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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgtatttgtactgttttggtgaaataatattaaacagattaaacatacttgtgtgttctatgaagttcactgataacagtttattcctttcttcctgcagCCAAAATCATCTTAATCTTGTAGTGGTGAATAATGTTCCTCTATTTTTCAATATACGTGATGGTCCTTACATGCCAACCCTGCGTCTTCTTCATCAGT

Basic information

species Zea mays
transcript GRMZM2G180990_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G180990_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g21180.1 (Oryza sativa), 3'ss of exon 3
---cgtatttgtactgttttggtgaaata-ata-ttaaacagatta-aacatacttgtgtgttctat---gaagttcactgataacagtttattcctttcttcctgcagCCAAAATCATCTTAATCTTGTAGTGGTGAATAATGTTCCTCTATTTTTCAATATACGTGATGGTCCTTACATGCCAACCCTGCGTCTTCTTCATCAGT
    ||| || ||   ||    | | ||  ||  ||| | ||   | ||  | |  |  ||| ||||    | || ||||||| ||||||  || |||||||     |||||||||||||| |||||||| |||||||||||||| || || ||||||||||| |||||||||||||||||||||||| |||| |||||||||||||
gtgagtagttttatccttcatatcatatgcatgcttagatagccaataatttgcaagattgtactatttaaatgtgcactgatcacagttggtttctttcttt----agCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAATATCCGTGATGGTCCTTACATGCCAACCTTGCGCCTTCTTCATCAGT

upper sequence: GRMZM2G180990_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os01g21180.2 (Oryza sativa), 3'ss of exon 3
---cgtatttgtactgttttggtgaaata-ata-ttaaacagatta-aacatacttgtgtgttctat---gaagttcactgataacagtttattcctttcttcctgcagCCAAAATCATCTTAATCTTGTAGTGGTGAATAATGTTCCTCTATTTTTCAATATACGTGATGGTCCTTACATGCCAACCCTGCGTCTTCTTCATCAGT
    ||| || ||   ||    | | ||  ||  ||| | ||   | ||  | |  |  ||| ||||    | || ||||||| ||||||  || |||||||     |||||||||||||| |||||||| |||||||||||||| || || ||||||||||| |||||||||||||||||||||||| |||               
gtgagtagttttatccttcatatcatatgcatgcttagatagccaataatttgcaagattgtactatttaaatgtgcactgatcacagTTGGTTTCTTTCTTT----AGCCAAAATCATCTGAATCTTGTGGTGGTGAATAATGTCCCACTGTTTTTCAATATCCGTGATGGTCCTTACATGCCAACCTTGC---------------
















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|32830385|gb|CD970063.1|CD970063
EST:     TTGCTAGATGACTTGCTCCCAAAAAAGTCACCTATGATTGTTGTTAAATG                         CCAAAATCATCTTAATCTTGTAGTGGTGAATAATGTTCCTCTATTTTTCAA
genomic: TTGCTAGATGACTTGCTCCCAAAAAAGTCACCTATGATTGTTGTTAAATGgttagtagtt ... cttcctgcagCCAAAATCATCTTAATCTTGTAGTGGTGAATAATGTTCCTCTATTTTTCAA
EST: gi|60337104|gb|DN204077.1|DN204077
EST:     TTGCTAGATGACTTGCTCCCAAAAAAGTCACCTATGATTGTTGTTAAATG                         CCAAAATCATCTTAATCTTGTAGTGGTGAATAATGTTCCTCTATTTTTCAA
genomic: TTGCTAGATGACTTGCTCCCAAAAAAGTCACCTATGATTGTTGTTAAATGgttagtagtt ... cttcctgcagCCAAAATCATCTTAATCTTGTAGTGGTGAATAATGTTCCTCTATTTTTCAA
EST: gi|32830364|gb|CD970042.1|CD970042
EST:     TTGCTAGATGACTTGCTCCCAAAAAAGTCACCTATGATTGTTGTTAAATG                         CCAAAATCATCTTAATCTTGTAGTGGTGAATAATGTTCCTCTATTTTTCAA
genomic: TTGCTAGATGACTTGCTCCCAAAAAAGTCACCTATGATTGTTGTTAAATGgttagtagtt ... cttcctgcagCCAAAATCATCTTAATCTTGTAGTGGTGAATAATGTTCCTCTATTTTTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacttgtgtgttctatgaagttcactgataacagtttattcctttcttcctgcagCCAAAATCATCTTAATCTTGTAGTGGTGAATAATGTTCCTCTATTTTTCAATATACGTGATGGTCCTTACATGCCAACCCTGCGTCTTCTTCATCAGT
                         tgataac  putative branch site (score: 2)
                                  tttattcctttcttcc  putative PPT
                                agtttatt  TA-rich tract