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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATAGGGCTCCAGAGCTCATATTTGGTGCCACTGAGTATACCACAGCGATTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtatggtgtcttcgatatttattggcatgtttattttttcaagtcaacaaaaaaagtcttttgaagttcacattttcttacaagaactatttcaacag

Basic information

species Zea mays
transcript GRMZM5G835235_T04
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G835235_T03 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os01g14860.3 (Oryza sativa), 5'ss of exon 7
CTATAGGGCTCCAGAGCTCATATTTGGTGCCACTGAGTATACCACAGCGATTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtatg-----gtgtcttcgatatttatt---ggcatgtttattttttcaagtcaacaaaaaaagtcttttgaagttcacattttcttacaagaactat---ttcaacag
|||||||||||| |||||||||||||||||||| || || || ||||| |||||||| ||||||||||| |||||||||||||| |||||| ||||||||||| |     |  | |||  |    |||   || | |||| || |||     || |    |   | || |  |  ||    |  |||||||    | |   ||| ||||
CTATAGGGCTCCGGAGCTCATATTTGGTGCCACCGAATACACTACAGCTATTGACATCTGGTCTGCTGGATGTGTTCTTGCTGAACTTATGTTAGGGCAGgtaagcggctggattttctttgcacattttggggaagtttgttgttt---accaccctggactctattgtcgaagtcggtatgccttacaattgttttctgttcgacag
















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|213187425|gb|FM190443.1|FM190443
EST:     TTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAG                         CCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG
genomic: TTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtatggtgtc ... atttcaacagCCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG
EST: gi|33093876|gb|CF053870.1|CF053870
EST:     TTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAG                         CCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG
genomic: TTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtatggtgtc ... atttcaacagCCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG
EST: gi|213187001|gb|FM192338.1|FM192338
EST:     TTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAG                         CCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG
genomic: TTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtatggtgtc ... atttcaacagCCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG
EST: gi|20803001|gb|BQ294051.1|BQ294051
EST:     TTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAG                         CCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG
genomic: TTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtatggtgtc ... atttcaacagCCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG
EST: gi|32830913|gb|CD970591.1|CD970591
EST:     TTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAG                         CCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG
genomic: TTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtatggtgtc ... atttcaacagCCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG
EST: gi|32865481|gb|CF005163.1|CF005163
EST:     TTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAG                         CCTTTGTTTCCAGGTGAAAGGGGTGTGGACCAACTCGTCGAAATCATCAAG
genomic: TTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtatggtgtc ... atttcaacagCCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG
EST: gi|32865499|gb|CF005181.1|CF005181
EST:     TTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAG                         CCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG
genomic: TTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtatggtgtc ... atttcaacagCCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG
EST: gi|32830394|gb|CD970072.1|CD970072
EST:     TTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGTCAT                         CCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCGAG
genomic: TTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtatggtgtc ... atttcaacagCCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG
EST: gi|32831124|gb|CD970802.1|CD970802
EST:     TTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAG                         CCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG
genomic: TTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtatggtgtc ... atttcaacagCCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG
EST: gi|26456580|gb|CA828163.1|CA828163
EST:     TTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAG                         CCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG
genomic: TTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtatggtgtc ... atttcaacagCCTTTGTTTCCAGGTGAAAGTGGTGTGGACCAACTCGTCGAAATCATCAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTATAGGGCTCCAGAGCTCATATTTGGTGCCACTGAGTATACCACAGCGATTGACATTTGGTCTGCTGGTTGTGTTCTTGCTGAGCTTATGCTAGGGCAGgtatggtgtcttcgatatttattggcatgtttattttttcaagtcaacaaaaaaagtcttttgaagttcacattttcttacaagaactatttcaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT