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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatttgctattttctttaggttaacttttgtcactataactctgatgttggcaaacctttcagGTTCCAAAAACTTTTAATTTTAGCCTATCTGGGGCTTCGTCAAGATCTTGCAAATATGTTTTAAATACTCTCATGCAG

Basic information

species Oryza sativa
transcript LOC_Os01g60040.2
intron # 42
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 42
lower sequence: GRMZM2G068755_T01 (Zea mays), 3'ss of exon 43
gtaagcatttgctattttctttaggtta-acttttgtcactataactctgatgttggcaaacctttcagGTTCCAAAAACTTTTAATTTTAGCCTATCTGGGGCTTCGTCAAGATCTTGCAAATATGTTTTAAATACTCTCATGCAG
|| || ||||  | | || || | |||    |||  | | | | | | ||||  |||   | ||| |||||||| ||||| || ||||||||| ||||||| ||||| ||||| |||||||||||||| ||||| || |||||||||
gttagtatttattgtgttattcatgttctgttttcctgagtcttattttgattatgg---atcttgcagGTTCCGAAAACCTTCAATTTTAGCTTATCTGGTGCTTCTTCAAGGTCTTGCAAATATGTGTTAAACACACTCATGCAG

upper sequence: LOC_Os01g60040.2 (Oryza sativa), 3'ss of exon 42
lower sequence: GRMZM2G009849_T02 (Zea mays), 3'ss of exon 25
gtaagcatttgctattttctttaggttaacttttgtcactataactctgatgttggcaaacctttcagGTTCCAAAAACTTTTAATTTTAGCCTATCTGGGGCTTCGTCAAGATCTTGCAAATATGTTTTAAATACTCTCATGCAG
|| || ||||  ||  || || |||||   ||||  ||       | ||||  |||   | ||  |||||||||||||| || ||||||||| ||||||||||||| ||||| |||||||||||||| ||||| || |||||||||
gttagtatttcttacgttattcaggttctgttttcccaagtcttatttgatcatgg---atctagcagGTTCCAAAAACCTTCAATTTTAGCTTATCTGGGGCTTCTTCAAGGTCTTGCAAATATGTCTTAAACACACTCATGCAG
















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|58612256|gb|CK039968.1|CK039968
EST:     GACAGATTAGTTTCATGCTTGGCTGTTATG                         GTTCCAAAAACCTTTAATTTTAGCCTATCTGGGGCTTCGTCAAGATCTTGC
genomic: GACAGATTAGTTTCATGCTTGGCTGTTATGgtaagcattt ... aacctttcagGTTCCAAAAACTTTTAATTTTAGCCTATCTGGGGCTTCGTCAAGATCTTGC
EST: gi|33679052|gb|CF307291.1|CF307291
EST:     ATGATCTGATCAAGGAAGCTGACAGATTAGTTTCATGCTTGGCTGTTATG                         GTTCCAAAAACTTTTAATTTTAGCCTATCTGGGGCTTCGTCAAGATCTTGC
genomic: ATGATCTGATCAAGGAAGCTGACAGATTAGTTTCATGCTTGGCTGTTATGgtaagcattt ... aacctttcagGTTCCAAAAACTTTTAATTTTAGCCTATCTGGGGCTTCGTCAAGATCTTGC
EST: gi|300216015|gb|HO088641.1|HO088641
EST:     ATGATCTGATCAAGGAAGCTGACAGATTAGTTTCATGCTTGGCTGTTATG                         GTTCCAAAAACCTTTAATTTTAGCCTATCTGGGGCTTCGTCAAGATCTTGC
genomic: ATGATCTGATCAAGGAAGCTGACAGATTAGTTTCATGCTTGGCTGTTATGgtaagcattt ... aacctttcagGTTCCAAAAACTTTTAATTTTAGCCTATCTGGGGCTTCGTCAAGATCTTGC
EST: gi|58673525|gb|CK062211.1|CK062211
EST:     ATGATCTGATCAAGGAAGCTGACAGATTAGTTTCATGCTTGGCTGTTATG                         GTTCCAAAAACCTTTAATTTTAGCCTATCTGGGGCTTCGTCAAGATCTTGC
genomic: ATGATCTGATCAAGGAAGCTGACAGATTAGTTTCATGCTTGGCTGTTATGgtaagcattt ... aacctttcagGTTCCAAAAACTTTTAATTTTAGCCTATCTGGGGCTTCGTCAAGATCTTGC
EST: gi|163921634|gb|EG714160.1|EG714160
EST:     TCATGCTTGGCTGTTATG                         GTTCCAAAAACTTTTAATTTTAGCCTATCTGGGGCTTCGTCAAGATCTTGC
genomic: TCATGCTTGGCTGTTATGgtaagcattt ... aacctttcagGTTCCAAAAACTTTTAATTTTAGCCTATCTGGGGCTTCGTCAAGATCTTGC
EST: gi|58587630|gb|CF985938.1|CF985938
EST:     ATGATCTGATCAAGGAAGCTGACAGATTAGTTTCATGCTTGGCTGTTATG                         GTTCCAAAAACCTTTAATTTTAGCCTATCTGGGGCTTCGTCAAGATCTTGC
genomic: ATGATCTGATCAAGGAAGCTGACAGATTAGTTTCATGCTTGGCTGTTATGgtaagcattt ... aacctttcagGTTCCAAAAACTTTTAATTTTAGCCTATCTGGGGCTTCGTCAAGATCTTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttctttaggttaacttttgtcactataactctgatgttggcaaacctttcagGTTCCAAAAACTTTTAATTTTAGCCTATCTGGGGCTTCGTCAAGATCTTGCAAATATGTTTTAAATACTCTCATGCAG
                                               cctttc  CT-rich tract
            ttaactttt  TA-rich tract