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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGTGATTTAAGGGACTGGCATGAGTTTCCACAGTGGAAGCCCCAGGGTTTGGCACGTGTCGTCCCAACACTGGAACCTGAAGGAGTTGACCTTCTATCGgtaagttataagggtgatttacatgcccatttagtgtgttctcttaacctggaagtgtgttaatcaagtaaccttgcttcagttacatacttcgatccac...

Basic information

species Zea mays
transcript GRMZM2G495626_T04
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G495626_T03 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os01g67160.1 (Oryza sativa), 5'ss of exon 6
GAGTGATTTAAGGGACTGGCATGAGTTTCCACAGTGGAAGCCCCAGGGTTTGGCACGTGTCGTCCCAACACTGGAACCTGAAGGAGTTGACCTTCTATCGgtaagttataagggtgat-ttacatgcccatttagtgtgttctcttaacctggaagtgtgttaatcaagt--aaccttgcttcagttacata-cttcgatccac
 | |||||| |||||||||||||||||||||||||||||||| |||  ||| | ||||   |||||| || |||| |||||||||||||||||| ||||||||||  |   |    ||  |   |  |||||| ||   |  ||  ||      ||  ||| |   || |  ||  |  |   | ||  ||| |||| |     
AACTGATTTGAGGGACTGGCATGAGTTTCCACAGTGGAAGCCACAGATTTTAGAACGTCAAGTCCCATCATTGGAGCCTGAAGGAGTTGACCTTTTATCGgtaagaaaactgatctatactggttttccattttgtcactattcgaaattatttaggctgtaagataatttgaagttctccctaatttaatagcttcaaa----
















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|94473281|gb|EB702239.1|EB702239
EST:     TGGCACGTGTCGTCCCAACACTGGAACCTGAAGGAGTTGACCTTCTATCG                         AAAATGCTTCAGCTTGATCCTTCAAACAGGATATCAGCTTTAGCTGCGATG
genomic: TGGCACGTGTCGTCCCAACACTGGAACCTGAAGGAGTTGACCTTCTATCGgtaagttata ... tgtgttgcagAAAATGCTTCAGCTTGATCCTTCAAACAGGATATCAGCTTTAGCTGCGATG
EST: gi|5686848|gb|AI939762.1|AI939762
EST:     TGGCACGTGTCGTCCCAACACTGGAACCTGAAGGAGTTGACCTTCTATCG                         AAAATGCTTCAGCTTGATCCTTCAAACAGGATATCAGCTTTAGCTGCGATG
genomic: TGGCACGTGTCGTCCCAACACTGGAACCTGAAGGAGTTGACCTTCTATCGgtaagttata ... tgtgttgcagAAAATGCTTCAGCTTGATCCTTCAAACAGGATATCAGCTTTAGCTGCGATG
EST: gi|94473655|gb|EB702613.1|EB702613
EST:     TGGCACGTGTCGTCCCAACACTGGAACCTGAAGGAGTTGACCTTCTATCG                         AAAATGCTTCAGCTTGATCCTTCAAACAGGATATCAGCTTTAGCTGCGATG
genomic: TGGCACGTGTCGTCCCAACACTGGAACCTGAAGGAGTTGACCTTCTATCGgtaagttata ... tgtgttgcagAAAATGCTTCAGCTTGATCCTTCAAACAGGATATCAGCTTTAGCTGCGATG
EST: gi|5081226|gb|AI738383.1|AI738383
EST:     TGGCACGTGTCGTCCCAACACTGGAACCTGAAGGAGTTGACCTTCTATCG                         AAAATGCTTCAGCTTGATCCTTCAAACAGGATATCAGCTTTAGCTGCGATG
genomic: TGGCACGTGTCGTCCCAACACTGGAACCTGAAGGAGTTGACCTTCTATCGgtaagttata ... tgtgttgcagAAAATGCTTCAGCTTGATCCTTCAAACAGGATATCAGCTTTAGCTGCGATG
EST: gi|213190990|gb|FM191595.1|FM191595
EST:     ACGTGTCGTCCCAACACTGGAACCTNNNGGAGTTGACCTTCTATCG                         AAAATGCTTCAGCTTGATCCTTCAAACAGGATATCAGCTTTAGCTGCGATG
genomic: ACGTGTCGTCCCAACACTGGAACCTGAAGGAGTTGACCTTCTATCGgtaagttata ... tgtgttgcagAAAATGCTTCAGCTTGATCCTTCAAACAGGATATCAGCTTTAGCTGCGATG
EST: gi|31558281|gb|CD527493.1|CD527493
EST:     TGGCACGTGTCGTCCCAACACTGGAACCTGAAGGAGTTGACCTTCTATCG                         AAAATGCTTCAGCTTGATCCTTCAAACAGGATATCAGCTTTAGCTGCGATG
genomic: TGGCACGTGTCGTCCCAACACTGGAACCTGAAGGAGTTGACCTTCTATCGgtaagttata ... tgtgttgcagAAAATGCTTCAGCTTGATCCTTCAAACAGGATATCAGCTTTAGCTGCGATG
EST: gi|32912602|gb|CF017414.1|CF017414
EST:     TGGCACGTGTCGTCCCAACACTGGAACCTGAAGGAGTTGACCTTCTATCG                         AAAATGCTTCAGCTTGATCCTTCAAACAGGATATTATTTTTAGCTGCGATG
genomic: TGGCACGTGTCGTCCCAACACTGGAACCTGAAGGAGTTGACCTTCTATCGgtaagttata ... tgtgttgcagAAAATGCTTCAGCTTGATCCTTCAAACAGGATATCAGCTTTAGCTGCGATG
EST: gi|26559634|gb|CA831869.1|CA831869
EST:     TGGCACGTGTCGTCCCAACACTGGAACCTGAAGGAGTTGACCTTCTATCG                         AAAATGCTTCAGCTTGATCCTTCAAACAGGATATCAGCTTTAGCTGCGATG
genomic: TGGCACGTGTCGTCCCAACACTGGAACCTGAAGGAGTTGACCTTCTATCGgtaagttata ... tgtgttgcagAAAATGCTTCAGCTTGATCCTTCAAACAGGATATCAGCTTTAGCTGCGATG
EST: gi|78027249|gb|DV495636.1|DV495636
EST:     TGGCACGTGTCGTCCCAACACTGGAACCTGAAGGAGTTGACCTTCTATCG                         AAAATGCTTCAGCTTGATCCTTCAAACAGGATATCAGCTTTAGCTGCGATG
genomic: TGGCACGTGTCGTCCCAACACTGGAACCTGAAGGAGTTGACCTTCTATCGgtaagttata ... tgtgttgcagAAAATGCTTCAGCTTGATCCTTCAAACAGGATATCAGCTTTAGCTGCGATG
EST: gi|18178648|gb|BM379858.1|BM379858
EST:     TGGCACGTGTCGTCCCAACACTGGAACCTGAAGGAGTTGACCTTCTATCG                         AAAATGCTTCAGCTTGATCCTTCAAACAGGATATCAGCTTTAGCTGCGATG
genomic: TGGCACGTGTCGTCCCAACACTGGAACCTGAAGGAGTTGACCTTCTATCGgtaagttata ... tgtgttgcagAAAATGCTTCAGCTTGATCCTTCAAACAGGATATCAGCTTTAGCTGCGATG
EST: gi|9825079|gb|BE575296.1|BE575296
EST:     TGGCACGTGTCGTCCCAACACTGGAACCTGAAGGAGTTGACCTTCTATCG                         AAAATGCTTCAGCTTGATCCTTCAAACAGGATATCAGCTTTAGCTGCGATG
genomic: TGGCACGTGTCGTCCCAACACTGGAACCTGAAGGAGTTGACCTTCTATCGgtaagttata ... tgtgttgcagAAAATGCTTCAGCTTGATCCTTCAAACAGGATATCAGCTTTAGCTGCGATG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGTGATTTAAGGGACTGGCATGAGTTTCCACAGTGGAAGCCCCAGGGTTTGGCACGTGTCGTCCCAACACTGGAACCTGAAGGAGTTGACCTTCTATCGgtaagttataagggtgatttacatgcccatttagtgtgttctcttaacctggaagtgtgttaatcaagtaaccttgcttcagttacatacttcgatccac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG