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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgttttaccctagggtgctaatagtattccattttttaatatgcatgcctggcacatgagtatttttgttcaaactttaacggtggctgtctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGT

Basic information

species Zea mays
transcript GRMZM2G122039_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G122039_T07 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g06340.2 (Oryza sativa), 3'ss of exon 2
-tgttttaccctagggtgctaatagtattccattttttaatatgcatgcctggcacatgagtatttttgttcaaactttaacggtggctgtctg-ttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGT----------
   ||| |||||||| |  |||||      |   ||   |     ||||       |||| | |    | | |||   ||| ||||  ||| || ||  ||||| |||||||||||||| ||||| ||||||||||| || |||||||||||||||||||| || || || ||||||||||| |||||||||          
ccctttcaccctaggctcataatatcgcgacgacttagcaatgatatgcgctatg-atgaat-tcaacgcttaaatcctaatggtgtttgtatggtttgcagAAGTGCGTCAAGAGAGTGGAGAAGGATGATACTGGGCATAAACACTGCACTGGGCAATATTTCGACTATTGGTCATGCATTGACAAATGTGTAAGTATCT

upper sequence: GRMZM2G122039_T07 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g06340.1 (Oryza sativa), 3'ss of exon 2
-tgttttaccctagggtgctaatagtattccattttttaatatgcatgcctggcacatgagtatttttgttcaaactttaacggtggctgtctg-ttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGT
   ||| |||||||| |  |||||      |   ||   |     ||||       |||| | |    | | |||   ||| ||||  ||| || ||  ||||| |||||||||||||| ||||| ||||||||||| || |||||||||||||||||||| || || || ||||||||||| |||||||||
ccctttcaccctaggctcataatatcgcgacgacttagcaatgatatgcgctatg-atgaat-tcaacgcttaaatcctaatggtgtttgtatggtttgcagAAGTGCGTCAAGAGAGTGGAGAAGGATGATACTGGGCATAAACACTGCACTGGGCAATATTTCGACTATTGGTCATGCATTGACAAATGT

upper sequence: GRMZM2G122039_T07 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA08G19380.1 (Glycine max), 3'ss of exon 2
tgttttaccctagggtgctaa--tagtattccatttt-ttaatatgcatgcctggcacatgagtatttttgttcaaactttaacggtggctgtctg--ttat--cagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGT
          ||   ||| ||  |  | |||    || || || |  ||  ||   |  | ||  || ||| |    |   ||  ||   ||| |   ||    |||   ||| | || ||  |  |   ||||||  |||| || |||||||||||||| ||||| |||||||| ||||| || || |||||||||
-----agtgataaattgccaaatttttgttctgccttatttatttttatttcttcaaattaag--ttcttgcttggccgagaaaagtaattgtttaaattgctacagGCGTGCATTAAAAGGATACATGGTGATGAATCTGGGCAGAAACACTGCACTGGACAATATTTTGATTATTGGTCTTGTATTGACAAATGT

upper sequence: GRMZM2G122039_T07 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA15G05620.1 (Glycine max), 3'ss of exon 2
tgttttaccctagggtgctaatagtattccattttttaatatgcatgcctggcacatgagtatttttgttcaaactttaacggtggctgtctg--ttat--cagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGT
   |      ||   ||  ||   | |   ||   ||||| |          || || |   || ||| |    |   ||  ||   ||| ||  ||    |||   ||| | || ||  |  |   ||||||| |||| || |||||||||||||| ||||| |||||||| ||||| || || |||||||||
---tgagtgataaattgtcaaatttttgttatgccttaattttttatttcttcaaattaa-gttcttgcttggccgagaaaagtaattgtttgaattgctacagGCGTGCATTAAAAGGATACATGGTGATGATTCTGGGCAGAAACACTGCACTGGACAATATTTTGATTATTGGTCTTGTATTGACAAATGT

upper sequence: GRMZM2G122039_T07 (Zea mays), 3'ss of exon 2
lower sequence: AT2G01090.2 (Arabidopsis thaliana), 3'ss of exon 3
-----------------------------------------------------tgttttaccctagggtgctaatagtattccattttttaatatgcatgcctggcacatga----gtatttttgttca----aactttaacg----gtggctgtctgttat-cagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGT----------
                                                     |  |||  | ||| | |  | | | ||| | ||   |  |    ||   |  ||||| |    |  | || || |     |  ||||||     || | |||  ||  | |||   || ||||||||  |  |  |||||||  |||| |||||||| |||||||||||||| ||||||||||||   ||  | |||||||||          
gtgaatacgacttgagctgtcactggtcataaccttgttttgcattatacgagtcatttgacatagagagagagttg-attgctttcggtgctgcttatctatctcacatcacatggcttcttagtgctgctcagttttaacatcttgttgttgtgggtggttcagGCGTGTGTCAAGAGGATCCAAGATGATGAGTCTGGCCACAAACATTGCACTGGGCAATATTTTGATTACTGGCATTGTGTTGACAAATGTGTAAGTGTGT

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|56382672|gb|CV985341.1|CV985341
EST:     GAAGTAGCTGATTAAGGATACCTTACCAAATTAGTCGGGACATGATACTG                         AAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT
genomic: GAAGTAGCTGATTAAGGATACCTTACCAAATTAGTCGGGACATGATACTGgtattagtca ... ctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcctggcacatgagtatttttgttcaaactttaacggtggctgtctgttatcagAAATGCGTCAAGAGAGTTGAGAATGATGATACTGGTCACAAACACTGCACTGGGCAATACTTTGATTACTGGTCATGCATCGACAAATGT
                             ctttaac  putative branch site (score: 3)
               tatttttgttcaaa  TA-rich tract