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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGGATTCAAACAAAATTCTGGAATTAGGCGAACAGTTTGGCGTTGGCAAATATGCGAAGTACTTTCCTGTAATATTCACAGGGAGAACTATAGAAAGgtataccatgacatactaatcattatcattcagcaataaatattagaaagtttgtctcatcagcattcatagggcatcgtccttgagtcaggaatataaa...

Basic information

species Zea mays
transcript GRMZM2G040720_T03
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G040720_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os11g34830.1 (Oryza sativa), 5'ss of exon 10
TGTTGGATTCAAACAAAATTCTGGAATTAGGCGAACAGTTTGGCGTTGGCAAATATGCGAAGTACTTTCCTGTAATATTCACAGGGAGAACTATAGAAAGgtataccatgacatactaatcattatcattcagcaataaatattagaaagtttgtctcatcagcattcatagggcatcgtccttgagtcaggaatataaa
||||||||||  | ||||||||||| ||||| ||||||||||| |||||||||||||| ||||||||||| ||||||||||| ||||| ||||| ||||||||        ||| || || |   |    || |||    |  |    |  |||||  | | | |   ||  || |      || |||||   |      
TGTTGGATTCTCAAAAAATTCTGGAGTTAGGTGAACAGTTTGGTGTTGGCAAATATGCTAAGTACTTTCCCGTAATATTCACTGGGAGGACTATCGAAAGgta--------catgcttatgaccttttcccaacaaagcctgatgcgta-cttgtcaaaactgtaaaaatgtggaaaatcatttcagtcattcag-----

upper sequence: GRMZM2G040720_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os11g34750.1 (Oryza sativa), 5'ss of exon 13
TGTTGGATTCAAACAAAATTCTGGAATTAGGCGAACAGTTTGGCGTTGGCAAATATGCGAAGTACTTTCCTGTAATATTCACAGGGAGAACTATAGAAAGgtataccatgacatactaatcattatcattcagcaataaatattagaaagtttgtctcatcagcattcatagggcatcgt-ccttgagtcaggaatataaa--------
||||||||||  | ||||||||||| ||||| ||||| ||||| |||||||||||||| ||||||||||| ||||||||||| ||||| ||||| ||||||||        ||| || || |   |    || |||    |  |    |  |||||  | | | |   ||  |  |   |   || |||||   | |||          
TGTTGGATTCTCAAAAAATTCTGGAGTTAGGTGAACACTTTGGTGTTGGCAAATATGCTAAGTACTTTCCCGTAATATTCACTGGGAGGACTATCGAAAGgta--------catgcttatgaccttttcccaacaaagcctgatgcgta-cttgtcaaaactgtaaaaatgtgaaaaaatattttcagtcattcagatattattggatt
















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|60338335|gb|DN205308.1|DN205308
EST:     AAATATGCGAAGTACTTTCCTGTAATATTCACAGGGAGAACTATAGAAAG                         CAAGTCAGCTCTTGGCACACAAATGTCTGGTGAAGAGCAGAGGCGTCTGAA
genomic: AAATATGCGAAGTACTTTCCTGTAATATTCACAGGGAGAACTATAGAAAGgtataccatg ... taactatcagCAAGTCAGCTCTTGGCACACAAATGTCTGGTGAAGAGCAGAGGCGTCTGAA
EST: gi|37381459|gb|CF627617.1|CF627617
EST:     AACTATAGAAAG                         CAAGTCAGCTCTTGGCACACAAATGTCTGGTGAAGAGCAGAGGCGTCTGAA
genomic: AACTATAGAAAGgtataccatg ... taactatcagCAAGTCAGCTCTTGGCACACAAATGTCTGGTGAAGAGCAGAGGCGTCTGAA
EST: gi|9824900|gb|BE574997.1|BE574997
EST:     AAATATGCGAAGTACTTTCCTGTAATATTCACAGGGAGAACTATAGAAAG                         CAAGTCAGCTCTTGGCACACAAATGTCTGGTGAAGAGCAGAGGCGTCTGAA
genomic: AAATATGCGAAGTACTTTCCTGTAATATTCACAGGGAGAACTATAGAAAGgtataccatg ... taactatcagCAAGTCAGCTCTTGGCACACAAATGTCTGGTGAAGAGCAGAGGCGTCTGAA
EST: gi|60341736|gb|DN208709.1|DN208709
EST:     AAATATGCGAAGTACTTTCCTGTAATATTCACAGGGAGAACTATAGAAAG                         CAAGTCAGCTCTTGGCACACAAATGTCTGGTGAAGAGCAGAGGCGTCTGAA
genomic: AAATATGCGAAGTACTTTCCTGTAATATTCACAGGGAGAACTATAGAAAGgtataccatg ... taactatcagCAAGTCAGCTCTTGGCACACAAATGTCTGGTGAAGAGCAGAGGCGTCTGAA
EST: gi|60344633|gb|DN211606.1|DN211606
EST:     AAATATGCGAAGTACTTTCCTGTAATATTCACAGGGAGAACTATAGAAAG                         CAAGTCAGCTCTTGGCACACAAATGTCTGGTGAAGAGCAGAGGCGTCTGAA
genomic: AAATATGCGAAGTACTTTCCTGTAATATTCACAGGGAGAACTATAGAAAGgtataccatg ... taactatcagCAAGTCAGCTCTTGGCACACAAATGTCTGGTGAAGAGCAGAGGCGTCTGAA
EST: gi|86474242|gb|DY240612.1|DY240612
EST:     AAATATGCGAAGTACTTTCCTGTAATATTCACAGGGAGAACTATAGAAAG                         CAAGTCAGCTCTTGGCACACAAATGTCTGGTGAAGAGCAGAGGCGTCTGAA
genomic: AAATATGCGAAGTACTTTCCTGTAATATTCACAGGGAGAACTATAGAAAGgtataccatg ... taactatcagCAAGTCAGCTCTTGGCACACAAATGTCTGGTGAAGAGCAGAGGCGTCTGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTGGATTCAAACAAAATTCTGGAATTAGGCGAACAGTTTGGCGTTGGCAAATATGCGAAGTACTTTCCTGTAATATTCACAGGGAGAACTATAGAAAGgtataccatgacatactaatcattatcattcagcaataaatattagaaagtttgtctcatcagcattcatagggcatcgtccttgagtcaggaatataaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA