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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagattcttctccattcctactgtaatcaatatatatttgaattttaattatgaactgaaacaagatgttgtttctgaagCAATTGATAATGATGCAACAATTTGCTCTCCGCGAATCAAGAGAAGCACAAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAG

Basic information

species Oryza sativa
transcript LOC_Os01g06590.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g06590.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G165044_T01 (Zea mays), 3'ss of exon 4
gtagat--tcttctccattcctactgt---aatcaatatatatttgaattttaattatgaactgaaacaagatgttgtttctgaa---gCAATTGATAATGATGCAACAATTTGCTCTCCGCGAATCAAGAGAAGCACAAG---ACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAG
||||||   ||| | | | ||||||||   ||| ||  |   ||| | | ||  |    | |||||||  ||||||| | |||     | |   | | |||||| | || || |   ||  |||||| |||| ||||   |   |||||||||||| ||||||||||||||||||||| ||||| || |||
gtagatagcctttttcttccctactgtttcaatgaagttgagtttaagtctttgtcg-aacctgaaact-gatgttgctgctggtcgtgaagCGGTTCATGATGGACCACTTGGTCTTCTACGAATCGAGAGCAGCAGCTGCTGACCCCCACAGGGACATGAGACTGGACATTGACAACATGAGCTACGAG

upper sequence: LOC_Os01g06590.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G305901_T01 (Zea mays), 3'ss of exon 4
gtagatt-cttctccattcctactgtaatcaatatatatttgaatttta-attatgaactgaaacaagatgttgtttc-tgaagCAATTGATAATGATGCAACAATTTGCTCTCCGCGAATCAAGAGAAGCACAAG---ACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAG
||||||  ||| ||    ||      ||| ||  ||   | |  || || |   ||||    |    | || || ||  ||||||  ||    |||||| | || || |   |   ||||||||||| ||||   |   |||||||||||| ||||||||||||||| ||||| ||||| || |||
gtagatagcttttcttcccccgtctcaatgaagttaagctagcgttgtagagcctgaaactgatgttgctgctgctttgtgaagCGGTTC---ATGATGGACCAGTTGGTCTTTTACGAATCAAGAGCAGCAGCCGCTGACCCCCACAGGGACATGAGACTGGACATCGACAACATGAGCTACGAG
















