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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cataatcgaattccttggtattaatgctgctcactatctgtttgtttcatgtatatgttttggcacctaccattcttacatcatgctattgcaatgacagTTCAAGATGGAATTGGCTCAAACTAACACCGGGAATACACCTAAGAGCTACTCTTTGAATATGTTCAAAGATTTCGTTCCTATGTGTGTTTTCTCCGAAT

Basic information

species Zea mays
transcript GRMZM2G060284_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060284_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g43450.1 (Oryza sativa), 3'ss of exon 1
cataat--cgaattccttggtattaatgctgctcactatctgtttgtttcatgtatatgttttggcacctaccattcttacatcatgctattgcaatgacagTTCAAGATGGAATTGGCTCAAACTAACACCGGGAATACACCTAAGAGCTACTCTTTGAATATGTTCAAAGATTTCGTTCCTATGTGTGTTTTCTCCGAAT
 ||  |  |   |||  || || |       |||| | ||| |||| ||   ||   | |  |  || |   |||| | ||||  ||||||||  ||| ||||||||||||||  |||||||||||||||| || |||||||| ||||| ||||| |||||||||| ||| ||||| || || |||||||||||||| || |
-attgttccccgttctatgttagtttcatcactcatt-tctttttgcttgtggtgcctatagttacatcattcattataacatggtgctattggcatggcagTTCAAGATGGAGATGGCTCAAACTAACACTGGCAATACACCAAAGAGTTACTCCTTGAATATGTCCAAGGATTTTGTACCAATGTGTGTTTTCTCTGAGT

upper sequence: GRMZM2G060284_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA04G03030.1 (Glycine max), 3'ss of exon 1
cataatcgaatt-ccttggtattaatgc-tgctcactatc--tgtttgtttcatgtatatgttttggcacctaccattcttacatcatgctattgcaatgacagTTCAAGATGGAATTGGCTCAAACTAACACCGGGAATACACCTAAGAGCTACTCTTTGAATATGTTCAAAGATTTCGTTCCTATGTGTGTTTTCTCCGAAT
  |  | |||||  |   ||||  ||   ||||    ||   | |||||| | |||||   | |  |    |  ||||  |  || ||   ||    ||| ||||| |  |||||  |||||    |  |  | | |||||  || || |  || || ||||||||||| ||||| || |||||||||||||| ||||||||  
-cttctagaattgtcacagtatagatatgtgcttctgattaatatttgttgcttgtattgatgtaagagagt--cattgatttataat-tcataattatgtcagTTTACAATGGAGATGGCTGGCTCCGAAGCTGTGAATATGCCAAAAACTTATTCATTGAATATGTTTAAAGACTTTGTTCCTATGTGTGTCTTCTCCGAGA

upper sequence: GRMZM2G060284_T02 (Zea mays), 3'ss of exon 1
lower sequence: GLYMA06G03070.1 (Glycine max), 3'ss of exon 1
--cataatcgaattccttggtat-taatgctgctcactatctgtttgtttcatgtatatgttttggcacctaccattcttacatcatgctattgcaatgacagTTCAAGATGGAATTGGCTCAAACTAACACCGGGAATACACCTAAGAGCTACTCTTTGAATATGTTCAAAGATTTCGTTCCTATGTGTGTTTTCTCCGAAT
   ||  || |     | | ||  |  | ||| | | ||| ||||  ||      || |    | |    |   |||  ||  ||||   ||    ||| ||||| |  |||||  ||||    ||  |  | | |||||   | || |  || || ||||| ||||| ||||| ||||||||||||||||| ||||| ||  
agaattgtcaacaatatagataagtgcttctgattaatatttgttgattgtgctgatgtaagatagtcattg--atttatagctcat-tcataattatgccagTTTACAATGGAGATGGCAGGCACAGAAGCTGTGAATATGTCCAAAACTTATTCATTGAACATGTTTAAAGACTTCGTTCCTATGTGTGTCTTCTCTGAGA

upper sequence: GRMZM2G060284_T02 (Zea mays), 3'ss of exon 1
lower sequence: Vv18s0001g13370.t01 (Vitis vinifera), 3'ss of exon 1
--cataatcgaattccttggtattaatgctgctcactatctgtttgtttcatgtatat-gttttggcacctaccattcttacatcatgctattgcaatgacagTTCAAGATGGAATTGGCTCAAACTAACACCGGGAATACACCTAAGAGCTACTCTTTGAATATGTTCAAAGATTTCGTTCCTATGTGTGTTTTCTCCGAAT
   ||  | | |  | ||| |  |  | ||  |   |    | || |||  |||  || || ||| |||||  |   |||||||  | || |    ||  |||||||  |||||| || ||   |||    |    ||||  || || || ||||| |||||||||||||||||||| ||||||||||||||||| || ||  
agaatttttgcacccattgttggttgttctaatatgttagagattatttgttgtgaattgtcttgccaccttgc---cttacatgcttctttaatgatagcagTTCACAATGGAAATGACTGGCACTGGGGCTCCTAATATGCCAAAAAGTTACTCCTTGAATATGTTCAAAGATTTTGTTCCTATGTGTGTTTTTTCTGAGA

