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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggaagtttactaatttttggttgcattgcaagtttgaggtagtggcttctaatgtatgaatccacctcatttgttagGTCCTTGGAGATTCAAAAAGCACTGTACAGGATTGAACTGTACAGACAAGGTATATCAAGGCGGGCATATTGATGGAAGATCTGAGAAGCCAGTTGGGTT

Basic information

species Oryza sativa
transcript LOC_Os03g62730.3
intron # 4
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|8527221|gb|AU092036.1|AU092036
EST:     CTCGAACCTTACCTCGCCAATCTTCAGCTGTCTAGCGCATTGTTCAAGTG                         GTCCTTGGAGATTCAAAAAGCACTGTACAGGATTGAACTGTACAGACAAGG
genomic: CTCGAACCTTACCTCGCCAATCTTCAGCTGTCTAGCGCATTGTTCAAGTGgtaaggaagt ... catttgttagGTCCTTGGAGATTCAAAAAGCACTGTACAGGATTGAACTGTACAGACAAGG
EST: gi|86835542|gb|CI347999.1|CI347999
EST:     CTCGAACCTTACCTCGCCAATCTTCAGCTGTCTAGCGCATTGTTCAAGTG                         GTCCTTGGAGATTCAAAAAGCACTGTACAGGATTGAACTGTACAGACAAGG
genomic: CTCGAACCTTACCTCGCCAATCTTCAGCTGTCTAGCGCATTGTTCAAGTGgtaaggaagt ... catttgttagGTCCTTGGAGATTCAAAAAGCACTGTACAGGATTGAACTGTACAGACAAGG
EST: gi|8527217|gb|AU092032.1|AU092032
EST:     CTCGAACCTTACCTCGCCAATCTTCAGCTGTCTAGCGCATTGTTCAAGTG                         GTCCTTGGAGATTCAAAAAGCACTGTACAGGATTGAACTGTACAGACAAGG
genomic: CTCGAACCTTACCTCGCCAATCTTCAGCTGTCTAGCGCATTGTTCAAGTGgtaaggaagt ... catttgttagGTCCTTGGAGATTCAAAAAGCACTGTACAGGATTGAACTGTACAGACAAGG
EST: gi|88998115|gb|CI038000.1|CI038000
EST:     CTCGAACCTTACCTCGCCAATCTTCAGCTGTCTAGCGCATTGTTCAAGTG                         GTCCTTGGAGATTCAAAAAGCACTGTACAGGATTGAACTGTACAGACAAGG
genomic: CTCGAACCTTACCTCGCCAATCTTCAGCTGTCTAGCGCATTGTTCAAGTGgtaaggaagt ... catttgttagGTCCTTGGAGATTCAAAAAGCACTGTACAGGATTGAACTGTACAGACAAGG
EST: gi|89177886|gb|CI391065.1|CI391065
EST:     CAATCTTCAGCTGTCTAGCGCATTGTTCAAGTG                         GTCCTTGGAGATTCAAAAAGCACTGTACAGGATTGAACTGTACAGACAAGG
genomic: CAATCTTCAGCTGTCTAGCGCATTGTTCAAGTGgtaaggaagt ... catttgttagGTCCTTGGAGATTCAAAAAGCACTGTACAGGATTGAACTGTACAGACAAGG
EST: gi|29628052|gb|CB633063.1|CB633063
EST:     CTCGAACCTTACCTCGCCAATCTTCAGCTGTCTAGCGCATTGTTCAAGTG                         GTCCTTGGAGATTCAAAAAGCATTGTACAGGATTGAACTGTACAGACAAGG
genomic: CTCGAACCTTACCTCGCCAATCTTCAGCTGTCTAGCGCATTGTTCAAGTGgtaaggaagt ... catttgttagGTCCTTGGAGATTCAAAAAGCACTGTACAGGATTGAACTGTACAGACAAGG
EST: gi|88271300|gb|CI387353.1|CI387353
EST:     CTCGAACCTTACCTCGCCAATCTTCAGCTGTCTAGCGCATTGTTCAAGTG                         GTCCTTGGAGATTCAAAAAACACTGTACAGGATTGAACTGTACAGACAAGG
genomic: CTCGAACCTTACCTCGCCAATCTTCAGCTGTCTAGCGCATTGTTCAAGTGgtaaggaagt ... catttgttagGTCCTTGGAGATTCAAAAAGCACTGTACAGGATTGAACTGTACAGACAAGG
EST: gi|88259193|gb|CI363486.1|CI363486
EST:     AATCTTCAGCTGTCTAGCGCATTGTTCAAGTG                         GTCCTTGGAGATTCAAAAAGCACTGTACAGGATTGAACTGTACAGACAAGG
genomic: AATCTTCAGCTGTCTAGCGCATTGTTCAAGTGgtaaggaagt ... catttgttagGTCCTTGGAGATTCAAAAAGCACTGTACAGGATTGAACTGTACAGACAAGG

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: 59 (upstream exon), 75 (downstream exon)
Score: 17

GGAAGAGATGGCATCAGCAAAAGCAACGAGTGGAGCAGCTGTGCTTGTCTCTCGAACCTTACCTCGCCAATCTTCAGCTGTCTAGCGCATTGTTCAAGTGgtaaggaagt ... catttgttagGTCCTTGGAGATTCAAAAAGCACTGTACAGGATTGAACTGTACAGACAAGGTATATCAAGGCGGGCATATTGATGGAAGATCTGAGAAGCCAGTTGGGTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcattgcaagtttgaggtagtggcttctaatgtatgaatccacctcatttgttagGTCCTTGGAGATTCAAAAAGCACTGTACAGGATTGAACTGTACAGACAAGGTATATCAAGGCGGGCATATTGATGGAAGATCTGAGAAGCCAGTTGGGTT
                        ttctaat  putative branch site (score: 17)
                                      tccacctc  putative PPT
                           taatgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggaagtttactaatttttggttgcattgcaagtttgaggtagtggcttctaatgtatgaatccacctcatttgttagGTCCTTGGAGATTCAAAAAGCACTGTACAGGATTGAACTGTACAGACAAGGTATATCAAGGCGGGCATATTGATGGAAGATCTGAGAAGCCAGTTGGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC