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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcccaacttataattaaggattatataatataaaccaatagagtactcaagatatcattaaatttatccttttctacttaattttacagTTCAACGAAATGGCGTACCAATTGGACAGCAG

Basic information

species Oryza sativa
transcript LOC_Os03g49610.1
intron # 8
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|58657560|gb|CK046240.1|CK046240
EST:     TCAGCAAGTAGCAACTAGCTACTCATCTGATTGGCATGTTTCATTTATCT                         TTCAACGAAATGGCGTACCAATTGGACAG
genomic: TCAGCAAGCAGCAACTAGCTACTCATCTGATTGGCATGTTTCATTTATCTgtaagttccc ... aattttacagTTCAACGAAATGGCGTACCAATTGGACAG
EST: gi|27554361|gb|CA998261.1|CA998261
EST:     TCAGCAAGCAGCAACTAGCTACTCATCTGATTGGCATGTTTCATTTATCT                         TTCAACGAAATGGCGTACCAATTGGACAGCAG
genomic: TCAGCAAGCAGCAACTAGCTACTCATCTGATTGGCATGTTTCATTTATCTgtaagttccc ... aattttacagTTCAACGAAATGGCGTACCAATTGGACAGCAG
EST: gi|58669788|gb|CK058474.1|CK058474
EST:     TCAGCAAGCAGCAACTAGCTACTCATCTGATTGGCATGTTTCATTTATCT                         TTCAACGAAATGGCGTACCAATTGGACAGCAG
genomic: TCAGCAAGCAGCAACTAGCTACTCATCTGATTGGCATGTTTCATTTATCTgtaagttccc ... aattttacagTTCAACGAAATGGCGTACCAATTGGACAGCAG
EST: gi|58596985|gb|CK007513.1|CK007513
EST:     TCAGCAAGCAGCAACTAGCTACTCATCTGATTGGCATGTTTCATTTATCT                         TTCAACGAAATGGCGTACCAATTGGACAGCAG
genomic: TCAGCAAGCAGCAACTAGCTACTCATCTGATTGGCATGTTTCATTTATCTgtaagttccc ... aattttacagTTCAACGAAATGGCGTACCAATTGGACAGCAG
EST: gi|58673908|gb|CK062594.1|CK062594
EST:     TCAGCAAGCAGCAACTAGCTACTCATCTGATTGGCATGTTTCATTTATCT                         TTCAACGAAATGGCGTACCAATTGGACAGCAG
genomic: TCAGCAAGCAGCAACTAGCTACTCATCTGATTGGCATGTTTCATTTATCTgtaagttccc ... aattttacagTTCAACGAAATGGCGTACCAATTGGACAGCAG
EST: gi|58660033|gb|CK048713.1|CK048713
EST:     TCAGCAAGCAGCAACTAGCTACTCATCTGATTGGCATGTTTCATTTATCT                         TTCAACGAAATGGCGTACCAATTGGACAGCAG
genomic: TCAGCAAGCAGCAACTAGCTACTCATCTGATTGGCATGTTTCATTTATCTgtaagttccc ... aattttacagTTCAACGAAATGGCGTACCAATTGGACAGCAG
EST: gi|163925553|gb|EG715398.1|EG715398
EST:     TCAGCAAG-AGCAACTAGCTACTCATCTGATTGGCATGTTTCATTTATCT                         TTCAACGAAATGGCGTACCAATTGGACAGCAG
genomic: TCAGCAAGCAGCAACTAGCTACTCATCTGATTGGCATGTTTCATTTATCTgtaagttccc ... aattttacagTTCAACGAAATGGCGTACCAATTGGACAGCAG
EST: gi|58674306|gb|CK062992.1|CK062992
EST:     TCAGCAAGCAGCAACTAGCTACTCATCTGATTGGCATGTTTCATTTATCT                         TTCAACGAAATGGCGTACCAATTGGACAGCAG
genomic: TCAGCAAGCAGCAACTAGCTACTCATCTGATTGGCATGTTTCATTTATCTgtaagttccc ... aattttacagTTCAACGAAATGGCGTACCAATTGGACAGCAG
EST: gi|58674546|gb|CK063233.1|CK063233
EST:     TCAGCAAGCAGCAACTAGCTACTCATCTGATTGGCATGTTTCATTTATCT                         TTCAACGAAATGGCGTACCAATTGGACAGCAG
genomic: TCAGCAAGCAGCAACTAGCTACTCATCTGATTGGCATGTTTCATTTATCTgtaagttccc ... aattttacagTTCAACGAAATGGCGTACCAATTGGACAGCAG
EST: gi|58604470|gb|CK014998.1|CK014998
EST:     TCAGCAAGCAGCAACTAGCTACTCATCTGATTGGCATGTTTCATTTATCT                         TTCAACGAAATGGCGTACCAATTGGACAGCAG
genomic: TCAGCAAGCAGCAACTAGCTACTCATCTGATTGGCATGTTTCATTTATCTgtaagttccc ... aattttacagTTCAACGAAATGGCGTACCAATTGGACAGCAG
EST: gi|58597512|gb|CK008040.1|CK008040
EST:     TCAGCAAGCAGCAACTAGCTACTCATCTGATTGGCATGTTTCATTTATCT                         TTCAACGAAATGGCGTACCAATTGGACAGCAG
genomic: TCAGCAAGCAGCAACTAGCTACTCATCTGATTGGCATGTTTCATTTATCTgtaagttccc ... aattttacagTTCAACGAAATGGCGTACCAATTGGACAGCAG
EST: gi|58598545|gb|CK009073.1|CK009073
EST:     TCAGCAAGCAGCAACTAGCTACTCATCTGATTGGCATGTTTCATTTATCT                         TTCAACGAAATGGCGTACCAATTGGACAGCAG
genomic: TCAGCAAGCAGCAACTAGCTACTCATCTGATTGGCATGTTTCATTTATCTgtaagttccc ... aattttacagTTCAACGAAATGGCGTACCAATTGGACAGCAG
EST: gi|58668081|gb|CK056767.1|CK056767
EST:     TCAGCAAGCAGCAACTAGCTACTCATCTGATTGGCATGTTTCATTTATCT                         TTCAACGAAATGGCGTACCAATTGGACAGCAG
genomic: TCAGCAAGCAGCAACTAGCTACTCATCTGATTGGCATGTTTCATTTATCTgtaagttccc ... aattttacagTTCAACGAAATGGCGTACCAATTGGACAGCAG
EST: gi|33684008|gb|CF312247.1|CF312247
EST:     TCAGCAAGCAGCAACTAGCTACTCATCTGATTGGCATGTTTCATTTATCT                         TTCAACGAAATGGCGTACCAATTGGACAGCAG
genomic: TCAGCAAGCAGCAACTAGCTACTCATCTGATTGGCATGTTTCATTTATCTgtaagttccc ... aattttacagTTCAACGAAATGGCGTACCAATTGGACAGCAG
EST: gi|27554359|gb|CA998259.1|CA998259
EST:     TCAGCAAGCAGCAACTAGCTACTCATCTGATTGGCATGTTTCATTTATCT                         TTCAACGAAATGGCGTACCAATTGGACAGCAG
genomic: TCAGCAAGCAGCAACTAGCTACTCATCTGATTGGCATGTTTCATTTATCTgtaagttccc ... aattttacagTTCAACGAAATGGCGTACCAATTGGACAGCAG
EST: gi|58671037|gb|CK059723.1|CK059723
EST:     TCAGCAAGCAGCAACTAGCTACTCATCTGATTGGCATGTTTCATTTATCT                         TTCAACGAAATGGCGTACCAATTGGACAGCAG
genomic: TCAGCAAGCAGCAACTAGCTACTCATCTGATTGGCATGTTTCATTTATCTgtaagttccc ... aattttacagTTCAACGAAATGGCGTACCAATTGGACAGCAG

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), 69 (downstream exon)
Score: 25

TTTGGGATCAATCAATATACTGCTAACTACATGGCAGACCAACCAGCACCTCAGCAAGCAGCAACTAGCTACTCATCTGATTGGCATGTTTCATTTATCTgtaagttccc ... aattttacagTTCAACGAAATGGCGTACCAATTGGACAGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaatagagtactcaagatatcattaaatttatccttttctacttaattttacagTTCAACGAAATGGCGTACCAATTGGACAGCAG
                                         acttaat  putative branch site (score: 25)
                                tccttttctactta  CT-rich tract
                 atatcattaaatttat  TA-rich tract