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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGGGAGGATGGTCCATCTGAGGAGCATAGTGACCTATTGTTCTATGAGTATGTTGAAGCTGTAAAATTAACAGGGGACAACCTCATGCCAGCTGGTCAGgtatggattattgtaacttccactgggtttttattaccatataggaatagcgtttgtaagtagctaagtaatacgtgccttctggttcacggtcttcctg...

Basic information

species Zea mays
transcript GRMZM2G048435_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G048435_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os10g34400.2 (Oryza sativa), 5'ss of exon 8
GCGGGAGGATGGTCCATCTGAGGAGCATAGTGACCTATTGTTCTATGAGTATGTTGAAGCTGTAAAATTAACAGGGGACAACCTCATGCCAGCTGGTCAGgtatggattattgtaacttccactgggtttttattaccatataggaatagcgtttgtaagtagc-taagtaatacgtgccttctggttcacggtcttcctg-----------------
||| ||||||| | ||||||| ||||| || ||||||  |||||||||||||||||| |||||||| || || || ||||||||  ||||||| ||||||||||       | |  |||| |||      || |  ||||| |  | || |      |||||   ||||||||| ||     || |||   | ||||||                   
GCGAGAGGATGATTCATCTGAAGAGCACAGGGACCTACAGTTCTATGAGTATGTTGAGGCTGTAAAGTTGACCGGTGACAACCTTGTGCCAGCGGGTCAGgtat-------tatgccttcaact-----cttgtagccatacaaaactaac------aagtactgtaagtaatatgtattcccttgtttttgttcttcccacttgttgaagaaataaa
















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|32928804|gb|CF033616.1|CF033616
EST:     ATGTTGAAGCTGTAAAATTAACAGGGGACAACCTCATGCCAGCTGGTCAG                         GTTGTTTTCCGTGCAAAAGTTGGTGAACACTATCGGCTCCCTCATAAGGGA
genomic: ATGTTGAAGCTGTAAAATTAACAGGGGACAACCTCATGCCAGCTGGTCAGgtatggatta ... cctttgctagGTTGTTTTCCGTGCAAAAGTTGGTGAACACTATCGGCTCCCTCATAAGGGA
EST: gi|60358610|gb|DN225583.1|DN225583
EST:     GCCAGCTGGTCAG                         GTTGTTTTCCGTGCAAAAGTTGGTGAACACTATCGGCTCCCTCATAAGGGA
genomic: GCCAGCTGGTCAGgtatggatta ... cctttgctagGTTGTTTTCCGTGCAAAAGTTGGTGAACACTATCGGCTCCCTCATAAGGGA
EST: gi|113704299|gb|EE681803.1|EE681803
EST:     ATGTTGAAGCTGTAAAATTAACAGGGGACAACCTCATGCCAGCTGGTCAG                         GTTGTTTTCCGTGCAAAAGTTGGTGAACACTATCGGCTCCCTCATAAGGGA
genomic: ATGTTGAAGCTGTAAAATTAACAGGGGACAACCTCATGCCAGCTGGTCAGgtatggatta ... cctttgctagGTTGTTTTCCGTGCAAAAGTTGGTGAACACTATCGGCTCCCTCATAAGGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGGGAGGATGGTCCATCTGAGGAGCATAGTGACCTATTGTTCTATGAGTATGTTGAAGCTGTAAAATTAACAGGGGACAACCTCATGCCAGCTGGTCAGgtatggattattgtaacttccactgggtttttattaccatataggaatagcgtttgtaagtagctaagtaatacgtgccttctggttcacggtcttcctg

- - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG