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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttgattgcctgaaaacttgacgtagagcgctcttgttttgacttttgaggaaggatggtgcttatgtttctgagcagattgtcatcttgttgtccatgggagcttatggcatcttgttaatctgtggtttagGTGAGGGCGCGGTGCAGGAAGGAATGGGGCATGTTCCAGACCAGGATGGCGGAGGCGGAGAAGGCGTATTACAAGATGATGGGCATCACCCCTCCAAACT

Basic information

species Zea mays
transcript GRMZM5G846339_T02
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G846339_T02 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os05g01760.1 (Oryza sativa), 3'ss of exon 14
gtacgttgattgcctgaaaacttgacgtagagcgctcttgttttgacttttgaggaaggatggtgcttatgtttctgagcagattgtcatcttgttgtccatgggagcttatggcatcttgttaatctgtggtttagGTGAGGGCGCGGTGCAGGAAGGAATGGGGCATGTTCCAGACCAGGATGGCGGAGGCGGAGAAGGCGTATTACAAGATGATGGGCATCACCCCTCCAAACT
                               |      | |||  | ||||  | |   |||      |       || | |   |||  ||||||               ||  | | |  |  |   | ||| ||||||||||||||||||||||||||||||| ||||| ||||| || ||||||||||||||||||||||| |||||||||||||||||||||||||| ||||
-------------------------------gtaagagtctttgaaattttccgcagacatga-----acacactagaactgcgagtccccttgtt---------------tgtaaccataatgtttgttcgttcagGTGAGGGCGCGGTGCAGGAAGGAATGGGGGATGTTTCAGACGAGAATGGCGGAGGCGGAGAAGGCGTACTACAAGATGATGGGCATCACCCCTCCGAACT
















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|148929009|gb|EC874209.2|EC874209
EST:     GGGCAGTCAGAAAACGGAAGGGCGCCATGGGAAGGG                         GTGAGGGCGCGGTGCAGGAAGGAATGGGGCATGTTCCAGACCAGGATGGCG
genomic: GGGCAGTCAGAAAACGGAAGGGCGCCATGGGAAGGGgtacgttgat ... tgtggtttagGTGAGGGCGCGGTGCAGGAAGGAATGGGGCATGTTCCAGACCAGGATGGCG
EST: gi|148950257|gb|EC895809.2|EC895809
EST:     GGGCAGTCAGAAAACGGAAGGGCGCCATGGGAAGGG                         GTGAGGGCGCGGTGCAGGAAGGAATGGGGCATGTTCCAGACCAGGATGGCG
genomic: GGGCAGTCAGAAAACGGAAGGGCGCCATGGGAAGGGgtacgttgat ... tgtggtttagGTGAGGGCGCGGTGCAGGAAGGAATGGGGCATGTTCCAGACCAGGATGGCG
EST: gi|148945517|gb|EC890762.2|EC890762
EST:     GGGCAGTCAGAAAACGGAAGGGCGCCATGGGAAGGG                         GTGAGGGCGCGGTGCAGGAAGGAATGGGGCATGTTCCAGCCCAGGATGGCG
genomic: GGGCAGTCAGAAAACGGAAGGGCGCCATGGGAAGGGgtacgttgat ... tgtggtttagGTGAGGGCGCGGTGCAGGAAGGAATGGGGCATGTTCCAGACCAGGATGGCG
EST: gi|211435723|gb|FL461646.1|FL461646
EST:     GGGCAGTCAGAAAACGGAAGGGCGCCATGGGAAGGG                         GTGAGGGCGCGGTGCAGGAAGGAATGGGGCATGTTCCAGACCAGGATGGCG
genomic: GGGCAGTCAGAAAACGGAAGGGCGCCATGGGAAGGGgtacgttgat ... tgtggtttagGTGAGGGCGCGGTGCAGGAAGGAATGGGGCATGTTCCAGACCAGGATGGCG
EST: gi|211015300|gb|FL437092.1|FL437092
EST:     GGGCAGTCAGAAAACGGAAGGGCGCCATGGGAAGGG                         GTGAGGGCGCGGTGCAGGAAGGAATGGGGCATGTTCCAGACCAGGATGGCG
genomic: GGGCAGTCAGAAAACGGAAGGGCGCCATGGGAAGGGgtacgttgat ... tgtggtttagGTGAGGGCGCGGTGCAGGAAGGAATGGGGCATGTTCCAGACCAGGATGGCG
EST: gi|12046797|gb|BF728936.1|BF728936
EST:     GGGCAGTCAGAAAACGGAAGGGCGCCATGGGAAGGG                         GTGAGGGCGCGGTGCAGGAAGGAATGGTGTTTTGTTCCAGACCAGGATGGC
genomic: GGGCAGTCAGAAAACGGAAGGGCGCCATGGGAAGGGgtacgttgat ... tgtggtttagGTGAGGGCGCGGTGCAGGAAGGAATGG-GGCATGTTCCAGACCAGGATGGC
EST: gi|149070556|gb|EE158958.2|EE158958
EST:     GGGCAGTCAGAAAACGGAAGGGCGCCATGGGAAGGG                         GTGAGGGCGCGGTGCAGGAAGGAATGGGGCATGTTCCAGACCAGGATGGCG
genomic: GGGCAGTCAGAAAACGGAAGGGCGCCATGGGAAGGGgtacgttgat ... tgtggtttagGTGAGGGCGCGGTGCAGGAAGGAATGGGGCATGTTCCAGACCAGGATGGCG
EST: gi|37399165|gb|CF636908.1|CF636908
EST:     GGGCAGTCAGAAAACGGAAGGGTGCCATGGGAAGGG                         GTGAGGGCGCGGTGCAGGAAGGAATGGGGCATGTTCCAGACCAGGATGGCG
genomic: GGGCAGTCAGAAAACGGAAGGGCGCCATGGGAAGGGgtacgttgat ... tgtggtttagGTGAGGGCGCGGTGCAGGAAGGAATGGGGCATGTTCCAGACCAGGATGGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtcatcttgttgtccatgggagcttatggcatcttgttaatctgtggtttagGTGAGGGCGCGGTGCAGGAAGGAATGGGGCATGTTCCAGACCAGGATGGCGGAGGCGGAGAAGGCGTATTACAAGATGATGGGCATCACCCCTCCAAACT
                                     tgttaat  putative branch site (score: 3)
                                    ttgttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgttgattgcctgaaaacttgacgtagagcgctcttgttttgacttttgaggaaggatggtgcttatgtttctgagcagattgtcatcttgttgtccatgggagcttatggcatcttgttaatctgtggtttagGTGAGGGCGCGGTGCAGGAAGGAATGGGGCATGTTCCAGACCAGGATGGCGGAGGCGGAGAAGGCGTATTACAAGATGATGGGCATCACCCCTCCAAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG