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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggtatttatgtggttatgttcaagataagttactgtgcatactaattctagatagataaaatattttgatgaaaattagatcatagcatgacttatgttgtgcttccattgcctttacagGTTAAACCAATTTCTGTCCAATACGGGATTGGCATACGTGAACATGATCATGAGGGCAGGGTTATTACTCTGGAGTTTGATGGTTTTTACTTGGTAAATG

Basic information

species Oryza sativa
transcript LOC_Os01g58690.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g58690.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G086246_T01 (Zea mays), 3'ss of exon 3
-----------------------------gtatggtatttatg-tggttat---gttcaagataagttactgtgca-tactaattctagata-gataaaatattttgatgaaaattagat-catagcatgacttatgttgtgcttccat-tgcctttacagGTTAAACCAATTTCTGTCCAATACGGGATTGGCATACGTGAACATGATCATGAGGGCAGGGTTATTACTCTGGAGTTTGATGGTTTTTACTTGGTAAATG
                              | |    ||| |  ||  ||    ||    |   ||   |  |||| ||    ||||  |    |||  ||   |||||  | | || ||   || | | ||||    ||| |||   | ||| || ||||||  ||||||| || || ||||| ||| |||||||||  || |||||||| || |||||| |||||||  |||||||||||| ||||||||||       
gtatgttcttcctgtggttaatgcccaacatctcccttttgtactgactaaaaagtcagtggatagcagcattgcaataaatcttctgaacccaatactatcagttgatacatagtatatatctaacctcactttccgtgttcttttgtatgcattaacagGTACAACCAATCTCAGTTCAATATGGGCTTGGCATACCAGAGCATGATCAGGAAGGCAGGCTTATTACCTTGGAGTTTGATGATTTTTACTTG-------

upper sequence: LOC_Os01g58690.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM5G800154_T01 (Zea mays), 3'ss of exon 5
-----------------------------gtatggtatttatg-tggttatgttcaagataagttactgtgc-atactaattct----agatagataaaatattttgatgaaaattagat-catagcatgacttatgttgtgcttccat-tgcctttacagGTTAAACCAATTTCTGTCCAATACGGGATTGGCATACGTGAACATGATCATGAGGGCAGGGTTATTACTCTGGAGTTTGATGGTTTTTACTTGGTAAATG
                              | |    ||| |  ||  ||    |    |   |  | |      | ||| |||    |     |||  ||   |||||  | | || ||   || | | ||||    ||| |||   | ||| || ||||||  ||||||| || || ||||| ||| |||||||||  || | |||||| || |||| | |||||||  |||||||||||| |||||||||||| ||||
gtatgttctttctatggttaatgcccaacatctcccttttgtactgactaaaaactcagtggatagcagcattgcaataaatcttctgaacccaatactatcagttgatacatagtatatatctaacctcactttctgtgttcttttgtatgcattaacagGTACAACCAATCTCAGTTCAATATGGGCTTGGCATACCAGAGCGTGATCAGGAAGGCATGCTTATTACCTTGGAGTTTGATGATTTTTACTTGGTCAATG

upper sequence: LOC_Os01g58690.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G139329_T02 (Zea mays), 3'ss of exon 3
---------------------------gtatggtatttatgtggttatgttcaagataagttactgt-gcatactaat------tctagata-gataaaatattttgatgaaaattagat-catagcatgacttatgttgtgcttccat-tgcctttacagGTTAAACCAATTTCTGTCCAATACGGGATTGGCATACGTGAACATGATCATGAGGGCAGGGTTATTACTCTGGAGTTTGATGGTTTTTACTTGGTAAATG
                           | ||     || |||  | |     |||  |    |  |  ||||   |||      |||  |    |||  ||   |||||  | | || ||   || | | ||||    ||| |||   | ||| || ||||||  ||||||| || || ||||| ||| |||||||||  || |||||||| || |||||| |||||||  |||||||||||| |||||||||||| ||||
gtatgttcttcctgtggttaatgcccagcatctcccttttgtactgactaaaaagtcagtggatagcagcattgcaataaatcttctgaacccaatactatcagttgatacatagtatatatctaacctcactttccgtgttcttttgtatgcattaacagGTACAACCAATCTCAGTTCAATATGGGCTTGGCATACCAGAGCATGATCAGGAAGGCAGGCTTATTACCTTGGAGTTTGATGATTTTTACTTGGTCAATG

upper sequence: LOC_Os01g58690.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G134072_T02 (Zea mays), 3'ss of exon 4
-----------------------------gtatggtatttatg-tggttat---gttcaagataagttactgtgca-tactaattctagata-gataaaatattttgatgaaaattagat-catagcatgacttatgttgtgcttccat-tgcctttacagGTTAAACCAATTTCTGTCCAATACGGGATTGGCATACGTGAACATGATCATGAGGGCAGGGTTATTACTCTGGAGTTTGATGGTTTTTACTTGGTAAATG
                              | |    ||| |  ||  ||    ||  | |   ||   |  |||| ||    ||||  |    |||  ||   |||||  | | || ||   || | | ||||    ||| |||   | ||| || ||||||  ||||||| || || ||||| ||| ||| ||||   || | |||||| || |||||| |||||||  |||||||||||| |||||||||||| ||||
gtatgttcttcttatggttaatgcccaacatctcccttttgtactgactaaaaagtcaatggatagcagcattgcaataaatcttctgaacccaatactatcagttgatacatagtatatatctaacctcactttccgtgttcttttgtatgcattaacagGTACAACCAATCTCAGTTCAATATGGGCTTGACATAACAGAGCGTGATCAGGAAGGCAGGCTTATTACCTTGGAGTTTGATGATTTTTACTTGGTCAATG

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|27546396|gb|CA764589.2|CA764589
EST:     CATGCAGCGTCTCGAGGCTTGGCTATTCAGGGACTGCTGTAATTTCACGG                         GTTAAACCAATTTCTGTCCAATACGGGATTGGCATACGTGAACATGATCAT
genomic: CATGCAGCGTCTCGAGGCTTGGCTATTCAGGGACTGCAGTAATTTCACGGgtatggtatt ... gcctttacagGTTAAACCAATTTCTGTCCAATACGGGATTGGCATACGTGAACATGATCAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatgaaaattagatcatagcatgacttatgttgtgcttccattgcctttacagGTTAAACCAATTTCTGTCCAATACGGGATTGGCATACGTGAACATGATCATGAGGGCAGGGTTATTACTCTGGAGTTTGATGGTTTTTACTTGGTAAATG
 ttttgat  putative branch site (score: 4)
                                     cttccattgccttt  putative PPT
      aaaattagatcata  TA-rich tract