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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctgtatgccagtaccatgtgctattcttgtttcctttcaaaaattaatggtagattgaagttatgtcagggttcctattttttatgtaattcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAGTGGTGCCAGACAGCCAACAATGCTCTCTCCCTTTTGTCTACAAATGATA

Basic information

species Zea mays
transcript GRMZM2G165418_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g36770.1 (Oryza sativa), 3'ss of exon 3
-tgctgtatgccagtaccatgtgctattcttgtt---tcctttcaaaaattaatggtagattgaagtt-atgtcagggttcctattttttatgtaattcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAGTGGTGCCAGACAGCCAACAATGCTCTCTCCCTTTTGTCTACAAATGATA
 ||  | ||  || ||   ||   |  |||||||   | ||| |   ||||| | | | || |||  | |  ||   |||    ||||| ||| || | || |||||||| |||||||||||||||||||||||||| |||||||||| ||||| |||||||||||||||||| ||| | ||||||||| |||||||||||||||
atgaagcattacattattgtgctatgctcttgttttgttcttgcttgaattacttgcatatggaaactcacatctatgtt----tttttgatg-aactgttctagTTTGATTACCTCAAAAGTTTGGAAATAGAGGAGAAGATCAACAAGATCAGGTGGTGCCAGACAGCCAATAATTCACTCTCCCTTCTGTCTACAAATGATA

upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA08G20830.4 (Glycine max), 3'ss of exon 3
tgctgtatgccagtaccatgtgcta-ttcttgtttcctttcaaaaattaatggtagattgaagttatgtcagggttcctattttttatgtaattcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAGTGGTGCCAGACAGCCAACAATGCTCTCTCCCTTTTGTCTACAAATGATA
        |  | |  ||    ||  ||  || | |||      || |  | || ||    |   |||| |   ||  |    | |   |  || ||  |||||||||| || || |||||||||||||| || || || ||||  ||||| |||||||| ||||||||   |||| | | |||| | || ||||||||||
--------gtaattttcagtcactggttaatgctgcct-----gaaatgcttgtggagcagaa--atgttaacatttatgacatgtg-attgttgtttcagTTTGACTATCTTAAGAGTTTGGAAATAGAAGAGAAAATTAACAAAATCAAATGGTGCCAAACAGCCAATGGTGCTTTGTTCCTTCTATCCACAAATGATA

upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv09s0002g02470.t01 (Vitis vinifera), 3'ss of exon 3
-------tgctgtatgccagtaccatgtgctattcttgtttcctttcaaaaattaatggtagattgaagttatgtcagggttcctattttttatgtaattcttgt--agTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAGTGGTGCCAGACAGCCAACAATGCTCTCTCCCTTTTGTCTACAAATGATA
       |    |  |  | | |    ||   ||  | |   |   |      | |        |||| |  | | |  | | | |  ||   | |  |   ||   |||||||||| || || || |||||||||||||| || ||||| | |||||  |||||||||||||| ||   ||| || |  ||| | ||||| |||||||
gtatttctttcatcagttactcctgcctgaagtttgtttgcaccaccctttgctcactaggctctgaaatgttttaattgatgccacattgcttattctctgtgctcagTTTGACTATCTGAAGAGCTTGGAAATAGAGGAGAAAATCAATAAGATCAGATGGTGCCAGACAGCAAATGGTGCCCTGTTTCTTCTATCTACGAATGATA

upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 4
lower sequence: PP1S100_124V6.1 (Physcomitrella patens), 3'ss of exon 3
tgctgtatgccagtaccatgtgctattcttgtttcctttcaaaaattaatggtagattgaagttatgtcagggttcctattttttatgtaattctt---gtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAGTGGTGCCAGACAGCCAACAATGCTCTCTCCCTTTTGTCTACAAATGATA
   ||| |     |||  | ||    |  |           | | ||  ||||  ||   | ||     |    | || || |  ||||| ||  |   | |||| || ||||| || ||||||||||||||||| ||||||||||  || |  |||||||||||  ||||   ||| |  |  ||  | ||||||||||| |
---tgtgtagggatactgtttgacggtaatccagttgcattacacttgttggtcaatcctattttacgaacacgtgcttttctgaatgtattttgttatgcagTTCGATTACCTGAAGAGTTTGGAAATAGAGGAGAAGATCAACAAAATAAGATGGTGCCAGACCACCAATGCTGCCCAGTTTCTACTTTCTACAAATGACA

upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ09063 (Selaginella moellendorffii), 3'ss of exon 3
tgctgtatgccagtaccatgtgctattcttgtttcctttcaaaaattaatggtagattgaagttatgtcagggttcctattttttatgtaattcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAGTGGTGCCAGACAGCCAACAATGCTCTCTCCCTTTTGTCTACAAATGATA
                             ||       || |   || |  |    |||| | ||  |         || ||||  | |   |     |||||||||||||||| ||  |||| |||||||||||||||||||  ||||  ||||| || || || |||   ||||  |   |||| || || ||||| |
----------------------------gtgcgcttgctctatcgttga-agcgtgttgatgctacat---------tacttttgttttggcttccccagTTTGACTACCTCAAGAGCCTGGAGATAGAGGAAAAGATCAACAAAATCAGATGGTGTCACACGGCTAACGGCGCTCGTTTTGTTTTATCCACTAATGACA

upper sequence: GRMZM2G165418_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ08844 (Selaginella moellendorffii), 3'ss of exon 3
tgctgtatgccagtaccatgtgctattcttgtttcctttcaaaaattaatggtagattgaagttatgtcagggttcctattttttatgtaattcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAGTGGTGCCAGACAGCCAACAATGCTCTCTCCCTTTTGTCTACAAATGATA
                             ||       || |   || |  |    |||| | ||  | |         |||||| | |   |     |||||||||||||||| ||  |||| |||||||||||||||||||  ||||  ||||| || || || |||   ||||  |   |||| || || ||||| |
----------------------------gtgcgcttgctctatcgttga-agcgtgttgatgctacatta-------ctttttttttttggcttccccagTTTGACTACCTCAAGAGCCTGGAGATAGAGGAAAAGATCAACAAAATCAGATGGTGTCACACGGCTAACGGCGCTCGTTTTGTTTTATCCACTAATGACA

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|31352864|gb|CD437221.1|CD437221
EST:     GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
genomic: GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAGgttaataagc ... attcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
EST: gi|18649538|gb|BM498357.1|BM498357
EST:     GCTACAAAACTGAATTTCAGAGTCATGAACCTGAG                         TTGGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGGTCAACAGGATCAAG
genomic: GCTACAAAACTGAATTTCAGAGTCATGAACCTGAGgttaataagc ... attcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG
EST: gi|19822589|gb|BQ048613.1|BQ048613
EST:     GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAG                         TTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGGTCAACAGGATCAAG
genomic: GACACCCAGAGTTCCGCTACAAAACTGAATTTCAGAGTCATGAACCTGAGgttaataagc ... attcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaatggtagattgaagttatgtcagggttcctattttttatgtaattcttgtagTTTGACTACCTCAAAAGTTTGGAAATAGAGGAAAAGATCAACAGGATCAAGTGGTGCCAGACAGCCAACAATGCTCTCTCCCTTTTGTCTACAAATGATA
 aattaat  putative branch site (score: 3)
                                              ttcttgt  putative PPT
                                tattttttatgtaatt  TA-rich tract