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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatactgtagtgatgaattagtagtaccgaatgatttttttattttttttggtcaaagaaagcttttgtttgttggtcttgttgatgaaacatttgtataacttcataataattatttttcagGACTTCGGTGATGACAAGCCTATGGGTTGGAGCCACTTCACTGCTGAAGGAGATGTTGAGTTCAAAGCTTTGCTCTTCATTCCACCGAAGGCTCCGCATG

Basic information

species Zea mays
transcript GRMZM2G399073_T03
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G399073_T02 (Zea mays), 3'ss of exon 11
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 3'ss of exon 9
gtaatactgtagtgatgaattagtagtaccgaatgatttttttattttttttggtcaaagaaagcttttgtttgttggtcttgttgatgaaac--atttgtataacttcataataa-ttatttttcagGACTTCGGTGATGACAAGCCTATGGGTTGGAGCCACTTCACTGCTGAAGGAGATGTTGAGTTCAAAGCTTTGCTCTTCATTCCACCGAAGGCTCCGCATG
                         ||||  |  || |    |  |   |||     |  | | | ||| | |||  | ||||  || ||||   | |    | | || |||  || |||||||  ||||||| ||||||||||||||  ||  ||||||||||||||||||||| |||||||||||||||||||||||||||||  |||| || |||||||| ||||
-------------------------gtacaca--gactgcagtgatgaatttacaggagcataacattt-tatgtaagccttgcagaagaaagcaagtaacctcatttaatatcaaattattttgtagGACTTTGGTGATGACAAGCCCTTGTCTTGGAGCCACTTCACTGCTGAGGGAGATGTTGAGTTCAAAGCTTTGCTCTTTGTTCCTCCCAAGGCTCCACATG

upper sequence: GRMZM2G399073_T02 (Zea mays), 3'ss of exon 11
lower sequence: PP1S126_38V6.1 (Physcomitrella patens), 3'ss of exon 9
-----------------------------------------------------------gtaatactgtagtgatgaattagtagtaccgaatgat--ttttttattttttttggtcaaagaaagcttttgtttgttggtcttgttgatgaaacat-ttgtataacttcataataattattttt-------cagGACTTCGGTGATGACAAGCCTATGGGTTGGAGCCACTTCACTGCTGAAGGAGATGTTGAGTTCAAAGCTTTGCTCTTCATTCCACCGAAGGCTCCGCATG
                                                           |  |    || |       ||   | |   | | | |  | | | | | | | ||   |  | ||   |  | | ||   | ||||||| |  ||   ||||   | |   |  |  |  |||||       ||||| ||| ||   |||||||| |||   |||||||| |||| |||||| |||||||| |||||||||||  |  | |  || || || ||||||||  |||
gtgagggttggacttcaaatcctatgatagacttggctatctgtcaaacgtgtgattaagacaagaggttgccgcatgttgagacttgtggaagttggtctctgaatctatatgactaggggaataatcagctcgtca-tgttgttgaagtgacgggttgtcctaatcttttgttgtccttttttctcattcagGATTTCAGTACCGACAAGCCAATGTCGTGGAGCCATTTCAATGCTGAGGGAGATGTGGAGTTCAAAGCAGTCATATATATCCCTCCTAAGGCTCCTTATG

upper sequence: GRMZM2G399073_T02 (Zea mays), 3'ss of exon 11
lower sequence: EFJ17496 (Selaginella moellendorffii), 3'ss of exon 10
gtaatactgtagtgatgaattagtagtaccgaatgatttttttattttttttggtcaaagaaagcttttgtttgttggtcttgttgatgaaacatttgtataacttcataataattatttttcagGACTTCGGTGATGACAAGCCTATGGGTTGGAGCCACTTCACTGCTGAAGGAGATGTTGAGTTCAAAGCTTTGCTCTTCATTCCACCGAAGGCTCCGCATG
                                                                     ||  | || | |  |||   ||    ||||  || || |     ||| ||   ||||| |        |||||||| |||   ||||| || ||| |||| ||||||||||| |||||||| ||| || | |||||||| ||||||||||||||||
---------------------------------------------------------------------gtgagctgatgtgattggcaaat--gttgt-caattttacgtgcattgtt---cagGATTATAACCCCGACAAGCCAATGTCCTGGAGTCATTTCTCTGCGGAAGGAGATGTCGAGTTCAAGGCTGTGTTGTTCATTCCTCCGAAGGCTCCGCATG

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|211478283|gb|FL245116.1|FL245116
EST:     GAAGTTTTACCACTCACTAGCCAAG                         GACTTCAGTGATGACAAGCCTATGGGGTGGAGCCACTTCACTGCTGAAGGA
genomic: GAAGTTTTACCACTCACTAGCCAAGgtaatactgt ... tatttttcagGACTTCGGTGATGACAAGCCTATGGGTTGGAGCCACTTCACTGCTGAAGGA
EST: gi|22489665|gb|BU049575.1|BU049575
EST:     AGGAGGTTACTGACGAAGAATACTCAAAGTTTTACCACTCACTAGCCAAG                         GACTTCGGTGATGACAAGCCTATGGGTTGGAGCCACTTCACTGCTGAAGGA
genomic: AGGAGGTTACTGATGAGGAATACTCGAAGTTTTACCACTCACTAGCCAAGgtaatactgt ... tatttttcagGACTTCGGTGATGACAAGCCTATGGGTTGGAGCCACTTCACTGCTGAAGGA
EST: gi|19822479|gb|BQ048503.1|BQ048503
EST:     GGAGGTTACTGCCGAAGAATACTCAAAGTTTT-CCACTTCACTAGCCAAG                         GACTTCGGTGATGACAAGCCTATGGGTTGGAGCCACTTCACTGCTGAAGGA
genomic: GGAGGTTACTGATGAGGAATACTCGAAGTTTTACCAC-TCACTAGCCAAGgtaatactgt ... tatttttcagGACTTCGGTGATGACAAGCCTATGGGTTGGAGCCACTTCACTGCTGAAGGA
EST: gi|211478285|gb|FL245118.1|FL245118
EST:     GAAGTTTTACCACTCACTAGCCAAG                         GACTTCAGTGATGACAAGCCTATGGGTTGGAGCCACTTCACTGCTGAAGGA
genomic: GAAGTTTTACCACTCACTAGCCAAGgtaatactgt ... tatttttcagGACTTCGGTGATGACAAGCCTATGGGTTGGAGCCACTTCACTGCTGAAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgttggtcttgttgatgaaacatttgtataacttcataataattatttttcagGACTTCGGTGATGACAAGCCTATGGGTTGGAGCCACTTCACTGCTGAAGGAGATGTTGAGTTCAAAGCTTTGCTCTTCATTCCACCGAAGGCTCCGCATG
                           gtataac  putative branch site (score: 3)
                                            ttatttttc  putative PPT
                atgaaacatttgtata  TA-rich tract