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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agctgcaatgcatctttctttctgctaatggtaatagcaagtttaatcctttccattatggatcttcttaatctattcacacttggttcatcccttgcagATCGTGGCCTTTGCGTGTGGACTTGTGCATTACAAGTCTTCAGCCAAAAGGCATCCAAGCATGCAACCTTGGAATTTGGGCGG

Basic information

species Oryza sativa
transcript LOC_Os05g09360.1
intron # 18
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|8324505|gb|AU091654.1|AU091654
EST:     GTCTTGCTCGTGTGTATGCNCTGTGGAATATTACATCATTGGTTAATGTT                         ATCGTGGCCTTTGCGTGTGGACTTGTGCATTACAAGTCTTCAGCCAAAAGG
genomic: GTCTTGCTCGTGTGTATGCGCTGTGGAATATTACATCATTGGTTAATGTTgtgagtactc ... tcccttgcagATCGTGGCCTTTGCGTGTGGACTTGTGCATTACAAGTCTTCAGCCAAAAGG
EST: gi|29616296|gb|CB621308.1|CB621308
EST:     GTCTTGCTCGTGTGTATGCGCTGTGGAATATTACATCATTGGTTAATGTT                         ATCGTGGCCTTTGCGTGTGGACTTGTGCATTACAAGTCTTCAGCCAAAAGG
genomic: GTCTTGCTCGTGTGTATGCGCTGTGGAATATTACATCATTGGTTAATGTTgtgagtactc ... tcccttgcagATCGTGGCCTTTGCGTGTGGACTTGTGCATTACAAGTCTTCAGCCAAAAGG
EST: gi|88905396|gb|CI712695.1|CI712695
EST:     GTCTTGCTCGTGTGTATGCGCTGTGGAATATTACATCATTGGTTAATGTT                         ATCGTGNGC-TTTGCGTGTGGACTTGTGCATTACAAGTCTTCAGCCAAAAG
genomic: GTCTTGCTCGTGTGTATGCGCTGTGGAATATTACATCATTGGTTAATGTTgtgagtactc ... tcccttgcagATCGTG-GCCTTTGCGTGTGGACTTGTGCATTACAAGTCTTCAGCCAAAAG
EST: gi|88670113|gb|CI724229.1|CI724229
EST:     GTCTTGCTCGTGTGTATGCGCTGTGGAATATTACATCATTGGTTAATGTT                         ATCGTGGCCTTTGCGTGTGGACTTGTGCATTACAAGTCTTCAGCCAAAAGG
genomic: GTCTTGCTCGTGTGTATGCGCTGTGGAATATTACATCATTGGTTAATGTTgtgagtactc ... tcccttgcagATCGTGGCCTTTGCGTGTGGACTTGTGCATTACAAGTCTTCAGCCAAAAGG
EST: gi|88669953|gb|CI724069.1|CI724069
EST:     GTCTTGCTCGTGTGTATGCGCTGTGGAATATTACATCATTGGTTAATGTT                         ATCGTGGCCTTTGCGTGTGGACTTGTGCATTACAAGTCTTCACCCAAAAGG
genomic: GTCTTGCTCGTGTGTATGCGCTGTGGAATATTACATCATTGGTTAATGTTgtgagtactc ... tcccttgcagATCGTGGCCTTTGCGTGTGGACTTGTGCATTACAAGTCTTCAGCCAAAAGG
EST: gi|88672075|gb|CI726191.1|CI726191
EST:     GTCTTGCTCGTGTGTATGCGCTGTGGAATATTACATCATTGGTTAATGTT                         ATCGTGGCCTTTGCGTGTGGACTTGTGCATTACAAGTCTTCAGCCAAAAGG
genomic: GTCTTGCTCGTGTGTATGCGCTGTGGAATATTACATCATTGGTTAATGTTgtgagtactc ... tcccttgcagATCGTGGCCTTTGCGTGTGGACTTGTGCATTACAAGTCTTCAGCCAAAAGG
EST: gi|88669249|gb|CI719387.1|CI719387
EST:     GTCTTGCTCGTGTGTATGCGCTGTGGAATATTACATCATTGGTTAATGTT                         ATCGTGGCCTTTGCGTGTGGACTTGTGCATTACAAGTCTTCAGCCAAAAGG
genomic: GTCTTGCTCGTGTGTATGCGCTGTGGAATATTACATCATTGGTTAATGTTgtgagtactc ... tcccttgcagATCGTGGCCTTTGCGTGTGGACTTGTGCATTACAAGTCTTCAGCCAAAAGG
