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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcgatgagtttatctccttccggccttacctattctcgatcttctctgctcccttagttcttgttcctttattttccttgttccccactgtctcttcctgattagtgttatttcgcttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGAGGAGCAGTTCATCCTCCGCGTGCCGCCATCCGTCGCAGAGCGGATCGAG

Basic information

species Zea mays
transcript GRMZM2G147614_T01
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|86472598|gb|DY238968.1|DY238968
EST:     AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACG                         AGATCCCTAAGTTTCGATCCTCTGTCCCAGTGGATTTGGGACTGCGATGGA
genomic: AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACGgtgagtcgat ... cttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
EST: gi|211005527|gb|FL375718.1|FL375718
EST:     AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACG                         AGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
genomic: AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACGgtgagtcgat ... cttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
EST: gi|93013166|gb|EB638686.1|EB638686
EST:     AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACG                         AGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
genomic: AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACGgtgagtcgat ... cttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
EST: gi|22543273|gb|BU093711.1|BU093711
EST:     GGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACG                         AGATCCCTAAGTTTCGATCCACTGTCCCAGCGGATTTGGGACTGCGATGGA
genomic: AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACGgtgagtcgat ... cttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
EST: gi|32931457|gb|CF036269.1|CF036269
EST:     AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACG                         AGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
genomic: AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACGgtgagtcgat ... cttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
EST: gi|32931995|gb|CF036807.1|CF036807
EST:     AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACG                         AGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
genomic: AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACGgtgagtcgat ... cttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
EST: gi|60345606|gb|DN212579.1|DN212579
EST:     AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACG                         AGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
genomic: AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACGgtgagtcgat ... cttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
EST: gi|32865677|gb|CF005359.1|CF005359
EST:     AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACG                         AGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
genomic: AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACGgtgagtcgat ... cttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
EST: gi|211322003|gb|FL424973.1|FL424973
EST:     AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACG                         AGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
genomic: AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACGgtgagtcgat ... cttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
EST: gi|40334273|gb|CK368343.1|CK368343
EST:     GGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACG                         AGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
genomic: AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACGgtgagtcgat ... cttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
EST: gi|9254486|gb|BE344954.1|BE344954
EST:     GGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACG                         AGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
genomic: AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACGgtgagtcgat ... cttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
EST: gi|116819180|gb|EC862277.1|EC862277
EST:     AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACG                         AGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
genomic: AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACGgtgagtcgat ... cttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
EST: gi|211527102|gb|FL390752.1|FL390752
EST:     AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACG                         AGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
genomic: AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACGgtgagtcgat ... cttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
EST: gi|26457225|gb|CA828808.1|CA828808
EST:     GGGGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACG                         AGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
genomic: AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACGgtgagtcgat ... cttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
EST: gi|211416221|gb|FL415023.1|FL415023
EST:     AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACG                         AGATCCCTAAGTTTCGATCCACTGTCCCAGT-GATTTGGGACTGCGATGGA
genomic: AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACGgtgagtcgat ... cttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
EST: gi|71435867|gb|DR816917.1|DR816917
EST:     AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACG                         AGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
genomic: AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACGgtgagtcgat ... cttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
EST: gi|211526828|gb|FL377016.1|FL377016
EST:     AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACG                         AGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
genomic: AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACGgtgagtcgat ... cttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
EST: gi|74235860|gb|DT643774.1|DT643774
EST:     AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACG                         AGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
genomic: AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACGgtgagtcgat ... cttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
EST: gi|211161653|gb|FL415254.1|FL415254
EST:     AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACG                         AGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA
genomic: AGTGGAGAAAATCAGCGGCACAGCGTGGGTCTCGCGACCTCCAGCGAACGgtgagtcgat ... cttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttccttgttccccactgtctcttcctgattagtgttatttcgcttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGAGGAGCAGTTCATCCTCCGCGTGCCGCCATCCGTCGCAGAGCGGATCGAG
                         tcctgat  putative branch site (score: 3)
                                        tttcgctt  putative PPT
                                   tgttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcgatgagtttatctccttccggccttacctattctcgatcttctctgctcccttagttcttgttcctttattttccttgttccccactgtctcttcctgattagtgttatttcgcttgagtcagAGATCCCTAAGTTTCGATCCACTGTCCCAGTGGATTTGGGACTGCGATGGAGGAGCAGTTCATCCTCCGCGTGCCGCCATCCGTCGCAGAGCGGATCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG