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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttaccttccacacttaaaacagattggtttttgccttcctttaatagctagctgagtttcttccgtgcttgcctactcttgaagtaggaccaaatgagcaatagcttgttcttgttggatatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCGCCCAAGAAGAAAAACCTTCAGGCGTCGAAGCTCAGCGTGGAAGGCCGTGGCATGATCAAGTACCTGTAGA

Basic information

species Zea mays
transcript GRMZM2G085254_T02
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085254_T02 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os01g05420.1 (Oryza sativa), 3'ss of exon 10
gtttaccttccacacttaaaacagattggtttttgccttcctttaatagctagctgagtttcttccgtgcttgcctactcttgaagtaggaccaaatgagcaatagcttgttcttgttggatatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCGCCCAAGAAGAAAAACCTTCAGGCGTCGAAGCTCAGCGTGGAAGGCCGTGGCATGATCAAGTACCTGTAGA
   | |  |||   | || ||  || | | | ||       |||  ||||  | |   || ||     | ||  | |  |   | ||  |      |  |||||   |  |||||||  |  ||||||||||||||||||||||||||||||||||| || ||||||||||||||||||||||| || ||||| || ||||| ||||| |||||||||||| |||| |
--gttctgtccctgcctacaa--gacttgctgtt-------tttgctagcatgttacattgctggacggttttgccatgcc--atgtgagt-----tacgcaattaatcattcttgtctgtcatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAGGCGTCAAAACTCAGTGTTGAAGGGCGTGGAATGATCAAGTACTTGTAAA
















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|148996258|gb|EE035537.2|EE035537
EST:     AGATACGGGCTCGTGCTAAGCAGGCTGTCCAAGACCAGCGTCGGCTGAAG                         ATGAACAAGAAATTGCAGCAGCTGAAAGCGCCCAAGAAGAAAAACCTTCAG
genomic: AGATACGGGCTCGTGCTAAGCAGGCTGTCCAAGACCAGCGTCGGCTGAAGgtttaccttc ... ggatatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCGCCCAAGAAGAAAAACCTTCAG
EST: gi|149065683|gb|EE286806.2|EE286806
EST:     AGATACGGGCTCGTGCTAAGCAGGCTGTCCAAGACCAGCGTCGGCTGAAG                         ATGAACAAGAAATTGCAGCAGCTGAAAGCGCCCAAGAAGAAAAACCTTCAG
genomic: AGATACGGGCTCGTGCTAAGCAGGCTGTCCAAGACCAGCGTCGGCTGAAGgtttaccttc ... ggatatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCGCCCAAGAAGAAAAACCTTCAG
EST: gi|4874506|gb|AI674026.1|AI674026
EST:     AGATACGGGCTCGTGCTAAGCAGGCTGTCCAAGACCAGCGTCGGCTGAAG                         ATGAACAAGAAATTGCAGCAGCTGAAAGCGCCCAAGAAGAAAAACCTTCAG
genomic: AGATACGGGCTCGTGCTAAGCAGGCTGTCCAAGACCAGCGTCGGCTGAAGgtttaccttc ... ggatatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCGCCCAAGAAGAAAAACCTTCAG
EST: gi|22549113|gb|BU101314.1|BU101314
EST:     AGATACGGGCTCGTGCTAAGCAGGCTGTCCAAGACCAGCGTCGGCTGAAG                         ATGAACAAGAAATTGCAGCAGCTGAAAGCGCCCCAGAAGAAAAACCTTCAG
genomic: AGATACGGGCTCGTGCTAAGCAGGCTGTCCAAGACCAGCGTCGGCTGAAGgtttaccttc ... ggatatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCGCCCAAGAAGAAAAACCTTCAG
EST: gi|14202472|gb|BG836149.1|BG836149
EST:     AGATACGGGCTCGTGCTAAGCAGGCTGTCCAAGACCAGCGTCGGCTGAAG                         ATGAACAAGAAATTGCAGCAGCTGAAAGCGCCCAAGAAGAAAAACCTTCAG
genomic: AGATACGGGCTCGTGCTAAGCAGGCTGTCCAAGACCAGCGTCGGCTGAAGgtttaccttc ... ggatatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCGCCCAAGAAGAAAAACCTTCAG
EST: gi|67025420|gb|CO454169.1|CO454169
EST:     AGATACGGGCTCGTGCTAAGCAGGCTGTCCAAGACCAGCGTCGGCTGAAG                         ATGAACAAGAAATTGCAGCAGCTGAAAGCGCCCAAGAAGAAAAACCTTCAG
genomic: AGATACGGGCTCGTGCTAAGCAGGCTGTCCAAGACCAGCGTCGGCTGAAGgtttaccttc ... ggatatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCGCCCAAGAAGAAAAACCTTCAG
EST: gi|31353907|gb|CD438264.1|CD438264
EST:     AGATACGGGCTCGTGCTAAGCAGGCTGTCCAAGACCAGCGTCGGCTGAAG                         ATGAACAAGAAATTGCAGCAGCTGAAAGCGCCCAAGAAGAAAAACCTTCAG
genomic: AGATACGGGCTCGTGCTAAGCAGGCTGTCCAAGACCAGCGTCGGCTGAAGgtttaccttc ... ggatatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCGCCCAAGAAGAAAAACCTTCAG
EST: gi|18171074|gb|BM340914.1|BM340914
EST:     AGATACGGGCTCGTGCTAAGCAGGCTGTCCAAGACCAGCGTCGGCTGAAG                         ATGAACAAGAAATTGCAGCAGCTGAAAGCGCCCAAGAAGAAAAACCTTCAG
genomic: AGATACGGGCTCGTGCTAAGCAGGCTGTCCAAGACCAGCGTCGGCTGAAGgtttaccttc ... ggatatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCGCCCAAGAAGAAAAACCTTCAG
EST: gi|5361086|gb|AI795701.1|AI795701
EST:     AGATACGGGCTCGTGCTAAGCAGGCTGTCCAAGACCAGCGTCGGCTGAAG                         ATGAACAAGAAATTGCAGCAGCTGAAAGCGCCCAAGAAGAAAAACCTTCAG
genomic: AGATACGGGCTCGTGCTAAGCAGGCTGTCCAAGACCAGCGTCGGCTGAAGgtttaccttc ... ggatatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCGCCCAAGAAGAAAAACCTTCAG
EST: gi|18165422|gb|BM335261.1|BM335261
EST:     TCGTGCTAAGCAGGCTGTCCAAGACCAGCGTCGGCTGAAG                         ATGAACAAGAAATTGCAGCAGCTGAAAGCGCCCAAGAAGAAAAACCTTCAG
genomic: TCGTGCTAAGCAGGCTGTCCAAGACCAGCGTCGGCTGAAGgtttaccttc ... ggatatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCGCCCAAGAAGAAAAACCTTCAG
EST: gi|5005912|gb|AI711974.1|AI711974
EST:     AAGCAGGCTGTCCAAGACCAGCGTCGGCTGAAG                         ATGAACAAGAAATTGCAGCAGCTGAAAGCGCCCAAGAAGAAAAACCTTCAG
genomic: AAGCAGGCTGTCCAAGACCAGCGTCGGCTGAAGgtttaccttc ... ggatatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCGCCCAAGAAGAAAAACCTTCAG
EST: gi|24768922|gb|CA404051.1|CA404051
EST:     AGATACGGGCTCGTGCTAAGCAGGCTGTCCAAGACCAGCGTCGGCTGAAG                         ATGAACAAGAAATTGCAGCAGCTGAAAGCGCCCAAGAAGAAAAACCTTCAG
genomic: AGATACGGGCTCGTGCTAAGCAGGCTGTCCAAGACCAGCGTCGGCTGAAGgtttaccttc ... ggatatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCGCCCAAGAAGAAAAACCTTCAG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttaccttccacacttaaaacagattggtttttgccttcctttaatagctagctgagtttcttccgtgcttgcctactcttgaagtaggaccaaatgagcaatagcttgttcttgttggatatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCGCCCAAGAAGAAAAACCTTCAGGCGTCGAAGCTCAGCGTGGAAGGCCGTGGCATGATCAAGTACCTGTAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG