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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaggagtttacattaaatctagattcatatctttctgctataacttaataaatttatatcatctctaaatgtttttgatagtagtcatgttgatatctctccacagGTACATCTCATATCTACCTTTAGCTCACATCTATGAGAGAGTTAACCAGATTGCACTGCTTCACTATGGAGTTGCCATTGGATTCTACCAAGGG

Basic information

species Oryza sativa
transcript LOC_Os11g04980.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g04980.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 2
gtgaggagtttacat-taaatctagattcatatctttctgcta---taacttaataaatttatatcatctctaaatgtttttgatagtagtcatgttgatatctctccacagGTACATCTCATATCTACCTTTAGCTCACATCTATGAGAGAGTTAACCAGATTGCACTGCTTCACTATGGAGTTGCCATTGGATTCTACCAAGGG
|| || | ||| ||| || |   | ||  |  | ||| ||||     | ||||   |||| | |||  | || ||  ||| ||| | ||    ||| |||  |||||| |||||| ||||||||||| ||||| |||||||| || ||||| |||||||||||||||   || |||| ||| ||||||||||||||||||||||||
gttagtattttgcatatacactcaaataaaattgtttgtgcttgatcagcttatccaattcacatctgcacttaacatttgtgaaaataactctgtggatcactctcctcagGTATATCTCATATCTGCCTTTGGCTCACATTTACGAGAGGGTTAACCAGATTGCAGCACTGCACTGTGGTGTTGCCATTGGATTCTACCAAGGG
















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|29679207|gb|CB675482.1|CB675482
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|29671403|gb|CB667678.1|CB667678
EST:     GCAAATGTAGCAGGATCAAGTGTGGTCATTAAGTTTTACCCATCTGATGT                         GTACATCTCATATCTACCTTTAGCTCACATCTATGAGAGAGTTAACCAGAT
genomic: GCAAATGTAGCAGGATCAAGTGTGGTCATTAAGTTTTACCCATCTGATGTgtgaggagtt ... ctctccacagGTACATCTCATATCTACCTTTAGCTCACATCTATGAGAGAGTTAACCAGAT
EST: gi|58663800|gb|CK052486.1|CK052486
EST:     GCAAATGTAGCAGGATCAAGTGTGGTCATTAAGTTTTACCCATCTGATGT                         GTACATCTCATATCTACCTTTAGCTCACATCTATGAGAGAGTTAACCAGAT
genomic: GCAAATGTAGCAGGATCAAGTGTGGTCATTAAGTTTTACCCATCTGATGTgtgaggagtt ... ctctccacagGTACATCTCATATCTACCTTTAGCTCACATCTATGAGAGAGTTAACCAGAT
EST: gi|58688175|gb|CK076862.1|CK076862
EST:     TTTA-CCATCTGATGT                         GTACATCTCATATCTACCTTTAGCTCACATCTATGAGAGAGTTAACCAGAT
genomic: TTTACCCATCTGATGTgtgaggagtt ... ctctccacagGTACATCTCATATCTACCTTTAGCTCACATCTATGAGAGAGTTAACCAGAT
EST: gi|29670550|gb|CB666825.1|CB666825
EST:     GCAAATGTAGCAGGATCAAGTGTGGTCATTAAGTTTTACCCATCTGATGT                         GTACATCTCATATCTACCTTTAGCTCACATCTATGAGAGAGTTAACCAGAT
genomic: GCAAATGTAGCAGGATCAAGTGTGGTCATTAAGTTTTACCCATCTGATGTgtgaggagtt ... ctctccacagGTACATCTCATATCTACCTTTAGCTCACATCTATGAGAGAGTTAACCAGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttatatcatctctaaatgtttttgatagtagtcatgttgatatctctccacagGTACATCTCATATCTACCTTTAGCTCACATCTATGAGAGAGTTAACCAGATTGCACTGCTTCACTATGGAGTTGCCATTGGATTCTACCAAGGG
                                          tatctctcc  CT-rich tract
              taaatgtttttgata  TA-rich tract