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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgaatgtttcttcttgatcttctcatgtaatcaagtatggtttgcacaatgcactgctgaatttgggcctggcctgattacaccatttgttcatttcagACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTATGCGTCATGGGTGCAGTGACGTTGCAATACTGCTGGCAAATGGTATGGC

Basic information

species Oryza sativa
transcript LOC_Os02g17280.1
intron # 5
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|88268165|gb|CI377902.1|CI377902
EST:     GAAGTGATCAAGTATTTGTCCCACTTGTTCATCTGATTGCTTCTGTAATG                         ACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
genomic: GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATGgtaagaacta ... ttcatttcagACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
EST: gi|86546412|gb|CI186618.1|CI186618
EST:     GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATG                         ACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
genomic: GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATGgtaagaacta ... ttcatttcagACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
EST: gi|88255900|gb|CI354724.1|CI354724
EST:     GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATG                         ACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
genomic: GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATGgtaagaacta ... ttcatttcagACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
EST: gi|88296751|gb|CI540103.1|CI540103
EST:     GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATG                         ACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
genomic: GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATGgtaagaacta ... ttcatttcagACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
EST: gi|88205852|gb|CI205701.1|CI205701
EST:     GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATG                         ACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
genomic: GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATGgtaagaacta ... ttcatttcagACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
EST: gi|88488734|gb|CI426005.1|CI426005
EST:     GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATG                         ACACTAATCAATCTTGCACCTNNNNNNNCTGCGTAATTGGTACACCACTAT
genomic: GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATGgtaagaacta ... ttcatttcagACACTAATCAATCTTGCACCT--GGGGGCTGCGTAATTGGTACACCACTAT
EST: gi|89187835|gb|CI009819.1|CI009819
EST:     GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATG                         ACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
genomic: GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATGgtaagaacta ... ttcatttcagACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
EST: gi|86886214|gb|CI321250.1|CI321250
EST:     GAAATGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATG                         ACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
genomic: GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATGgtaagaacta ... ttcatttcagACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
EST: gi|88273370|gb|CI393776.1|CI393776
EST:     GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATG                         ACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
genomic: GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATGgtaagaacta ... ttcatttcagACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
EST: gi|396941389|gb|HO188598.1|HO188598
EST:     GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATG                         ACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA
genomic: GAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATGgtaagaacta ... ttcatttcagACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTA

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: 69 (upstream exon), 75 (downstream exon)
Score: 26

CCACACATTCTCAATGATTATTGCTTTTAATGGGTACGACGAGAGAAAGAGAAGTGATCAAGTATTTGTCCCAGTTGTTCATCTGATTGCTTCTGTAATGgtaagaacta ... ttcatttcagACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTATGCGTCATGGGTGCAGTGACGTTGCAATACTGCTGGCAAATGGTATGGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacaatgcactgctgaatttgggcctggcctgattacaccatttgttcatttcagACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTATGCGTCATGGGTGCAGTGACGTTGCAATACTGCTGGCAAATGGTATGGC
                           gcctgat  putative branch site (score: 26)
                                             ttcatttc  putative PPT
             tgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaatgtttcttcttgatcttctcatgtaatcaagtatggtttgcacaatgcactgctgaatttgggcctggcctgattacaccatttgttcatttcagACACTAATCAATCTTGCACCTGGGGGCTGCGTAATTGGTACACCACTATTATGCGTCATGGGTGCAGTGACGTTGCAATACTGCTGGCAAATGGTATGGC

gtgaatg
- - - - - cttcttg
- - - - - - - - - - - - catgtaa
- - - - - - - - - - - - - - - - - - - - gtttgca
- - - - - - - - - - - - - - - - - - - - - - - -caatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gggcctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcctgat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatttg