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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaagcttgaactttgatggatactttaatttgatgatctacagtatctgtttcccctttgccaaactagatttccaatatctgtctctgcaattgcattccatgcgtatcgcagGATGGGGATGGCGACGAAGAGCTGAAAGAAGCTTTCGAGGTCCTAGACAAGGATCAGAATGGTTTTATCTCCCCAACTGAG

Basic information

species Oryza sativa
transcript LOC_Os03g53200.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g53200.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G149923_T01 (Zea mays), 3'ss of exon 2
gtgaagcttgaactttgatggatactttaatttgatgatctacagtatctgtttcccc--tttgccaaactagatttccaatatctgtctctgcaattgcattccatgcgtatcgcagGATGGGGATGGCGACGAAGAGCTGAAAGAAGCTTTCGAGGTCCTAGACAAGGATCAGAATGGTTTTATCTCCCCAACTGAG
                   |  | || |   |   |  ||||       |  | ||    ||  |||    ||   ||| | |  || |    ||  ||| |||  |||   | ||||||||| || |||||||||||||| || ||||| || |||||||| ||||| || ||||| || || ||||||||   ||||
-----------------gcgagt-ctctctctcatttgtctatcacgaatactcccgaaattaaccatcgcag---tccgaaagttgacagcacacctgc-ttcgttgc---ttgcagGATGGCGACGGCGACGAAGAGCTCAAGGAAGCCTTTGAGGTCCTGGACAAAGACCAGAACGGCTTCATCTCCCCGGTTGAG
















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|88299931|gb|CI579992.1|CI579992
EST:     GGATAATAGATTTTCAGGAGTTCCTGAGCCTCATTGCAAGGAAGATGAAG                         GATGGGGATGGCGACGAAGAGCTGAAAGAAGCTTTCGAGGTCCTAGACAAG
genomic: GGATCATAGATTTTCAGGAGTTCCTGAGCCTCATTGCCAGGAAGATGAAGgtgaagcttg ... cgtatcgcagGATGGGGATGGCGACGAAGAGCTGAAAGAAGCTTTCGAGGTCCTAGACAAG
EST: gi|38472151|gb|CF956282.1|CF956282
EST:     GGATCATAGATTTTCAGGAGTTCCTGAGCCTCATTGCCAGGAAGATGAAG                         GATGGGGATGGCGACGAAGAGCTGAAAGAAGCTTTTGAGGTCCTAGACAAG
genomic: GGATCATAGATTTTCAGGAGTTCCTGAGCCTCATTGCCAGGAAGATGAAGgtgaagcttg ... cgtatcgcagGATGGGGATGGCGACGAAGAGCTGAAAGAAGCTTTCGAGGTCCTAGACAAG
EST: gi|29667976|gb|CB664251.1|CB664251
EST:     GGATCATAGATTTTCAGGAGTTCCTGAGCCTCATTGCCAGGAAGATGAAG                         GATGGGGATGGCGACGAAGAGCTGAAAGAAGCTTTCGAGGTCCTAGACAAG
genomic: GGATCATAGATTTTCAGGAGTTCCTGAGCCTCATTGCCAGGAAGATGAAGgtgaagcttg ... cgtatcgcagGATGGGGATGGCGACGAAGAGCTGAAAGAAGCTTTCGAGGTCCTAGACAAG
EST: gi|88329564|gb|CI650016.1|CI650016
EST:     GGATCATAGATTTTCAGGAGTTCCTGAGCCTCATTGCCAGGAAGATGAAG                         GATGGGGATGGCGACGAAGAGCTGAAAGAAGCTTTCGAGGTCCTAGACAAG
genomic: GGATCATAGATTTTCAGGAGTTCCTGAGCCTCATTGCCAGGAAGATGAAGgtgaagcttg ... cgtatcgcagGATGGGGATGGCGACGAAGAGCTGAAAGAAGCTTTCGAGGTCCTAGACAAG
EST: gi|88299406|gb|CI572358.1|CI572358
EST:     GGATCATAGATTTTCAGGAGTTCCTGAGCCTCATTGCCAGGAAGATGAAG                         GATGGGGATGGCGACGAAGAGCTGAAAGAAGCTTTCGAGGTCCTAGACAAG
genomic: GGATCATAGATTTTCAGGAGTTCCTGAGCCTCATTGCCAGGAAGATGAAGgtgaagcttg ... cgtatcgcagGATGGGGATGGCGACGAAGAGCTGAAAGAAGCTTTCGAGGTCCTAGACAAG
EST: gi|88341641|gb|CI641393.1|CI641393
EST:     GGATCATAGATTTTCAGGAGTTCCTGAGCCTCATTGCCAGGAAGATGAAG                         GATGGGGATGGCGACGAAGAGCTGAAAGAAGCTTTCGAGGTCCCTAGACAA
genomic: GGATCATAGATTTTCAGGAGTTCCTGAGCCTCATTGCCAGGAAGATGAAGgtgaagcttg ... cgtatcgcagGATGGGGATGGCGACGAAGAGCTGAAAGAAGCTTTCGAGGTCC-TAGACAA
EST: gi|88310980|gb|CI657893.1|CI657893
EST:     GGATCATAGATTTTCAGGAGTTCCTGAGCCTCATTGCCAGGAAGATGAAG                         GATGGGGATGGCGACCAAGAGCTGAAAGAAGCTCTCCAGGTCCTAGACAAG
genomic: GGATCATAGATTTTCAGGAGTTCCTGAGCCTCATTGCCAGGAAGATGAAGgtgaagcttg ... cgtatcgcagGATGGGGATGGCGACGAAGAGCTGAAAGAAGCTTTCGAGGTCCTAGACAAG
EST: gi|88306356|gb|CI638139.1|CI638139
EST:     GGATCATAGATTTTCAGGAGTTCCTGAGCCTCATTGCCAGGAAGATGAAG                         GATGGGGATGGCGACGAAGAGCTGAAAGAAGCTTTCGAGGTCCTAGACAAG
genomic: GGATCATAGATTTTCAGGAGTTCCTGAGCCTCATTGCCAGGAAGATGAAGgtgaagcttg ... cgtatcgcagGATGGGGATGGCGACGAAGAGCTGAAAGAAGCTTTCGAGGTCCTAGACAAG
EST: gi|88404677|gb|CI581113.1|CI581113
EST:     GGATCATAGATTTTCAGGAGTTCCTGAGCCTCATTGCCAGGAAGGTGAAG                         GATGGGGATGGCGACGAAGAGCTGAAAGAAGCTTTCGAGGTCCTAGACAAG
genomic: GGATCATAGATTTTCAGGAGTTCCTGAGCCTCATTGCCAGGAAGATGAAGgtgaagcttg ... cgtatcgcagGATGGGGATGGCGACGAAGAGCTGAAAGAAGCTTTCGAGGTCCTAGACAAG
EST: gi|88827806|gb|CI778371.1|CI778371
EST:     GGATCATAGATTTTCAGGAGTTCCTGAGCCTCATTGCCAGGAAGATGAAG                         GATGGGGATGGCGACGAAGAGCTGAAAGAAGCTTTCGAGGTCCTA
genomic: GGATCATAGATTTTCAGGAGTTCCTGAGCCTCATTGCCAGGAAGATGAAGgtgaagcttg ... cgtatcgcagGATGGGGATGGCGACGAAGAGCTGAAAGAAGCTTTCGAGGTCCTA
EST: gi|88407027|gb|CI581114.1|CI581114
EST:     GGATCATAGATTTTCAGGAGTTCCTGAGCCTCATTGCCAGGAAGGTGAAG                         GATGGGGATGGCGACGAAGAGCTGAAAGAAGCTTTCGAGGTCCTAGACAAG
genomic: GGATCATAGATTTTCAGGAGTTCCTGAGCCTCATTGCCAGGAAGATGAAGgtgaagcttg ... cgtatcgcagGATGGGGATGGCGACGAAGAGCTGAAAGAAGCTTTCGAGGTCCTAGACAAG
EST: gi|58589123|gb|CF987431.1|CF987431
EST:     GGATCATAGATTTTCAGGAGTTCCTGAGCCTCATTGCCAGGAAGATGAAG                         GATGGGGATGGCGACGAAGAGCTGAAAGAAGCTTTTGAGGTCCTAGACAAG
genomic: GGATCATAGATTTTCAGGAGTTCCTGAGCCTCATTGCCAGGAAGATGAAGgtgaagcttg ... cgtatcgcagGATGGGGATGGCGACGAAGAGCTGAAAGAAGCTTTCGAGGTCCTAGACAAG
EST: gi|88471830|gb|CI409101.1|CI409101
EST:     GATCATAGATTTTCAGGAGTTCCTGAGCCTCATTGCCAGGAAGATGAAG                         GATGGGGATGGCGACGAAGAGCTGAAAGAAGCTTTCGAGGTCCTAGACAAG
genomic: GATCATAGATTTTCAGGAGTTCCTGAGCCTCATTGCCAGGAAGATGAAGgtgaagcttg ... cgtatcgcagGATGGGGATGGCGACGAAGAGCTGAAAGAAGCTTTCGAGGTCCTAGACAAG
EST: gi|88404667|gb|CI581103.1|CI581103
EST:     GGATCATAGATTTTCAGGAGTTCCTGAGCCTCATTGGCAGGAAGGTGAAG                         GATGGGGATGGCGACGAAGAGCTGAAAGAAGCTTTCGAGGTCCTAGACAAG
genomic: GGATCATAGATTTTCAGGAGTTCCTGAGCCTCATTGCCAGGAAGATGAAGgtgaagcttg ... cgtatcgcagGATGGGGATGGCGACGAAGAGCTGAAAGAAGCTTTCGAGGTCCTAGACAAG

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: 65 (upstream exon), 63 (downstream exon)
Score: 16

CGATCAGGAGCTCAACGACATGATGAGGGAAGTTGATACAGATGGCAATGGGATCATAGATTTTCAGGAGTTCCTGAGCCTCATTGCCAGGAAGATGAAGgtgaagcttg ... cgtatcgcagGATGGGGATGGCGACGAAGAGCTGAAAGAAGCTTTCGAGGTCCTAGACAAGGATCAGAATGGTTTTATCTCCCCAACTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccaaactagatttccaatatctgtctctgcaattgcattccatgcgtatcgcagGATGGGGATGGCGACGAAGAGCTGAAAGAAGCTTTCGAGGTCCTAGACAAGGATCAGAATGGTTTTATCTCCCCAACTGAG
       tagattt  TA-rich tract