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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtcacctctcatgtgaataggcctgcttttgttctattgctgaataatgtaatagtattgacgattcttgctgctattttccagTGATTGTTGGAGAAGTGGCTAACTTTGCAGCATATGCTTTTGCTCCTGCTATCTTGGTCACACCACTTGGTGCACTTAGCATCATAATTAG

Basic information

species Zea mays
transcript GRMZM2G110398_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G110398_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g65986.1 (Oryza sativa), 3'ss of exon 2
gtaggtcacctctcatgtgaataggcctgcttttgttctattgctgaataatgtaatagtattgacgattcttgctgctattttccagTGATTGTTGGAGAAGTGGCTAACTTTGCAGCATATGCTTTTGCTCCTGCTATCTTGGTCACACCACTTGGTGCACTTAGCATCATAATTAG
||| ||||    |  |    ||| |      ||  | ||| | || |  | ||| |||   |||||  |  |   |||| |||||||||||||||||||||||| |||||||||||||||||||| ||||||||||||||||| || || ||||||||||| || |||||||| || ||
gtaagtcaaaatttctaaatataagtaattattcatgctaatacttatcagtgtgata---ttgacagtattcagtgctgttttccagTGATTGTTGGAGAAGTAGCTAACTTTGCAGCATATGCCTTTGCTCCTGCTATCTTAGTAACCCCACTTGGTGCGCTAAGCATCATCATCAG

upper sequence: GRMZM2G110398_T01 (Zea mays), 3'ss of exon 2
lower sequence: PP1S49_181V6.2 (Physcomitrella patens), 3'ss of exon 2
gtaggtcacctctcatgtgaataggcctgcttttgttctattgctgaataatgtaatagtattgacgattcttgctgctattttccagTGATTGTTGGAGAAGTGGCTAACTTTGCAGCATATGCTTTTGCTCCTGCTATCTTGGTCACACCACTTGGTGCACTTAGCATCATAATTAG
||| |    ||      |   ||  | || |  | || | | |   | |     ||    ||||||  |      ||  |  |  |||||||||| ||||||||||| |||||  | || || || |||||||| ||| |||||||||| || ||||| ||||| ||||| ||| | ||
gtaagatcacttcagcttatttattcatggtgct-ttttgtggagaactttctcaacg--attgacc-tggaaagtgtgagctggcagTGATTGTGGGAGAAGTGGCCAACTTCACTGCCTACGCGTTTGCTCCGGCTGTCTTGGTCACTCCGCTTGGCGCACTGAGCATAATAGTCAG
















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|18384468|gb|BM417667.1|BM417667
EST:     TGGTTACTCTTACTTGTATGACCCATTATGGTGGGCAGGAATGATTACAA                         TGATTGTTGGAGAAGTGGCT
genomic: TGGTTACTCTTACTTGTATGAACCATTATGGTGGGCAGGAATGATTACAAgtaggtcacc ... tattttccagTGATTGTTGGAGAAGTGGCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttctattgctgaataatgtaatagtattgacgattcttgctgctattttccagTGATTGTTGGAGAAGTGGCTAACTTTGCAGCATATGCTTTTGCTCCTGCTATCTTGGTCACACCACTTGGTGCACTTAGCATCATAATTAG
                          tattgac  putative branch site (score: 2)
                                            ctattttcc  putative PPT
             aataatgtaatagtat  TA-rich tract