatgg ... tattttatagATGCCTTCTTGGAGACCCTCACAAGTCACAACCAGTTCAACTGAAGTGGGC
EST: gi|88831540|gb|CI083934.1|CI083934
EST:     GGACCATTGATGCATTGCTGACTGCTGAGCTCTGCGTTGGGTTTTATAAT                         ATGCCTTCTTGGAGACCCTCACAAGTCACAACCAGTTCAACTGAAGTGGGC
genomic: GGACCATTGATGCATTGCTGACTGCTGAGCTCTGCGTTGGGTTTTATAATgtatgtatgg ... tattttatagATGCCTTCTTGGAGACCCTCACAAGTCACAACCAGTTCAACTGAAGTGGGC
EST: gi|88845414|gb|CI084339.1|CI084339
EST:     GGACCATTGATGCATTGCTGACTGCTGAGCTCTGCGTTGGGTTTTATAAT                         ATGCCTTCTTGGAGACCCTCACAAGTCACAACCAGTTCAACTGAAGTGGGC
genomic: GGACCATTGATGCATTGCTGACTGCTGAGCTCTGCGTTGGGTTTTATAATgtatgtatgg ... tattttatagATGCCTTCTTGGAGACCCTCACAAGTCACAACCAGTTCAACTGAAGTGGGC
EST: gi|86504655|gb|CI147288.1|CI147288
EST:     GACACATTGATGCATTGCTGACTGCTGAGCTCTGCGTTGGGTTTTATAAT                         ATGCCTTCTTGGAGACCCTCACAAGTCACAACCAGTTCAACTGAAGTGGGC
genomic: GAC-CATTGATGCATTGCTGACTGCTGAGCTCTGCGTTGGGTTTTATAATgtatgtatgg ... tattttatagATGCCTTCTTGGAGACCCTCACAAGTCACAACCAGTTCAACTGAAGTGGGC
EST: gi|88841179|gb|CI080633.1|CI080633
EST:     GGACCATTGATGCATTGCTGACTGCTGAGCTCTGCGTTGGGTTTTATAAT                         ATGCCTTCTTGGAGACCCTCACAAGTCACAACCAGTTCAACTGAAGTGGGC
genomic: GGACCATTGATGCATTGCTGACTGCTGAGCTCTGCGTTGGGTTTTATAATgtatgtatgg ... tattttatagATGCCTTCTTGGAGACCCTCACAAGTCACAACCAGTTCAACTGAAGTGGGC

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: 73 (upstream exon), 75 (downstream exon)
Score: 5

AATACATAGACTACAAGGCTTGGGATGCTCTTCCCTGCTTGGAGAAACGTGGACCATTGATGCATTGCTGACTGCTGAGCTCTGCGTTGGGTTTTATAATgtatgtatgg ... tattttatagATGCCTTCTTGGAGACCCTCACAAGTCACAACCAGTTCAACTGAAGTGGGCGACTTTCATAATGCATCTGATTCTGAACACTGGGGTTGCATTTAGTTAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtactatctgaagttgtgaattgatctgcatagagtgtttgcctttattttatagATGCCTTCTTGGAGACCCTCACAAGTCACAACCAGTTCAACTGAAGTGGGCGACTTTCATAATGCATCTGATTCTGAACACTGGGGTTGCATTTAGTTAC
                  aattgat  putative branch site (score: 5)
                                     tttgcctttatttt  putative PPT
                                           tttattttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttattccagtgcatagctcttgcatcttattctgtgaattaccatgtactatctgaagttgtgaattgatctgcatagagtgtttgcctttattttatagATGCCTTCTTGGAGACCCTCACAAGTCACAACCAGTTCAACTGAAGTGGGCGACTTTCATAATGCATCTGATTCTGAACACTGGGGTTGCATTTAGTTAC

- - - - gtgcata
- - - - - - - - -tcttgca
- - - - - - - - - - - - - -tattctg
- - - - - - - - - - - - - - - - - - - - - catgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atctgca