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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccttccgcgtcctcctcttgctgctcgattggattccaatttttagaccgaccaaactagaattaggtaggttcagCAGTTAGATTGGATGCCCTAGCAGCGCCGGCGGCAGATGCTGACCCGGGAGCCGTCGGCGACAAGCTCGTCTTCGAAGCGCCGCCTCAGCCCGTGAGGGA

Basic information

species Zea mays
transcript GRMZM2G363460_T06
intron # 1
splice site 3'
intron type U2

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|211174721|gb|FL404361.1|FL404361
EST:     AGGCGAGGCCATGGCCTCCGGCATCGGCTCCGGCCAGCAGCAACCCCCAG                         CAGTTAGATTGGATGCCCTAGCAGCGCCGGCGGCAGATGCTGACCCGGGAG
genomic: AGGCGAGGCCATGGCCTCCGGCATCGGCTCCGGCCAGCAGCAACCCCCAGgtaccttccg ... gtaggttcagCAGTTAGATTGGATGCCCTAGCAGCGCCGGCGGCAGATGCTGACCCGGGAG
EST: gi|148934906|gb|EC878952.2|EC878952
EST:     AGGCGAGGCCATGGCCTCCGGCATCGGCTCCGGCCAGCAGCAACCCCCAGGTTCAG                    
genomic: AGGCGAGGCCATGGCCTCCGGCATCGGCTCCGGCCAGCAGCAA-CCCC-----CAGgtaccttccg ... gtagg
EST: gi|148946560|gb|EC885619.2|EC885619
EST:     AGGCGAGGCCATGGCCTCCGGCATCGGCTCCGGCCAGCAGCAA-CCCC--                         CAGTTAGATTGGATGCCCTAGCAGCGCCGGCGGCAGATGCTGACCCGGGAG
genomic: AGGCGAGGCCATGGCCTCCGGCATCGGCTCCGGCCAGCAGCAACCCCCAGgtaccttccg ... gtaggttcagCAGTTAGATTGGATGCCCTAGCAGCGCCGGCGGCAGATGCTGACCCGGGAG
EST: gi|148947997|gb|EC893497.2|EC893497
EST:     AGGCGAGGCCATGGCCTCCGGCATCGGCTCCGGCCAGCAGCAACCCCCAGGTTCAG                    
genomic: AGGCGAGGCCATGGCCTCCGGCATCGGCTCCGGCCAGCAGCAA-CCCC-----CAGgtaccttccg ... gtagg
EST: gi|148941345|gb|EC886254.2|EC886254
EST:     AGGCGAGGCCATGGCCTCCGGCATCGGCTCCGGCCAGCAGCAA-CCCC--                         CAGTTAGATTGGATGCCCTAGCAGCGCCGGCGGCAGATGCTGACCCGGGAG
genomic: AGGCGAGGCCATGGCCTCCGGCATCGGCTCCGGCCAGCAGCAACCCCCAGgtaccttccg ... gtaggttcagCAGTTAGATTGGATGCCCTAGCAGCGCCGGCGGCAGATGCTGACCCGGGAG
EST: gi|148980471|gb|EE027160.2|EE027160
EST:     AGGCGAGGCCATGGCCTCCGGCATCGGCTCCGGCCAGCAGCAA-CCCC--                         CAGTTAGATTGGATGCCCTAGCAGCGCCGGCGGCAGATGCTGACCCGGGAG
genomic: AGGCGAGGCCATGGCCTCCGGCATCGGCTCCGGCCAGCAGCAACCCCCAGgtaccttccg ... gtaggttcagCAGTTAGATTGGATGCCCTAGCAGCGCCGGCGGCAGATGCTGACCCGGGAG
EST: gi|78109256|gb|DV527672.1|DV527672
EST:     AGGCGAGGCCATGGCCTCCGGCATCGGCTCCGGCCAGCAGCAA-CCCC--                         CAGTTAGATTGGATGCCCTAGCAGCGCCGGCGGCAGATGCTGACCCGGGAG
genomic: AGGCGAGGCCATGGCCTCCGGCATCGGCTCCGGCCAGCAGCAACCCCCAGgtaccttccg ... gtaggttcagCAGTTAGATTGGATGCCCTAGCAGCGCCGGCGGCAGATGCTGACCCGGGAG
EST: gi|211092253|gb|FL379378.1|FL379378
EST:     AGGCGAGGCCATGGCCTCCGGCATCGGCTCCGGCCAGCAGCAACCCCCAGGTAGGTTCAG                
genomic: AGGCGAGGCCATGGCCTCCGGCATCGGCTCCGGCCAGCAGCAA-CCCC---------CAGgtaccttccg ... g
EST: gi|91873988|gb|EB403945.1|EB403945
EST:     AGGCGAGGCCATGGCCTCCGGCATCGGCTCCGGCCAGCAGCAACCCCCAG                         ---TTAGATTGGATGCCCTAGCAGCGCCGGCGGCAGATGCTGACCCGGGAG
genomic: AGGCGAGGCCATGGCCTCCGGCATCGGCTCCGGCCAGCAGCAACCCCCAGgtaccttccg ... gtaggttcagCAGTTAGATTGGATGCCCTAGCAGCGCCGGCGGCAGATGCTGACCCGGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctcgattggattccaatttttagaccgaccaaactagaattaggtaggttcagCAGTTAGATTGGATGCCCTAGCAGCGCCGGCGGCAGATGCTGACCCGGGAGCCGTCGGCGACAAGCTCGTCTTCGAAGCGCCGCCTCAGCCCGTGAGGGA
                aatttttaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaccttccgcgtcctcctcttgctgctcgattggattccaatttttagaccgaccaaactagaattaggtaggttcagCAGTTAGATTGGATGCCCTAGCAGCGCCGGCGGCAGATGCTGACCCGGGAGCCGTCGGCGACAAGCTCGTCTTCGAAGCGCCGCCTCAGCCCGTGAGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT