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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAGTTGTTCTTTCTCATAGGAACTTAATCGCAAATGTAGCAGGATCAAGTGTGGTCATTAAGTTTTACCCATCTGATGTgtgaggagtttacattaaatctagattcatatctttctgctataacttaataaatttatatcatctctaaatgtttttgatagtagtcatgttgatatctctccacag

Basic information

species Oryza sativa
transcript LOC_Os11g04980.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g04980.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G176546_T01 (Zea mays), 5'ss of exon 2
GGAGTTGTTCTTTCTCATAGGAACTTAATCGCAAATGTAGCAGGATCAAGTGTGGTCATTAAGTTTTACCCATCTGATGTgtgaggagtttacat-taaatctagattcatatctttctgcta---taacttaataaatttatatcatctctaaatgtttttgatagtagtcatgttgatatctctccacag
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GGAGCTGTTCTTTCTCATGGGAACTTAATTGCAAATGTAGCAGGATCAAGCCTAAACATTAAGTTTTACCCCTCCGATGTgttagtattttgcatatacactcaaataaaattgtttgtgcttgatcagcttatccaattcacatctgcacttaacatttgtgaaaataactctgtggatcactctcctcag
















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|29679209|gb|CB675484.1|CB675484
EST:     GCAAATGTAGCAGGATCAAGTGTGGTCATTAAGTTTTACCCATCTGATGT                         GTACATCTCATATCTACCTTTAGCTCACATCTATGAGAGAGTTAACCAGAT
genomic: GCAAATGTAGCAGGATCAAGTGTGGTCATTAAGTTTTACCCATCTGATGTgtgaggagtt ... ctctccacagGTACATCTCATATCTACCTTTAGCTCACATCTATGAGAGAGTTAACCAGAT
EST: gi|29671403|gb|CB667678.1|CB667678
EST:     GCAAATGTAGCAGGATCAAGTGTGGTCATTAAGTTTTACCCATCTGATGT                         GTACATCTCATATCTACCTTTAGCTCACATCTATGAGAGAGTTAACCAGAT
genomic: GCAAATGTAGCAGGATCAAGTGTGGTCATTAAGTTTTACCCATCTGATGTgtgaggagtt ... ctctccacagGTACATCTCATATCTACCTTTAGCTCACATCTATGAGAGAGTTAACCAGAT
EST: gi|33676001|gb|CF304240.1|CF304240
EST:     GCAAATGTAGCAGGATCAAGTGTGGTCATTAAGTTTTACCCATCTGATGT                         GTACATCTCATATCTACCTTT
genomic: GCAAATGTAGCAGGATCAAGTGTGGTCATTAAGTTTTACCCATCTGATGTgtgaggagtt ... ctctccacagGTACATCTCATATCTACCTTT
EST: gi|58696224|gb|CK084911.1|CK084911
EST:     GCGAATGTAGCAGGATCAAGTGTGGTCATTAAGTTTTACCCATCTGATGT                         GTACATCTCATATC
genomic: GCAAATGTAGCAGGATCAAGTGTGGTCATTAAGTTTTACCCATCTGATGTgtgaggagtt ... ctctccacagGTACATCTCATATC
EST: gi|29679207|gb|CB675482.1|CB675482
EST:     GCAAATGTAGCAGGATCAAGTGTGGTCATTAAGTTTTACCCATCTGATGT                         GTACATCTCATATCTACCTTTAGCTCACATCTATGAGAGAGTTAACCAGAT
genomic: GCAAATGTAGCAGGATCAAGTGTGGTCATTAAGTTTTACCCATCTGATGTgtgaggagtt ... ctctccacagGTACATCTCATATCTACCTTTAGCTCACATCTATGAGAGAGTTAACCAGAT
EST: gi|58688175|gb|CK076862.1|CK076862
EST:     TTTA-CCATCTGATGT                         GTACATCTCATATCTACCTTTAGCTCACATCTATGAGAGAGTTAACCAGAT
genomic: TTTACCCATCTGATGTgtgaggagtt ... ctctccacagGTACATCTCATATCTACCTTTAGCTCACATCTATGAGAGAGTTAACCAGAT
EST: gi|58663800|gb|CK052486.1|CK052486
EST:     GCAAATGTAGCAGGATCAAGTGTGGTCATTAAGTTTTACCCATCTGATGT                         GTACATCTCATATCTACCTTTAGCTCACATCTATGAGAGAGTTAACCAGAT
genomic: GCAAATGTAGCAGGATCAAGTGTGGTCATTAAGTTTTACCCATCTGATGTgtgaggagtt ... ctctccacagGTACATCTCATATCTACCTTTAGCTCACATCTATGAGAGAGTTAACCAGAT
EST: gi|29670550|gb|CB666825.1|CB666825
EST:     GCAAATGTAGCAGGATCAAGTGTGGTCATTAAGTTTTACCCATCTGATGT                         GTACATCTCATATCTACCTTTAGCTCACATCTATGAGAGAGTTAACCAGAT
genomic: GCAAATGTAGCAGGATCAAGTGTGGTCATTAAGTTTTACCCATCTGATGTgtgaggagtt ... ctctccacagGTACATCTCATATCTACCTTTAGCTCACATCTATGAGAGAGTTAACCAGAT

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: 66 (upstream exon), 46 (downstream exon)
Score: 8

GGAGTTGTTCTTTCTCATAGGAACTTAATCGCAAATGTAGCAGGATCAAGTGTGGTCATTAAGTTTTACCCATCTGATGTgtgaggagtt ... ctctccacagGTACATCTCATATCTACCTTTAGCTCACATCTATGAGAGAGTTAACCAGATTGCACTGCTTCACTATGGAGTTGCCATTGGATTCTACCAAGGG




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