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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtagtcggtttcaaaccgatgatgatactgcgttctccaaacgtcaatcgtttgtgcttcgagctacgacctattttcctgacgaaatttaaatctgcagTGGGACATCCTCTCGAACGGTGGTGCTGTCCAAGAAATGGCTCACATTGCCAACGGCCGGGACCATGGCAACTGTGTCTCCCTCCTTCGTGTCAAT

Basic information

species Zea mays
transcript GRMZM2G130442_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G130442_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os08g08820.1 (Oryza sativa), 3'ss of exon 9
gtagtcggtttcaaaccgatgatgatactgcgttctccaaacgtcaatcgtttgtgcttcgagctacgacctattttcctgacgaaatttaaat-ctgcagTGGGACATCCTCTCGAACGGTGGTGCTGTCCAAGAAATGGCTCACATTGCCAACGGCCGGGACCATGGCAACTGTGTCTCCCTCCTTCGTGTCAAT
||   |  |||    || ||    |       |   | |   |   | |   | |  | || | |   |   |||  ||||||||  ||  | | | |||||||||||| || || ||||| || || |||||||||||||||||||||||||||||||| ||||||||||||| |||||| || ||||||||||||
gtgcccaatttgccccccatccctagggaatttatccaatttgctgaccaaattttatacgtgatcaaattcatt--cctgacgagtttggatttccgcagTGGGACATTCTGTCCAACGGCGGCGCCGTCCAAGAAATGGCTCACATTGCCAACGGCCGTGACCATGGCAACTCTGTCTCGCTTCTTCGTGTCAAT

upper sequence: GRMZM2G130442_T02 (Zea mays), 3'ss of exon 8
lower sequence: EFJ10492 (Selaginella moellendorffii), 3'ss of exon 9
gtagtcggtttcaaaccgatgatgatactgcgttctccaaacgtcaatcgtttgtgcttcgagctacgacctattttcctgacgaaatttaaatctgcagTGGGACATCCTCTCGAACGGTGGTGCTGTCCAAGAAATGGCTCACATTGCCAACGGCCGGGACCATGGCAACTGTGTCTCCCTCCTTCGTGTCAAT
                   | |     || ||||    |  | ||||    | | | ||         | |  ||||| ||      |||   | | ||||||||||| ||||| ||||||||    || ||||| ||||||||||| ||||| || | ||| |  |||||| ||||||| ||||| |||||||| 
------------------gtaacagagcttcgtttg--atccatcaa--aatcgagtttttg-----tatcggttttcttgg-----ttt---ttttcagTGGGACATTCTCTCCAACGGTGGAATGGTGCAAGAGATGGCTCACATCGCCAAAGGACAGGATCCAGGCAACAGTGTCTCTCTCCTCCGTGTCAAC
















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|9794706|gb|BE553014.1|BE553014
EST:     CACCCAAGAGGGTCTTCGACTTCCTCCGCGATGAGACCTCTCGCAGCGAG                         TGGGACATCCTGTCGAACGGTGGTGCTGTCCAAGAAATGGCTCATATTGCC
genomic: CACCCAAGAGGGTCTTCGATTTCCTCCGCGATGAGACCTCTCGCAGCGAGgtatgtcaca ... aaatctgcagTGGGACATCCTCTCGAACGGTGGTGCTGTCCAAGAAATGGCTCACATTGCC
EST: gi|9732662|gb|BE511414.1|BE511414
EST:     CACCCAAGAGGGTCTTCGACTTCCTCCGCGATGAGACCTCTCGCAGCGAG                         TGGGACATCCTGTCGAACGGTGGTGCTGTCCAAGAAATGGCTCATATTGCC
genomic: CACCCAAGAGGGTCTTCGATTTCCTCCGCGATGAGACCTCTCGCAGCGAGgtatgtcaca ... aaatctgcagTGGGACATCCTCTCGAACGGTGGTGCTGTCCAAGAAATGGCTCACATTGCC
EST: gi|71428267|gb|DR809317.1|DR809317
EST:     TCGATTTCCTCCGCGATGAGACCTCTCGCAGCGAG                         TGGGACATCCTCTCGAACGGTGGTGCTGTCCAAGAAATGGCTCACATTGCC
genomic: TCGATTTCCTCCGCGATGAGACCTCTCGCAGCGAGgtatgtcaca ... aaatctgcagTGGGACATCCTCTCGAACGGTGGTGCTGTCCAAGAAATGGCTCACATTGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatcgtttgtgcttcgagctacgacctattttcctgacgaaatttaaatctgcagTGGGACATCCTCTCGAACGGTGGTGCTGTCCAAGAAATGGCTCACATTGCCAACGGCCGGGACCATGGCAACTGTGTCTCCCTCCTTCGTGTCAAT
                               tcctgac  putative branch site (score: 2)
                                       aaatttaaatct  TA-rich tract