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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCACAAGGAAAAATTGGCAGTGGGTTTGATGTTAGTGCTGCTGTCTATGGGAGTCAACGTTACACAAGGTTTTCTCCAGAAATATTATCCTCGGCTCAGgtataaaaaaaaaaactgtcattaccagatagttgtctatctaaaaggttttctattataaagcttgccatatctgattggctgataatatatctgcacaatatttacag

Basic information

species Oryza sativa
transcript LOC_Os03g14830.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g14830.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G030839_T02 (Zea mays), 5'ss of exon 7
AGCACAAGGAAAAATTGGCAGTGGGTTTGATGTTAGTGCTGCTGTCTATGGGAGTCAACGTTACACAAGGTTTTCTCCAGAAATATTATCCTCGGCTCAGgtataaaaaaaaaaactgtcattaccagatagttgtctatctaaaaggttttctattataaagcttgccatatctgattggctgataatatatctgcacaatatttacag
||||||||| |||||||||||||| ||||||||||||||||||||||||||||||||||| ||   ||||||||||||||||||| | |||||||||||||||       | ||||  ||| |  |||||  |   |     |  |  |||   | |||||  ||  | | || ||    | || |||| |||    |||||||||||||
AGCACAAGGGAAAATTGGCAGTGGTTTTGATGTTAGTGCTGCTGTCTATGGGAGTCAACGCTATGTAAGGTTTTCTCCAGAAATACTCTCCTCGGCTCAGgta-------agaaacc-tcagtggcagatgatatgcacctcatcaattttgtcagtataat-ctgactacatatggagagttggtaatttatggctacaatatttacag

upper sequence: LOC_Os03g14830.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G019260_T01 (Zea mays), 5'ss of exon 6
---AGCACAAGGAAAAATTGGCAGTGGGTTTGATGTTAGTGCTGCTGTCTATGGGAGTCAACGTTACACAAGGTTTTCTCCAGAAATATTATCCTCGGCTCAGgtataaaaaaaaaaactgtcattaccagatagttgtctatctaaaaggttttctattataaagcttgccatatctgattggctgataatatatctgcacaatatttacag
   |||||| || |||||||||||||| ||||||||||||||||||||||||||||||||||| ||   ||||||||||||||||||| |   |||| ||||||||       | ||||  ||| |  ||||| | | |  | || |    |||| |    || | ||  | | || |||   |||| |||| |||    |||||||||||||
TATAGCACAGGGGAAAATTGGCAGTGGTTTTGATGTTAGTGCTGCTGTCTATGGGAGTCAACGCTATGTAAGGTTTTCTCCAGAAATACT---CTCGTCTCAGgta-------agaaacc-tcaatggcagatggct-tgcacctcatgaattttgt-cagtatatctcactacatttgaagagctggtaatttatgactacaatatttacag
















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|58677829|gb|CK066516.1|CK066516
EST:     GGAGTCAACGTTACACAAGGTTTTCTCCAGAAATATTATCCTCGGCTCAG                         GTTACAGGTGGGCACTGCATGGCAGATGTGGTGGCA
genomic: GGAGTCAACGTTACACAAGGTTTTCTCCAGAAATATTATCCTCGGCTCAGgtataaaaaa ... atatttacagGTTACAGGTGGGCACTGCATGGCAGATGTGGTGGCA
EST: gi|218496898|gb|FG969050.1|FG969050
EST:     GGAGTCAACGTTACACAAGGTTTTCTCCAGAAATATTATCCTCGGCTCAG                         GTTACAGGTGGGCACTGCATGGCAGATGTGGTGGCAGATATTGTTACACAG
genomic: GGAGTCAACGTTACACAAGGTTTTCTCCAGAAATATTATCCTCGGCTCAGgtataaaaaa ... atatttacagGTTACAGGTGGGCACTGCATGGCAGATGTGGTGGCAGATATTGTTACACAG
EST: gi|58683922|gb|CK072609.1|CK072609
EST:     GGAGTCAACGTTACACAAGGTTTTCTCCAGAAATATTATCCTCGGCTCAG                         GTTACAGGTGGGCACTGCATGGCAGATGTGGTGGCAGATATTGTTACACAG
genomic: GGAGTCAACGTTACACAAGGTTTTCTCCAGAAATATTATCCTCGGCTCAGgtataaaaaa ... atatttacagGTTACAGGTGGGCACTGCATGGCAGATGTGGTGGCAGATATTGTTACACAG
EST: gi|58683493|gb|CK072180.1|CK072180
EST:     GGAGTCAACGTTACACAAGGTTTTCTCCAGAAATATTATCCTCGGCTCAG                         GTTACAGGTGGGCACTGCATGGCAGATGTGGTGGCAGATATTGTTACACAG
genomic: GGAGTCAACGTTACACAAGGTTTTCTCCAGAAATATTATCCTCGGCTCAGgtataaaaaa ... atatttacagGTTACAGGTGGGCACTGCATGGCAGATGTGGTGGCAGATATTGTTACACAG

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: 53 (upstream exon), 58 (downstream exon)
Score: 12

AGCACAAGGAAAAATTGGCAGTGGGTTTGATGTTAGTGCTGCTGTCTATGGGAGTCAACGTTACACAAGGTTTTCTCCAGAAATATTATCCTCGGCTCAGgtataaaaaa ... atatttacagGTTACAGGTGGGCACTGCATGGCAGATGTGGTGGCAGATATTGTTACACAGAGTTGGGATCATGAGAAGGTTAAGTTTTCCTTGCCTCCTCTAATGTCCC




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