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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcatttcatggtttggttaaattggataaacattgaattgttgccttttattgctaatacatttgactcattttacaattgttgtttcaacaatgtgtattatgattggaattgaagTGTACACTTGGTAGAGTTGTTGAATACAGGAGAATACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAG

Basic information

species Oryza sativa
transcript LOC_Os12g01140.4
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g01140.4 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G001457_T02 (Zea mays), 3'ss of exon 12
gtaatcatttc-atggtttggtt--aaattggataaacattgaattgttgcct-tttattgctaatacatttgactcatttta-----caattgttgtttcaaca------atgtgtattatgattggaattgaagTGTACACTTGGTAGAGTTGTTGAATACAGGAGAATACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAG
||||  | ||| ||  | | |||  || |  |  ||  | | | ||        |  |||    | ||   |  || |||||      | |||   |||| ||||      ||||| ||| |  ||| ||||| ||||| |||||||| |||||| |    ||||| ||||||||||||||||||||||||||||||||  ||||||||||||| || |||
gtaagtacttctatattatagtttcaactatggcaatgactcagtttgcatgaatccattagacacactcctttctaattttcactccctatttacgtttaaacagtaaacatgtgaattgttgttg-aattgtagTGTCCACTTGGTGGAGTTGCTTGGCACAGGTGAATACTTTGCCATGAAAGCTATGGATAAAAGTGTCATGCTTAACCGAAACAAG

upper sequence: LOC_Os12g01140.4 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv06s0004g03700.t01 (Vitis vinifera), 3'ss of exon 13
gtaatcatttcatggtttggttaaattggataaacattgaattgttgccttttattgctaatacatttgactcattttacaattgttgtttcaacaatgtgtatta--tgattggaattgaagTGTACACTTGGTAGAGTTGTTGAATACAGGAGAATACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAG
                           ||   |  ||  | |  ||    | |     |  |    ||  ||||   |     |||   ||  | ||| |  | |   |||||||  | | ||||| ||  |||| || || |     || || |||||||||||||||||||||||||||||||   ||||||| |||||||| |||
-----------------------ctcaggggtatgatcaagtccttattctctccattttgttttcttagctcaaacttttgctgtgtcttggaaaatttagactcattgattggtttggcagTGTGCATCTGGTGGAATTATGTGGAACTGGTGAATACTTTGCCATGAAAGCTATGGATAAAAATGTCATGCTCAACCGCAACAAG
















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|66913937|gb|CX100785.1|CX100785
EST:     GGCCAGTAAAACCATTAGGATCTGGTGACACTGGAAG                         TGTACACTTGGTAGAGTTGTTGAATACAGGAGAATACTTTGCCATGAAAGC
genomic: GGCCAGTAAAACCATTAGGATCTGGTGACACTGGAAGgtaatcattt ... ggaattgaagTGTACACTTGGTAGAGTTGTTGAATACAGGAGAATACTTTGCCATGAAAGC
EST: gi|29622723|gb|CB627734.1|CB627734
EST:     TTAAAACATTTTAGGCCAGTAAAACCATTAGGATCTGGTGACACTGGAAG                         TGTACACTTGGTAGAGTTGTTGAATACAGGAGAATACTTTGCCATGAAAGC
genomic: TTAAAACATTTTAGGCCAGTAAAACCATTAGGATCTGGTGACACTGGAAGgtaatcattt ... ggaattgaagTGTACACTTGGTAGAGTTGTTGAATACAGGAGAATACTTTGCCATGAAAGC
EST: gi|29672018|gb|CB668293.1|CB668293
EST:     TTAAAACATTTTAGGCCAGTAAAACCATTAGGATCTGGTGACACTGGAAG                         TGTACACTTGGTAGAGTTGTTGAATACAGGAGAATACTTTGCCATGAAAGC
genomic: TTAAAACATTTTAGGCCAGTAAAACCATTAGGATCTGGTGACACTGGAAGgtaatcattt ... ggaattgaagTGTACACTTGGTAGAGTTGTTGAATACAGGAGAATACTTTGCCATGAAAGC
EST: gi|29613611|gb|CB618624.1|CB618624
EST:     TTAAAACATTTTAGGCCAGTAAAACCATTAGGATCTGGTGACACTGGAAG                         TGTACACTTGGTAGAGTTGTTGAATACAGGAGAATACTTTGCCATGAAAGC
genomic: TTAAAACATTTTAGGCCAGTAAAACCATTAGGATCTGGTGACACTGGAAGgtaatcattt ... ggaattgaagTGTACACTTGGTAGAGTTGTTGAATACAGGAGAATACTTTGCCATGAAAGC
EST: gi|29641400|gb|CB646407.1|CB646407
EST:     TTAAAACATTTTAGGCCAGTAAAACCATTAGGATCTGGTGACACTGGAAG                         TGTACACTTGGTAGAGTTGTTGAATACAGGAGAATACTTTGCCATGAAAGC
genomic: TTAAAACATTTTAGGCCAGTAAAACCATTAGGATCTGGTGACACTGGAAGgtaatcattt ... ggaattgaagTGTACACTTGGTAGAGTTGTTGAATACAGGAGAATACTTTGCCATGAAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgactcattttacaattgttgtttcaacaatgtgtattatgattggaattgaagTGTACACTTGGTAGAGTTGTTGAATACAGGAGAATACTTTGCCATGAAAGCTATGGATAAAAGCATCATGCTTAACCGCAATAAG
 atttgac  putative branch site (score: 4)
       attttacaattgtt  TA-rich tract