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|29670363|gb|CB666638.1|CB666638
EST:     GGGCGAGAAGCTCATACTATGGTATTCAGCCTTTGATGATTGATGCACAG                         CAATTGATAATGATGCAACAATTTGCTCTCCGCGAATCAAGAGAAGCACAA
genomic: GGGCGAGAAGCTCATACTATGGTATTCAGCCTTTGATGATTGATGCACAGgtagattctt ... gtttctgaagCAATTGATAATGATGCAACAATTTGCTCTCCGCGAATCAAGAGAAGCACAA
EST: gi|29629980|gb|CB634989.1|CB634989
EST:     GGGCGAGAAGCTCATACTATGGTATTCAGCCTTTGATGATTGATGCACAG                         CAATTGATAATGATGCAACAATTTGCTCTCCGCGAATCAAGAGAAGCACAA
genomic: GGGCGAGAAGCTCATACTATGGTATTCAGCCTTTGATGATTGATGCACAGgtagattctt ... gtttctgaagCAATTGATAATGATGCAACAATTTGCTCTCCGCGAATCAAGAGAAGCACAA
EST: gi|33682425|gb|CF310664.1|CF310664
EST:     GGCGAGAAGCTCATACTATGGTATTCAGCCTTTGATGATTGATGCACAG                         CAATTGATAATGATTCAACAATTTGCTCTCCGCGAATCAAGAGAAGCACAA
genomic: GGCGAGAAGCTCATACTATGGTATTCAGCCTTTGATGATTGATGCACAGgtagattctt ... gtttctgaagCAATTGATAATGATGCAACAATTTGCTCTCCGCGAATCAAGAGAAGCACAA
EST: gi|29622198|gb|CB627209.1|CB627209
EST:     GGGCGAGAAGCTCATACTATGGTATTCAGCCTTTGATGATTGATGCACAG                         CAATTGATAATGATGCAACAATTTGCTCTCCGCGAATCAAGAGAAGCACAA
genomic: GGGCGAGAAGCTCATACTATGGTATTCAGCCTTTGATGATTGATGCACAGgtagattctt ... gtttctgaagCAATTGATAATGATGCAACAATTTGCTCTCCGCGAATCAAGAGAAGCACAA
EST: gi|29669273|gb|CB665548.1|CB665548
EST:     GGGCGAGAAGCTCATACTATGGTATTCAGCCTTTGATGATTGATGCACAG                         CAATTGATAATGATGCAACAATTTGCTCTCCGCGAATCAAGAGAAGCACAA
genomic: GGGCGAGAAGCTCATACTATGGTATTCAGCCTTTGATGATTGATGCACAGgtagattctt ... gtttctgaagCAATTGATAATGATGCAACAATTTGCTCTCCGCGAATCAAGAGAAGCACAA
EST: gi|3760896|gb|C98150.1|C98150
EST:     GGGCGAGAAGCTCATACTATGGTATTCAGCCTTTGATGATTGATGCACAG                         CAATTGATAATGATGCAACAATTTGCTCTCCGCGAATCAAGAGAAGCACAA
genomic: GGGCGAGAAGCTCATACTATGGTATTCAGCCTTTGATGATTGATGCACAGgtagattctt ... gtttctgaagCAATTGATAATGATGCAACAATTTGCTCTCCGCGAATCAAGAGAAGCACAA
EST: gi|29684935|gb|CB681210.1|CB681210
EST:     GGGCGAGAAGCTCATACTATGGTATTCAGCCTTTGATGATTGATGCACAG                         CAATTGATAATGATGCAACAATTTGCTCTCCGCGAATCAAGAGAAGCACAA
genomic: GGGCGAGAAGCTCATACTATGGTATTCAGCCTTTGATGATTGATGCACAGgtagattctt ... gtttctgaagCAATTGATAATGATGCAACAATTTGCTCTCCGCGAATCAAGAGAAGCACAA
EST: gi|3760897|gb|C98151.1|C98151
EST:     GCCTTTGATGATTGATGCACCAG                         CAATTGATAATGATGCAACAATTTGCTCTCCGCGAATCAAGAGAAGCACA
genomic: GCCTTTGATGATTGATGCA-CAGgtagattctt ... gtttctgaagCAATTGATAATGATGCAACAATTTGCTCTCCGCGAATCAAGAGAAGCACA
EST: gi|7839221|gb|AU090632.1|AU090632
EST:     GGGCGAGANGCTCATACTATGGTATTCAGCCTTTGATGATTGATGCACAG                         CAATTGATAATGATGCNACAATTTGCTCTCCGCGAATCAAGAGANGCACAA
genomic: GGGCGAGAAGCTCATACTATGGTATTCAGCCTTTGATGATTGATGCACAGgtagattctt ... gtttctgaagCAATTGATAATGATGCAACAATTTGCTCTCCGCGAATCAAGAGAAGCACAA
EST: gi|29669272|gb|CB665547.1|CB665547
EST:     GGGCGAGAAGCTCATACTATGGTATTCAGCCTTTGATGATTGATGCACAG                         CAATTGATAATGATGCAACAATTTGCTCTCCGCGAATCAAGAGAAGCACAA
genomic: GGGCGAGAAGCTCATACTATGGTATTCAGCCTTTGATGATTGATGCACAGgtagattctt ... gtttctgaagCAATTGATAATGATGCAACAATTTGCTCTCCGCGAATCAAGAGAAGCACAA
EST: gi|29623670|gb|CB628681.1|CB628681
EST:     GGGCGAGAAGCTCATACTATGGTATTCAGCCTTTGATGATTGATGCACAG                         CAATTGATAATGATGCAACAATTTGCTCTCCGCGAATCAAGAGAAGCACAA
genomic: GGGCGAGAAGCTCATACTATGGTATTCAGCCTTTGATGATTGATGCACAGgtagattctt ... gtttctgaagCAATTGATAATGATGCAACAATTTGCTCTCCGCGAATCAAGAGAAGCACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcaatatatatttgaattttaattatgaactgaaacaagatgttgtttctgaagCAATTGATAATGATGCAACAATTTGCTCTCCGCGAATCAAGAGAAGCACAAGACCCCCACAGGGCCATGAGACTGGACATTGACAATATGAGTTATGAG
                 ttttaat  putative branch site (score: 3)
                                           ttgtttct  putative PPT
     tatatatttgaatttt  TA-rich tract