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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTCTGAACGTGTCTGGTCCAGTGCAGCCATACAATCCCAGTCTGAAGAACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaaaacaacgtgcgattcaggcatttttttacgaggtcagagttagcagttgcagaaacttatgtttatttgatgtggtttgcgcattctcag

Basic information

species Oryza sativa
transcript LOC_Os10g41780.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g41780.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G038487_T01 (Zea mays), 5'ss of exon 4
GAGTCTGAACGTGTCTGGTCCAGTGCAGCCATACAATCCCAGTCTGAAGAACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaa---aacaacgtgcgattcag-gcatttttttacgaggtcagagttagcagttgcagaaacttatgtttatttgat--gtggtttgcgcattctcag
| | || ||||||||||| || ||| |||| ||||||||||| ||||||||||||||||||||||| || ||||||||||| || ||||| || || ||||||||   | ||  |   |  |||| ||  ||    |    | ||||| | | |||||| ||| | | ||| |  ||  |   ||   || ||||||||||
GGGCCTTAACGTGTCTGGCCCGGTGAAGCCGTACAATCCCAGCCTGAAGAACTTCTGGTACCCAGTCGCCTTCTCCAGTGATCTGAAAGATGACACCATGgtaaactaaccactgaatgcctcagagccattgcacagacagacagagctgggagttgctgaagcctgtgtgtgcttacttgatgagctgtgcattctcag

upper sequence: LOC_Os10g41780.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G171390_T05 (Zea mays), 5'ss of exon 4
GAGTCTGAACGTGTCTGGTCCAGTGCAGCCATACAATCCCAGTCTGAAGAACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaaaacaacgtgcgattcaggcatttttttacgaggtcagagttagcagttgcagaaacttatgtttatttgatgtggtttgcgcattctcag
    ||  ||||||| || |||||| |||| ||||| ||||| || |||||||||||||||||||| || |||||||| || || || |    |   |   |   |||   |  | |||||| | | | | |  | |  |    ||    | |  |  | ||  ||   |  |       ||      |  ||||
---GCTTGACGTGTCCGGCCCAGTGAAGCCTTACAACCCCAGCCTCAAGAACTTCTGGTACCCAGTCGCCTTCTCCAGCGATCTCAAGGCTCCTGACACCATGgtaactcagcac-attcag-cgtgtgtgtgtgtgtgcgtgcttgctcgcttaattacctgctgacaacctacgcgcattcaattctcatcag

upper sequence: LOC_Os10g41780.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G171390_T04 (Zea mays), 5'ss of exon 4
-------------------------GAGTCTGAACGTGTCTGGTCCAGTGCAGCCATACAATCCCAGTCTGAAGAACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaaaacaacgtgcgattcaggcatttttttacgaggtcagagttagcagttgcagaaacttatgtttatttgatgtggtttgcgcattctcag
                         ||| ||  ||||||| || |||||| |||| ||||| ||||| || |||||||||||||||||||| || |||||||| || || || |    |   |   |   |||   |  | |||||| | | | | |  | |  |    ||    | |  |  | ||  ||   |  | | |                  
GAGCCAAGAACAAACAGCCACGTCGGAGGCTTGACGTGTCCGGCCCAGTGAAGCCTTACAACCCCAGCCTCAAGAACTTCTGGTACCCAGTCGCCTTCTCcagcgatctcaaggctcctgacaccatggtaactcagcac-attcag-cgtgtgtgtgtgtgtgcgtgcttgctcgcttaattacctgctgacaacct-acgc-----------------

upper sequence: LOC_Os10g41780.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA14G23860.1 (Glycine max), 5'ss of exon 4
GAGTCTGAACGTGTCTGGTCCAGTGCAGCCATACAATCCCAGTCTGAAGAACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaaaacaacgtgcgattcaggcatttttttacgaggtcagagttagcagttgcagaaact-tatgtttatttgatgtggtttgcgcattctcag------
 ||  |||| || ||||||||||| ||| ||||| |||||    ||||||| |||||||| || ||||||||||| | ||||||||| || ||||| |||||||   ||   || | | || |  | |||||  || |  |    ||  |  | |  | | | | ||| |  |  || |   |         |||       
AAGCTTGAATGTATCTGGTCCAGTTCAGTCATACCATCCCCACTTGAAGAATTTCTGGTATCCCGTTGCTTTCTCTAATGACCTAAAGGATGATACCATGgtaagt-cagtatgtg-tccaagtgtctttttctgaagaaaattctattatatacttagaatatttgtgtcatctatttcaatcaaaagaaatcaactataa

upper sequence: LOC_Os10g41780.1 (Oryza sativa), 5'ss of exon 4
lower sequence: Vv18s0001g02700.t01 (Vitis vinifera), 5'ss of exon 3
GAGTCTGAACGTGTCTGGTCCAGTGCAGCCATACAATCCCAGTCTGAAGAACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaaaacaacgtgcga---ttcaggcatttttttacgaggtcagagttagcagttgcagaaacttatgtttatttgatg-tggtttgcgcattctcag---------------------------------------------------------------------------------------
 ||| |||| || || ||||| || ||||| ||| ||||  |||||||||| ||||||||||| |||||||||||||  ||||| || || ||||| |||||||        | | |   |  | |  |  | ||  | | | | |   ||   || || |   || ||  || |  |   ||  ||  | |     |                                                                                        
AAGTTTGAATGTTTCAGGTCCTGTTCAGCCTTACCATCCTCGTCTGAAGAATTTCTGGTACCCTGTTGCTTTCTCCACAGACCTGAAGGATGATACCATGgtaagccagttttccaaacatctaaggctcatatttagtgattaaatacagattttccaca---ttgtggctactcaacaatgtcttaagtagcaataagagaggaggcaaacatttatagcttatctggccttgtgataatctgtgagttttccttgtaacagttttcacctttttctgtttcag

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|29616566|gb|CB621578.1|CB621578
EST:     ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATG                         GTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
genomic: ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaaaacaa ... gcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
EST: gi|29673392|gb|CB669667.1|CB669667
EST:     ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATG                         GTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
genomic: ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaaaacaa ... gcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
EST: gi|29618942|gb|CB623954.1|CB623954
EST:     ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATG                         GTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
genomic: ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaaaacaa ... gcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
EST: gi|58591367|gb|CF989675.1|CF989675
EST:     ACTTCTGGTACCCAGTTGGTGGCTCCAGTGACCTAAAAGACGATACAATG                         GTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
genomic: ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaaaacaa ... gcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
EST: gi|29615262|gb|CB620274.1|CB620274
EST:     ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATG                         GTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
genomic: ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaaaacaa ... gcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
EST: gi|58673738|gb|CK062424.1|CK062424
EST:     ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATG                         GTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
genomic: ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaaaacaa ... gcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
EST: gi|29671985|gb|CB668260.1|CB668260
EST:     ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATG                         GTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAA-GGAT
genomic: ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaaaacaa ... gcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
EST: gi|29617556|gb|CB622568.1|CB622568
EST:     ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATG                         GTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
genomic: ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaaaacaa ... gcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
EST: gi|29614576|gb|CB619589.1|CB619589
EST:     ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTANAAGACGATACAATG                         GTGCCAATAGATTGTTTTGAG
genomic: ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaaaacaa ... gcattctcagGTGCCAATAGATTGTTTTGAG
EST: gi|66926053|gb|CX112901.1|CX112901
EST:     ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATG                         GTGCCAATAGATTTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGA
genomic: ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaaaacaa ... gcattctcagGTGCCAATAGATT-GTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGA
EST: gi|29613349|gb|CB618362.1|CB618362
EST:     ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATG                         GTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
genomic: ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaaaacaa ... gcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
EST: gi|700022|gb|D46313.1|D46313
EST:     ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATG                         GTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
genomic: ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaaaacaa ... gcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
EST: gi|29670404|gb|CB666679.1|CB666679
EST:     ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTANAAGACGATACAATG                         GTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTT
genomic: ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaaaacaa ... gcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTT
EST: gi|58611249|gb|CK038961.1|CK038961
EST:     ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATG                         GTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT
genomic: ACTTCTGGTACCCAGTTGCTTTCTCCAGTGACCTAAAAGACGATACAATGgtaaaaacaa ... gcattctcagGTGCCAATAGATTGTTTTGAGGAGCAGTGGGTAATTTTCCGAGGAAAGGAT