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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatgttcttttatcagcgttaatggaactgaatttccttgcaattcagaattctctccatttggtttacttatctcactgcagttcaatatcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCTTGTATATGACGTCACTCGCCACTCAACCTTTGAGAACGTTGAGCGTTGG

Basic information

species Zea mays
transcript GRMZM2G018619_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G018619_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os06g35814.1 (Oryza sativa), 3'ss of exon 1
taatgttcttttatcagcgttaatggaactgaatttccttgcaattcagaattctctccatttggtttacttat---ctcact-----gcagttcaatatcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCTTGTATATGACGTCACTCGCCACTCAACCTTTGAGAACGTTGAGCGTTGG
        |||| | ||   |    | ||||| ||  |||||||  |||||| ||  |  ||  |||||||| |    |||||         |    | |   |||||||||||||| || |||||||| ||||||||||| |||||||| ||||||||||| ||||| ||||| || ||||||||||||||||| |||||||| |||
--------tttttttagtagtttcagcactgatttatcttgcaaggcagaatgctgccttttcagtttacttctgccttcacttataaagcatctgttcttggtgcagATACCGTGCTATTACTAGTGCATATTACCGAGGTGCTGTTGGAGCGTTGCTTGTCTATGATGTCACCCGGCACTCAACCTTTGAGAATGTTGAGCGCTGG

upper sequence: GRMZM2G018619_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT4G18800.1 (Arabidopsis thaliana), 3'ss of exon 1
------------taatgttcttttatcagcgttaatggaactgaatttccttgcaattcagaattctctccatttggtttacttatctcactgcagttcaatatcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCTTGTATATGACGTCACTCGCCACTCAACCTTTGAGAACGTTGAGCGTTGG
            || | |  |  ||||     ||||  ||| || ||||  ||  | | ||     ||   |   |||||  || | || |  |  |||  |||   |  |||||||| |||||||||||||| || || ||||| |||||||||||| | ||||| || ||||| || || |||||||| || || ||||||||| | |||
catttcggttcttattatgttcctatcttt-ctaatttaacagagtttcaatg--actaag-----tcgttaacgggttt--ttgtttctcctcttttcgctattttt--agATACCGAGCAATCACTAGTGCTTACTATCGAGGAGCTGTTGGGGCGCTTCTTGTTTACGACGTAACCCGACACTCAACATTCGAAAACGTTGAGAGATGG

upper sequence: GRMZM2G018619_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT5G45750.1 (Arabidopsis thaliana), 3'ss of exon 1
taatgttcttttatcagcgttaatggaactgaatttccttgcaattca-gaattctctccattt-ggtttacttatctcactgca--gttcaat--atcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCTTGTATATGACGTCACTCGCCACTCAACCTTTGAGAACGTTGAGCGTTGG
      |   |  || |  ||        | ||  | |||||  ||   |  |||      ||| |||| |||||  || |||    ||| | |   |  |   || ||||| || ||||||||||||||||||||||| |||||||| ||| | ||||| || || || || || |||||||| ||||| |||||||||  ||||
------tgcatagtctgaattcgaaactgtaaagcttcttgccttttttgtgttcctgatgtttcggttaacttaattctctgtttcgttgactttgtttcaatagGTACCGAGCCATCACTAGTGCGTATTACCGAGGAGCTGTTGGAGCGCTTCTTGTCTACGATGTAACCCGACACTCAACATTTGAAAACGTTGAGACTTGG

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|211261234|gb|FL032912.1|FL032912
EST:     AGTACGCAGCAGTGCAGCAGGTGGCGTGGACTGAATAAGACTTTCTGAAG                         ATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT
genomic: AGTACGCAGCAGTGCAGCAGGTGGCGTGGACTGAATAAGACTTTCTGAAGgttagtaggt ... atcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCT
EST: gi|50338884|gb|CO534010.1|CO534010
EST:     AGTACGCAGCAGTGCAGCAGGTGGCGTGGACTGAATAAGACTTTCTGAAG                         ATACCGTGCAATCACTAGTGCGTA
genomic: AGTACGCAGCAGTGCAGCAGGTGGCGTGGACTGAATAAGACTTTCTGAAGgttagtaggt ... atcactgcagATACCGTGCAATCACTAGTGCGTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagaattctctccatttggtttacttatctcactgcagttcaatatcactgcagATACCGTGCAATCACTAGTGCGTATTACCGAGGCGCTGTTGGGGCGTTGCTTGTATATGACGTCACTCGCCACTCAACCTTTGAGAACGTTGAGCGTTGG
                           atctcac  putative branch site (score: 3)
                    tttacttat  TA-rich tract