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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATCTTGTCAAAAGCTTGGTAAATGCTCCAAATAGTCTCCTGTTGGGTAAAGGGGCCTTCTTTATCCATGTCAATAATATGATATTTCAAGTATTGAAAGgtgtgtaccacatgtcctgtttttccatgacgtgataacaacataaccttcttgtttatacatcatatatttgtacttaagctgcattgttcctgcataa...

Basic information

species Oryza sativa
transcript LOC_Os05g33810.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g33810.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G109354_T01 (Zea mays), 5'ss of exon 6
AATCTTGTCAAAAGCTTGGTAAATGCTCCAAATAGTCTCCTGTTGGGTAAAGGGGCCTTCTTTATCCATGTCAATAATATGATATTTCAAGTATTGAAAGgtgtgtaccacatgtcctgtttttccatgacgtgataacaacataaccttcttgtt-tatacatcatatatttgtacttaagctgcattgttcctgcataa
 ||||| ||| || |||||||||| | ||||| |||||  |||||||||||||||||||||| || ||||||||||| ||| ||||||||||| | ||||||||||         | ||||        | |  |||| ||  |   ||  |   | |||  ||  || ||  |||| | |  | |  ||||  | |||  
GATCTTCTCAGAAACTTGGTAAATTCCCCAAACAGTCTTTTGTTGGGTAAAGGGGCCTTCTTCATTCATGTCAATAACATGTTATTTCAAGTACTAAAAGgtgtgtctgcagcaacttgttacaatgccaggacataataatttgtgctattaactatatcgattctacatg-gtacatgaattactgtgtttgtacatgt
















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|29682373|gb|CB678648.1|CB678648
EST:     AGGGGCCTTCTTTATCCATGTCAATAATATGATATTTCAAGTATTGAAAG                         ATGGTGCAACATTGACCAGTACCAGATTAGAGGTACAGTCCCCGAGGATTC
genomic: AGGGGCCTTCTTTATCCATGTCAATAATATGATATTTCAAGTATTGAAAGgtgtgtacca ... tgtacttcagATGGTGCAACATTGACCAGTACCAGATTAGAGGTACAGTCCCCGAGGATTC
EST: gi|218482951|gb|FG948113.1|FG948113
EST:     AGGGGCCTTCTTTATCCATGTCAATAATATGATATTTCAAGTATTGAAAG                         ATGGTGCAACATTGACCAGTACCAGATTAGAGGTACAGTCCCCGAGGATTC
genomic: AGGGGCCTTCTTTATCCATGTCAATAATATGATATTTCAAGTATTGAAAGgtgtgtacca ... tgtacttcagATGGTGCAACATTGACCAGTACCAGATTAGAGGTACAGTCCCCGAGGATTC
EST: gi|58656998|gb|CK045678.1|CK045678
EST:     AGGGGCCTTCTTTATCCATGTCAATAATATGATATTTCAAGTATTGAAAG                         ATGGTGCAACATTGACCAGTACCAGATTAGAGGTACAG
genomic: AGGGGCCTTCTTTATCCATGTCAATAATATGATATTTCAAGTATTGAAAGgtgtgtacca ... tgtacttcagATGGTGCAACATTGACCAGTACCAGATTAGAGGTACAG
EST: gi|29619149|gb|CB624161.1|CB624161
EST:     AGGGGCCTTCTTTATCCATGTCAATAATATGATATTTCAAGTATTGAAAG                         ATGGTGCAACATTGACCAGTACCAGATTAGAGGTACAGTCCCCGAGGATTC
genomic: AGGGGCCTTCTTTATCCATGTCAATAATATGATATTTCAAGTATTGAAAGgtgtgtacca ... tgtacttcagATGGTGCAACATTGACCAGTACCAGATTAGAGGTACAGTCCCCGAGGATTC
EST: gi|88329499|gb|CI648561.1|CI648561
EST:     AGGGGCCTTCTTTATCCATGTCAATAATATGATATTTCAAGTATTGAAAG                         ATGGTGCAACATTGACCAGCACCAGATTAGAGGTACAGTCCCCGAGGATTC
genomic: AGGGGCCTTCTTTATCCATGTCAATAATATGATATTTCAAGTATTGAAAGgtgtgtacca ... tgtacttcagATGGTGCAACATTGACCAGTACCAGATTAGAGGTACAGTCCCCGAGGATTC
EST: gi|29679742|gb|CB676017.1|CB676017
EST:     AGGGGCCTTCTTTATCCATGTCAATAATATGATATTTCAAGTATTGAAAG                         ATGGTGCAACATTGACCAGTACCAGATTAGAGGTACAGTCCCCGAGGATTC
genomic: AGGGGCCTTCTTTATCCATGTCAATAATATGATATTTCAAGTATTGAAAGgtgtgtacca ... tgtacttcagATGGTGCAACATTGACCAGTACCAGATTAGAGGTACAGTCCCCGAGGATTC
EST: gi|88350419|gb|CI653484.1|CI653484
EST:     AGGGGCCTTCTTTATCCATGTCAATAATATGATATCTCAAGTATTGAAAG                         ATGGTGCAACATTGACCAGCACCACATTAGAGGTACAGTCCCCGAGGATTC
genomic: AGGGGCCTTCTTTATCCATGTCAATAATATGATATTTCAAGTATTGAAAGgtgtgtacca ... tgtacttcagATGGTGCAACATTGACCAGTACCAGATTAGAGGTACAGTCCCCGAGGATTC
EST: gi|58662678|gb|CK051364.1|CK051364
EST:     AGGGGCCTTCTTTATCCATGTCAATAATATGATATTTCAAGTATTGAAAG                         ATGGTGCAACATTGACCAGTACCAGATTAGAGGTACAGTCCCCGAGGATTC
genomic: AGGGGCCTTCTTTATCCATGTCAATAATATGATATTTCAAGTATTGAAAGgtgtgtacca ... tgtacttcagATGGTGCAACATTGACCAGTACCAGATTAGAGGTACAGTCCCCGAGGATTC
EST: gi|58670185|gb|CK058871.1|CK058871
EST:     AGGGGCCTTCTTTATCCATGTCAATAATATGATATTTCAAGTATTGAAAG                         ATGGTGCAACATTGACCAGTACCAGATTAGAGGTACAGTCCCCGAGGATTC
genomic: AGGGGCCTTCTTTATCCATGTCAATAATATGATATTTCAAGTATTGAAAGgtgtgtacca ... tgtacttcagATGGTGCAACATTGACCAGTACCAGATTAGAGGTACAGTCCCCGAGGATTC

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: 75 (upstream exon), 69 (downstream exon)
Score: 20

AATCTTGTCAAAAGCTTGGTAAATGCTCCAAATAGTCTCCTGTTGGGTAAAGGGGCCTTCTTTATCCATGTCAATAATATGATATTTCAAGTATTGAAAGgtgtgtacca ... tgtacttcagATGGTGCAACATTGACCAGTACCAGATTAGAGGTACAGTCCCCGAGGATTCACTATGTTCATCCATCATGGTTTGAAGCAGGAAAGCCCATCGATCTTAT




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