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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgattccatctaaatactatagtgttacattaaccgctgcataatttttatttggattagttaacagtaatattttcccttcccttttgtatgtatctagTGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT

Basic information

species Zea mays
transcript GRMZM5G825902_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G825902_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os12g05650.1 (Oryza sativa), 3'ss of exon 4
tgattccatctaaatactatagtgttacattaaccgctgca-taatttttatttggattagttaacagtaatattttcccttcccttttgtatgtatctagTGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT
  |   ||| ||   |||||  || | | |  |  | |    | ||||  ||        ||  |   | || |||| ||  | ||| ||| ||||||||| |||||||| ||||||||||||||||  || |||| ||| ||||||||  | || ||||||||||| ||||| ||||||
-taaaacatttagcaactatcatgcttcttatattgttttggtgatttggataatttcatgtctaatattatctttttccccctcttctgtctgtatctagGGGGCGCAAAGTTGAGGACCCTGACACATTGGAAAAGATACGGCTAACAGTTATTAACAACCTTCTGCAGTATCATCCT

upper sequence: GRMZM5G825902_T02 (Zea mays), 3'ss of exon 4
lower sequence: Vv13s0147g00220.t01 (Vitis vinifera), 3'ss of exon 4
--tgattccatctaaatactatagtgttaca-ttaaccgctgcataatttttatttggat-tagttaacagtaatattttcccttcccttttgtatgtatctagTGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT
  |  || |||      | |||  |  | || ||   |  |   |  | ||| ||||| | |  | | |  | | |    |  |     ||  ||||    |  ||| ||||| ||||| || |||||||||||||| || ||||| || || ||||||||||||||| |  |||| ||||| 
aatatttgcattagttaagtattttaatccagttgttcaatctttcctgtttttttgggtgttatcatcctttacaaaa-caatgttgattaatatgctagTGATGGACGCAAAGTTGAAGATCCTGACATGTTAGAGAGAATTCGACTTACAATCATCAACAACCTTTTGAAGTATCATCCA
















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|60394317|gb|DN227187.1|DN227187
EST:     CCATTGTGCAGCTAAGTTTTGGAGATCGTTTGGGGGCGCTACTTGACACG                         TGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT
genomic: CCATTGTGCAGCTAAGTTTTGGAGATCGCTTGGGGGCACTACTTGACACGgtatatattt ... atgtatctagTGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttatttggattagttaacagtaatattttcccttcccttttgtatgtatctagTGGGCGCAAGGTTGAGGACCCTGACATGTTAGAAAGGATTCGGCTAACCATCATCAACAACCTTCTCCAGTACCATCCT
             agttaac  putative branch site (score: 3)
                         tattttcccttccctt  putative PPT
          attagttaacagtaat  TA-rich tract