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|116816147|gb|EC858853.1|EC858853
EST:     CCCTTGACCTGTTGCGCCAAGAAGAACGCCCGGAAGAGCCTACGCTCCAG                         TTCAAGATGGAATTGGCTCAAACTAACACCGGGAATACACCTAAGAGCTAC
genomic: CCCTTGACCTGTTGCGCCAAGAAGAACGCCCGGAAGAGCCTACGCTCCAGgcaagtaccc ... gcaatgacagTTCAAGATGGAATTGGCTCAAACTAACACCGGGAATACACCTAAGAGCTAC
EST: gi|28187707|gb|CB179317.1|CB179317
EST:     CCCTTGACCTGTTGCGCCAAGAAGAACGCCCGGAAGAGCCTACGCTCCAG                         TTCAAGATGGAATTGGCTCAAACTAACACCGGGAATACACCTAAGAGCTAC
genomic: CCCTTGACCTGTTGCGCCAAGAAGAACGCCCGGAAGAGCCTACGCTCCAGgcaagtaccc ... gcaatgacagTTCAAGATGGAATTGGCTCAAACTAACACCGGGAATACACCTAAGAGCTAC
EST: gi|211224212|gb|FK968311.1|FK968311
EST:     GTTGCGCCAAGAAGAACGCCCGGAAGAGCCTACGCTCCAG                         TTCAAGATGGAATTGGCTCAAACTAACACCGGGAATACACCTAAGAGCTAC
genomic: GTTGCGCCAAGAAGAACGCCCGGAAGAGCCTACGCTCCAGgcaagtaccc ... gcaatgacagTTCAAGATGGAATTGGCTCAAACTAACACCGGGAATACACCTAAGAGCTAC
EST: gi|149085565|gb|EE175077.2|EE175077
EST:     CCCTTGACCTGTTGCGCCAAGAAGAACGCCCGGAAGAGCCTACGCTCCAG                         TTCAAGATGGAATTGGCTCAAACTAACACCGGGAATACACCTAAGAGCTAC
genomic: CCCTTGACCTGTTGCGCCAAGAAGAACGCCCGGAAGAGCCTACGCTCCAGgcaagtaccc ... gcaatgacagTTCAAGATGGAATTGGCTCAAACTAACACCGGGAATACACCTAAGAGCTAC
EST: gi|76937460|gb|DV175147.1|DV175147
EST:     CCCTTGACCTGTTGCGCCAAGAAGAACGCCCGGAAGAGCCTACGCTCCAG                         TTCAAGATGGAATTGGCTCAAACTAACACCGGGAATACACCTAAGAGCTAC
genomic: CCCTTGACCTGTTGCGCCAAGAAGAACGCCCGGAAGAGCCTACGCTCCAGgcaagtaccc ... gcaatgacagTTCAAGATGGAATTGGCTCAAACTAACACCGGGAATACACCTAAGAGCTAC
EST: gi|211224215|gb|FK968314.1|FK968314
EST:     CCCTTGACCTGTTGCGCCAAGAAGAACGCCCGGAAGAGCCTACGCTCCAG                         TTCAAGATGGAATTGGCTCAAACTAACACCGGGAATACACCTAAGAGCTAC
genomic: CCCTTGACCTGTTGCGCCAAGAAGAACGCCCGGAAGAGCCTACGCTCCAGgcaagtaccc ... gcaatgacagTTCAAGATGGAATTGGCTCAAACTAACACCGGGAATACACCTAAGAGCTAC
EST: gi|211224214|gb|FK968313.1|FK968313
EST:     GACCTGTTGCGCCAAGAAGAACGCCCGGAAGAGCCTACGCTCCAG                         TTCAAGATGGAATTGGCTCAAACTAACACCGGGAATACACCTAAGAGCTAC
genomic: GACCTGTTGCGCCAAGAAGAACGCCCGGAAGAGCCTACGCTCCAGgcaagtaccc ... gcaatgacagTTCAAGATGGAATTGGCTCAAACTAACACCGGGAATACACCTAAGAGCTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatgtatatgttttggcacctaccattcttacatcatgctattgcaatgacagTTCAAGATGGAATTGGCTCAAACTAACACCGGGAATACACCTAAGAGCTACTCTTTGAATATGTTCAAAGATTTCGTTCCTATGTGTGTTTTCTCCGAAT
                           ttcttac  putative branch site (score: 2)
      tatatgtttt  TA-rich tract