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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatatcaccctagtttttttgagtattcaattattgtttttctcactcgaattttatgtcatcattgcaatattttttatgttcagGTTGATACATTCTTTGCTGTTGGATCTCCCTTGGGTGTCTTCCTTTCCCTGCGTAATGTCCGTATTGGTATTG

Basic information

species Zea mays
transcript GRMZM2G318860_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G318860_T02 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os08g01920.1 (Oryza sativa), 3'ss of exon 13
gtgatatcaccctagtttttttgagtattcaattattgtttttctcactcgaattttatgtcatcattgcaatatttttta-tgttcagGTTGATACATTCTTTGCTGTTGGATCTCCCTTGGGTGTCTTCCTTTCCCTGCGTAATGTCCGTATTGGTATTG
        |  ||    |   | | ||| |||| ||   ||| ||    | |   |||||      || ||  ||||||   | |||||||||| ||||||| |||||||||||| ||||| || || ||| | |||||||| ||||| || ||||||||||
------gtagtctgtcctaaatcaatatccaataatctatttacttgtac-atcattatgctgc--ttacaccatttttggctattcagGTTGACACATTCTATGCTGTTGGATCCCCCTTAGGAGTTTTCTTGTCCCTGCGGAATGTTCGCATTGGTATTG

upper sequence: GRMZM2G318860_T02 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA09G36920.1 (Glycine max), 3'ss of exon 14
----------gtgatatcaccctagtttttttgag-tattcaattattgtttttctcactcgaattttatgtcatcattgcaatattttttatgt-tcagGTTGATACATTCTTTGCTGTTGGATCTCCCTTGGGTGTCTTCCTTTCCCTGCGTAATGTCCGTATTGGTATTG
           |  |||  || ||||   | | |   | |   | ||| || ||   |    ||  |  ||     ||  | | | |   ||| |  |||||||||||||||||||| |||||||| ||  | ||||| || ||| | || |||||| |||| ||||| ||||
acatgggccatttttatttccatagtaaatctaaaacaatgggtcatttttatttctatagtaacctattgctcatatgactaaactgcatatatgccagGTTGATACATTCTTTGCCGTTGGATCCCCTCTTGGTGTATTTCTTGCACTTCGTAATATCCGAATTGGCATTG
















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|31354196|gb|CD438553.1|CD438553
EST:     CAAACCAGTCCTACTCACCGCAAATCAAATACACGAAACTAAACTTTAAG                         GTTGATACATTCTTTGCTGTTGGATCTCCCTTGGGTGTCTTCCTTTCCCTG
genomic: CAAACCAGTCCTACTCACCGCAAATCAAATACACGAAACTAAACTTTAAGgtgatatcac ... ttatgttcagGTTGATACATTCTTTGCTGTTGGATCTCCCTTGGGTGTCTTCCTTTCCCTG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgtttttctcactcgaattttatgtcatcattgcaatattttttatgttcagGTTGATACATTCTTTGCTGTTGGATCTCCCTTGGGTGTCTTCCTTTCCCTGCGTAATGTCCGTATTGGTATTG
        ttctcac  putative branch site (score: 2)
                                       tatttttt  putative PPT
                                attgcaatatttttta  TA-rich tract