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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatacttcttcattatgttactagcttaccttccttgaactcctctaactagcttgatgggtaatatccagGACAAACCAATTCCTCTAAAGCTGAAACGCCTTGCACGTGACCATGAGAGATTTCTCTGGGCACTGAGTATAGTACAGTCTCGTTCTGTCAACTTGAAGT

Basic information

species Zea mays
transcript GRMZM5G807767_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G807767_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g50980.1 (Oryza sativa), 3'ss of exon 4
--------------------------gtatacttcttcattatgttactagcttaccttccttgaactcctctaac--tagcttgatgggtaatatccagGACAAACCAATTCCTCTAAAGCTGAAACGCCTTGCACGTGACCATGAGAGATTTCTCTGGGCACTGAGTATAGTACAGTCTCGTTCTGTCAACTTGAAGT
                          ||| ||||||  | ||| | |  | |||  ||  ||||    | ||||||  |||||||||||||||| ||||| | ||| |||| ||||||||||| || || ||||| | ||||||||| |||||||| |||||||||||||| || |||||||| |||||||| |||||  
caattgatttttggcaaaaacattgggtacacttctgtactatttgatcaacttcgctggcttgggtacatctaacactagcttgatgggtaatgtccagCATAAAACAATCCCTCTAAAGCTAAAGCGTCTTGCCCCTGACCATGAAAGATTTCTATGGGCACTGAGTATTGTTCAGTCTCGCTCTGTCAATTTGAAAC
















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|211020790|gb|FL433478.1|FL433478
EST:     AAATGTTAAAACACCAGGAACGAGCAATTGACTTTTGGCAAAAGCATTGG                         GACAAACCAATTCCTCTAAAGCTGAAACGCCTTGCACGTGACCATGAGAGA
genomic: AAATGTTAAAACACCAGGAACGAGCAATTGACTTTTGGCAAAAGCATTGGgtatacttct ... taatatccagGACAAACCAATTCCTCTAAAGCTGAAACGCCTTGCACGTGACCATGAGAGA
EST: gi|149101095|gb|EE187199.2|EE187199
EST:     AAATGTTAAAACACCAGGAACGAGCAATTGACTTTTGGCAAAAGCATTGG                         GACAAACCAATTCCTCTAAAGCTGAAACGCCTTGCACGTGACCATGAGAGA
genomic: AAATGTTAAAACACCAGGAACGAGCAATTGACTTTTGGCAAAAGCATTGGgtatacttct ... taatatccagGACAAACCAATTCCTCTAAAGCTGAAACGCCTTGCACGTGACCATGAGAGA
EST: gi|13557817|gb|BG549173.1|BG549173
EST:     AATGTTAAAACATTCATGAACGAGCAATTGACTTTTGGCAAAAGCATTGG                         GACAAACCAATTCCTCTAAAGCTGAAACGCCTTGCACGTGACCATGAGAGA
genomic: AATGTTAAAACA-CCAGGAACGAGCAATTGACTTTTGGCAAAAGCATTGGgtatacttct ... taatatccagGACAAACCAATTCCTCTAAAGCTGAAACGCCTTGCACGTGACCATGAGAGA
EST: gi|149029834|gb|EE286274.2|EE286274
EST:     AAATGTTAAAACACCAGGAACGAGCAATTGACTTTTGGCAAAAGCATTGG                         GACAAACCAATTCCTCTAAAGCTGAAACGCCTTGCACGTGACCATGAGAGA
genomic: AAATGTTAAAACACCAGGAACGAGCAATTGACTTTTGGCAAAAGCATTGGgtatacttct ... taatatccagGACAAACCAATTCCTCTAAAGCTGAAACGCCTTGCACGTGACCATGAGAGA
EST: gi|211112500|gb|FL459337.1|FL459337
EST:     AACACCAGGAACGAGCAATTGACTTTTGGCAAAAGCATTGG                         GACAAACCAATTCCTCTAAAGYTGAAACGCCTTGCACGTGACCATGAGAGA
genomic: AACACCAGGAACGAGCAATTGACTTTTGGCAAAAGCATTGGgtatacttct ... taatatccagGACAAACCAATTCCTCTAAAGCTGAAACGCCTTGCACGTGACCATGAGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttactagcttaccttccttgaactcctctaactagcttgatgggtaatatccagGACAAACCAATTCCTCTAAAGCTGAAACGCCTTGCACGTGACCATGAGAGATTTCTCTGGGCACTGAGTATAGTACAGTCTCGTTCTGTCAACTTGAAGT
                                             taatat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatacttcttcattatgttactagcttaccttccttgaactcctctaactagcttgatgggtaatatccagGACAAACCAATTCCTCTAAAGCTGAAACGCCTTGCACGTGACCATGAGAGATTTCTCTGGGCACTGAGTATAGTACAGTCTCGTTCTGTCAACTTGAAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG