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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTCCTGCGAGTCCAACTCGGTGGCAAGGAGAAACGTGTCGTCCAACAACAGTACGAGGAAGTCTCAATTCCACCACATCTGATGGTTGGAACTTCCATGgtaagcatttgctgcttgattttaaatttcttggagctgtacattccatgcttgtcttatgtattttctgactattaatgcag

Basic information

species Oryza sativa
transcript LOC_Os05g44760.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g44760.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G432801_T01 (Zea mays), 5'ss of exon 2
CGTCCTGCGAGTCCAACTCGGTGGCAAGGAGAAACGTGTCGTCCAACAACAGTACGAGGAAGTCTCAATTCCACCACATCTGATGGTTGGAACTTCCATGgtaagcatttgctgcttgattttaaatttcttggagct-gtacattcca---tgcttgtcttatgtattttctgactattaatgcag
 || |||||||||||||| || || | |||||||||||| ||| |||||||||||||||| || || |||||||| ||| ||||||| || |||||||| || || | | |||| |  ||||| | ||||||| |  | ||   ||| |   || ||||||||||||| ||   |  ||| || |||
TGTGCTGCGAGTCCAACTAGGAGGAAGGGAGAAACGTGTTGTCAAACAACAGTACGAGGAGGTTTCCATTCCACCGCATTTGATGGTCGGGACTTCCATTgtgagtactcgctgttctatttttagtttcttgaattttgtgttttcgacactgtttgtcttatgtatcttg-aatcattgatacag

upper sequence: LOC_Os05g44760.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G058745_T02 (Zea mays), 5'ss of exon 2
CGTCCTGCGAGTCCAACTCGGTGGCAAGGAGAAACGTGTCGTCCAACAACAGTACGAGGAAGTCTCAATTCCACCACATCTGATGGTTGGAACTTCCATGgtaagcatttgctgcttgattttaaatttcttggagctgtacattcca-----tgcttgtcttatgtattttctgactattaatgcag
 || ||||||||||| || || || |||||||||||||| ||| |||||||||| ||||| || || |||||||||||| ||||||| || ||||||||||| || | |||||| |  | ||| | ||||||| || ||| | ||        || ||||||||||||| ||   | |||| || |||
TGTGCTGCGAGTCCAGCTAGGAGGAAAGGAGAAACGTGTTGTCAAACAACAGTATGAGGAGGTTTCCATTCCACCACATTTGATGGTCGGGACTTCCATGgtgagtacttgctgttctaattttagtttcttgaagttgtgcgttttcaacactgtttgtcttatgtatcttg-aattattgatacag
















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|88392639|gb|CI625461.1|CI625461
EST:     AGTACGAGGAAGTCTCAATTCCACCACATCTGATGGTTGGAACTTCCATG                         GAAGTGTTTGATTTTATTGCTTCTGCATTGTCACAATTTGTTGATACTGA
genomic: AGTACGAGGAAGTCTCAATTCCACCACATCTGATGGTTGGAACTTCCATGgtaagcattt ... attaatgcagGAACTGTTTGATTTTATTGCTTCTGCATTGTCAAAATTTGTTGATACTGA
EST: gi|58676584|gb|CK065271.1|CK065271
EST:     AGTACGAGGAAGTCTCAATTCCACCACATCTGATGGTTGGAACTTCCATG                         GAACTGTTTGATTTTATTGCTTCTGCATTGTCAAAATTTGTTGATACTGAA
genomic: AGTACGAGGAAGTCTCAATTCCACCACATCTGATGGTTGGAACTTCCATGgtaagcattt ... attaatgcagGAACTGTTTGATTTTATTGCTTCTGCATTGTCAAAATTTGTTGATACTGAA
EST: gi|4880012|gb|AU064311.1|AU064311
EST:     AGTACGAGGAAGTCTCAATTCCACCACATCTGATGGTTGGAACTTCCATG                         GAACTGTTTGATTTTATTGCTTCTGCATTGTCAAAATTTGTTGATACTGAA
genomic: AGTACGAGGAAGTCTCAATTCCACCACATCTGATGGTTGGAACTTCCATGgtaagcattt ... attaatgcagGAACTGTTTGATTTTATTGCTTCTGCATTGTCAAAATTTGTTGATACTGAA
EST: gi|29629656|gb|CB634665.1|CB634665
EST:     AGTACGAGGAAGTCTCAATTCCACCACATCTGATGGTTGGAACTTCCATG                         GAACTGTTTGATTTTATTGCTTCTGCATTGTCAAAATTTGTTGATACTGAA
genomic: AGTACGAGGAAGTCTCAATTCCACCACATCTGATGGTTGGAACTTCCATGgtaagcattt ... attaatgcagGAACTGTTTGATTTTATTGCTTCTGCATTGTCAAAATTTGTTGATACTGAA
EST: gi|58667655|gb|CK056341.1|CK056341
EST:     AGTACGAGGAAGTCTCAATTCCACCACATCTGATGGTTGGAACTTCCATG                         GAACTGTTTGATTTTATTGCTTCTGCATTGTCAAAATTTGTTGATACTGAA
genomic: AGTACGAGGAAGTCTCAATTCCACCACATCTGATGGTTGGAACTTCCATGgtaagcattt ... attaatgcagGAACTGTTTGATTTTATTGCTTCTGCATTGTCAAAATTTGTTGATACTGAA
EST: gi|58612363|gb|CK040075.1|CK040075
EST:     GATGGTTGGAACTTCCATG                         GAACTGTTTGATTTTATTGCTTCTGCATTGTCAAAATTTGTTGATACTGAA
genomic: GATGGTTGGAACTTCCATGgtaagcattt ... attaatgcagGAACTGTTTGATTTTATTGCTTCTGCATTGTCAAAATTTGTTGATACTGAA
EST: gi|8404574|gb|AU091928.1|AU091928
EST:     AGTACGAGGAAGTCTCAATTNCACCACATCTGATGGTTGGA-CTTCCATG                         GA-CTGTTTGATTTTATTGCTTCTGCATTGTCAAAATTTGTTGATACTGA-
genomic: AGTACGAGGAAGTCTCAATTCCACCACATCTGATGGTTGGAACTTCCATGgtaagcattt ... attaatgcagGAACTGTTTGATTTTATTGCTTCTGCATTGTCAAAATTTGTTGATACTGAA

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: 70 (upstream exon), 63 (downstream exon)
Score: 13

CGTCCTGCGAGTCCAACTCGGTGGCAAGGAGAAACGTGTCGTCCAACAACAGTACGAGGAAGTCTCAATTCCACCACATCTGATGGTTGGAACTTCCATGgtaagcattt ... attaatgcagGAACTGTTTGATTTTATTGCTTCTGCATTGTCAAAATTTGTTGATACTGAAGGTGATGATTTCCACCTCCCAGAAGGGAGACAGAGAGAGCTGGGCTTCA




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