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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGATATTTGTTGGCAGGCTTCCACAAGAGGCAAACACGGAGGACCTAAGGCATTACTTTGGCAAATTTGGCCGAATTGTGGATGCATATATCCCAAAGgtaaggttaagactttctcattgtttgtaactgtactatgttaatctcaaccttttctaattgtattgaag

Basic information

species Oryza sativa
transcript LOC_Os01g71770.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g71770.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G060977_T05 (Zea mays), 5'ss of exon 12
AAAGATATTTGTTGGCAGGCTTCCACAAGAGGCAAACACGGAGGACCTAAGGCATTACTTTGGCAAATTTGGCCGAATTGTGGATGCATATATCCCAAAGgtaaggttaagactttctcattgtttgtaa--ctgtactatgttaa---tctcaaccttttctaattgtattgaag
 |||||||||||||| || ||||||||||| |||||||| || || |||||||| |||||||||| |||||| ||||| || ||||||||||| ||||||||  || |||||||  |  ||||||||  |  |   | ||| |||    ||| ||| | ||| ||||    |  ||
GAAGATATTTGTTGGTAGACTTCCACAAGAAGCAAACACAGATGATCTAAGGCAGTACTTTGGCAGATTTGGTCGAATCGTAGATGCATATATTCCAAAGgtgcggctaagactggc--attgtttggcataccacaatatattagatgtcttaac-tcttcgaatttctgtacag

upper sequence: LOC_Os01g71770.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G030902_T02 (Zea mays), 5'ss of exon 11
AAAGATATTTGTTGGCAGGCTTCCACAAGAGGCAAACACGGAGGACCTAAGGCATTACTTTGGCAAATTTGGCCGAATTGTGGATGCATATATCCCAAAGgtaaggttaagactttctcattgtttgtaac--tgtactatgttaat---ctcaaccttttctaattgtattgaag
 |||||||||||||| || ||||||||||| ||||||||||| |||||||| ||||||||||||| |||||| ||||| || ||||| ||||| ||||||||   | |||||||     ||||||||  |     || ||| ||| |   |||||| | ||| ||||    |  ||
GAAGATATTTGTTGGTAGACTTCCACAAGAAGCAAACACGGATGACCTAAGACATTACTTTGGCAGATTTGGTCGAATCGTAGATGCGTATATTCCAAAGgtgcagctaagactggt--attgtttggcatgtcataatatattagttgtctcaac-tcttcaaatttccatacag
















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|163926523|gb|EG712387.1|EG712387
EST:     GGCATTACTTTGGCAAATTTGGCCGAATTGTGGATGCATATATCCCAAAG                         GACCCTAAAAGAAGTGGACATCGAGGTTTTGGTTTTGTCACCTTTGCTGAT
genomic: GGCATTACTTTGGCAAATTTGGCCGAATTGTGGATGCATATATCCCAAAGgtaaggttaa ... tgtattgaagGACCCTAAAAGAAGTGGACATCGAGGTTTTGGTTTTGTCACCTTTGCTGAT
EST: gi|32947891|gb|BP184463.1|BP184463
EST:     GGCATTACTTTGGCAAATTTGGCCGAATTGTGGATGCATATATCCCAAAG                         GACCCTAAAAGAAGTGGACATCGAGGTTTTGGTTTTGTCACCTTTGCTGAT
genomic: GGCATTACTTTGGCAAATTTGGCCGAATTGTGGATGCATATATCCCAAAGgtaaggttaa ... tgtattgaagGACCCTAAAAGAAGTGGACATCGAGGTTTTGGTTTTGTCACCTTTGCTGAT
EST: gi|58603513|gb|CK014041.1|CK014041
EST:     GGCATTACTTTGGCAAATTTGGCCGAATTGTGGATGCATATATCCCAAAG                         GACCCTAAAAGAAGTGGACATCGAGGTT
genomic: GGCATTACTTTGGCAAATTTGGCCGAATTGTGGATGCATATATCCCAAAGgtaaggttaa ... tgtattgaagGACCCTAAAAGAAGTGGACATCGAGGTT
EST: gi|29677103|gb|CB673378.1|CB673378
EST:     GGCATTACTTTGGCAAATTTGGCCGAATTGTGGATGCATATATCCCAAAG                         GACCCTAAAAGAAGTGGACATCGAGGTTTTGGTTTTGTCACCTTTGCTGAT
genomic: GGCATTACTTTGGCAAATTTGGCCGAATTGTGGATGCATATATCCCAAAGgtaaggttaa ... tgtattgaagGACCCTAAAAGAAGTGGACATCGAGGTTTTGGTTTTGTCACCTTTGCTGAT
EST: gi|116875665|gb|EC366173.1|EC366173
EST:     GGCATTACTTTGGCAAATTTGGCCGAATTGTGGATGCATATATCCCAAAG                         GACCCTAAAAGAAGTGGACATCGAGGTTTTGGTTTTGTCACCTTTGCTGAT
genomic: GGCATTACTTTGGCAAATTTGGCCGAATTGTGGATGCATATATCCCAAAGgtaaggttaa ... tgtattgaagGACCCTAAAAGAAGTGGACATCGAGGTTTTGGTTTTGTCACCTTTGCTGAT
EST: gi|116875549|gb|EC366057.1|EC366057
EST:     GGCATTACTTTGGCAAATTTGGCCGAATTGCGGATGCATATATCCCAAAG                         GACCCTAAAAGAAGTGGACATCGAGGTTTTGGTTTTGTCACCTTTGCTGAT
genomic: GGCATTACTTTGGCAAATTTGGCCGAATTGTGGATGCATATATCCCAAAGgtaaggttaa ... tgtattgaagGACCCTAAAAGAAGTGGACATCGAGGTTTTGGTTTTGTCACCTTTGCTGAT

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), 67 (downstream exon)
Score: 24

AAAGATATTTGTTGGCAGGCTTCCACAAGAGGCAAACACGGAGGACCTAAGGCATTACTTTGGCAAATTTGGCCGAATTGTGGATGCATATATCCCAAAGgtaaggttaa ... tgtattgaagGACCCTAAAAGAAGTGGACATCGAGGTTTTGGTTTTGTCACCTTTGCTGATGAGGGTGTGGCAGATCGGGTAGCTCGCAGAAGTCATGAAATTCTAGGAC




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