EST: gi|58611103|gb|CK038815.1|CK038815
EST:     TGCTCGTGTGTATGCGCTGTGGAATATTACATCATTGGTTAATGTT                         ATCGTGGCCTTTGCGTGTGGACTTGTGCATTACAAGTCTTCAGCCAAAAGG
genomic: TGCTCGTGTGTATGCGCTGTGGAATATTACATCATTGGTTAATGTTgtgagtactc ... tcccttgcagATCGTGGCCTTTGCGTGTGGACTTGTGCATTACAAGTCTTCAGCCAAAAGG
EST: gi|88973622|gb|CI718050.1|CI718050
EST:     GTCTTGCTCGTGTGTATGCGCTGTGGAATATTACATCATTGGTTAATGTT                         ATCGTGGCCTTTGCGTGTGGACTTGTGCATTACAAGTCTTCAGCCAAAAGG
genomic: GTCTTGCTCGTGTGTATGCGCTGTGGAATATTACATCATTGGTTAATGTTgtgagtactc ... tcccttgcagATCGTGGCCTTTGCGTGTGGACTTGTGCATTACAAGTCTTCAGCCAAAAGG
EST: gi|88665993|gb|CI716149.1|CI716149
EST:     GTCTTGCTCGTGTGTATGCGCTGTGGAATATTACATCATTGGTTAATGTT                         ATCGTGGCCTTTGCGTGTGGACTTGTGCATTACAAGTCTTCAGCCAAAAGG
genomic: GTCTTGCTCGTGTGTATGCGCTGTGGAATATTACATCATTGGTTAATGTTgtgagtactc ... tcccttgcagATCGTGGCCTTTGCGTGTGGACTTGTGCATTACAAGTCTTCAGCCAAAAGG
EST: gi|88667639|gb|CI722378.1|CI722378
EST:     GTCTTGCTCGTGTGTATGCGCTGTGGAATATTACATCATTGGTTAATGTT                         ATCGTGGCCTTTGCGTGTGGACTTGTGCATTACAAGTCTTCAGCCAAAAGG
genomic: GTCTTGCTCGTGTGTATGCGCTGTGGAATATTACATCATTGGTTAATGTTgtgagtactc ... tcccttgcagATCGTGGCCTTTGCGTGTGGACTTGTGCATTACAAGTCTTCAGCCAAAAGG
EST: gi|88668494|gb|CI722056.1|CI722056
EST:     GTCTTGCTCGTGTGTATGCGCTGTGGAATATTACATCATTGGTTAATGTT                         ATCGTGGCCTTTGCGTGTGGACTTGTGCATTACAAGTCTTCAGCCAAAAGG
genomic: GTCTTGCTCGTGTGTATGCGCTGTGGAATATTACATCATTGGTTAATGTTgtgagtactc ... tcccttgcagATCGTGGCCTTTGCGTGTGGACTTGTGCATTACAAGTCTTCAGCCAAAAGG

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

TCCTGCTGGGATAAATGCTCTATTTAGTCATGGACCACGGCGGTCAGCAGGTCTTGCTCGTGTGTATGCGCTGTGGAATATTACATCATTGGTTAATGTTgtgagtactc ... tcccttgcagATCGTGGCCTTTGCGTGTGGACTTGTGCATTACAAGTCTTCAGCCAAAAGGCATCCAAGCATGCAACCTTGGAATTTGGGCGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcctttccattatggatcttcttaatctattcacacttggttcatcccttgcagATCGTGGCCTTTGCGTGTGGACTTGTGCATTACAAGTCTTCAGCCAAAAGGCATCCAAGCATGCAACCTTGGAATTTGGGCGG
                    tcttaat  putative branch site (score: 5)
                                         ttcatccctt  putative PPT
                      ttaatctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agctgcaatgcatctttctttctgctaatggtaatagcaagtttaatcctttccattatggatcttcttaatctattcacacttggttcatcccttgcagATCGTGGCCTTTGCGTGTGGACTTGTGCATTACAAGTCTTCAGCCAAAAGGCATCCAAGCATGCAACCTTGGAATTTGGGCGG

- - -caatgca
- - - - - - - - - -ttctgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcacac