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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCCACCAGCCGCCGCGACTTCCTCCGCAAGTTCGGCGAGTCCTTCCACCGCGAGGACCTCCTCATCAACAAGTACAAGAAGAACGACCCATCCGACCAGgtcagtccaggctcagctcccgatccaatccgaatccactccgccgcgggtcaacggcctcccctgctttgcttcctgccgctcctgatcggatcggaca...

Basic information

species Zea mays
transcript GRMZM2G476009_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G476009_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g59140.1 (Oryza sativa), 5'ss of exon 1
CGCCACCAGCCGCCGCGACTTCCTCCGCAAGTTCGGCGAGTCCTTCCACCGCGAGGACCTCCTCATCAACAAGTACAAGAAGAACGACCCATCCGACCAGgtcagtccaggctcagctcccgatccaatccg---aatccactccgccgcgggtcaacggcctcccctgctttgcttcctgcc-gctcctgatcggatcggaca
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CGCCATGGGCCGCCGCGACTTCCTCCGCAAGTACGGCGAGTCCTTCCACCGCGAGGACCTCCTCATCAACAAGTACAAGAAGAACGATCCCTCCGACCAGgtgag-ccatatgcatcctcacccccacttcgcccgatcgatccatccatccgcaagctagctacgcaagatcgatcaagcccagcagctagctctctctg---
















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|149013010|gb|EE042745.2|EE042745
EST:     GCGAGGACCTCCTCATCAACAAGTACAAGAAGAACGACCCATCCGACCAG                         ATATATGTCTTCTTCCCCAACGATGACAAGGTAGGGATGAAGCACATCAAG
genomic: GCGAGGACCTCCTCATCAACAAGTACAAGAAGAACGACCCATCCGACCAGgtcagtccag ... cttggatcagATATATGTCTTCTTCCCCAACGATGACAAGGTAGGGATGAAGCACATCAAG
EST: gi|4609494|gb|AI600333.1|AI600333
EST:     GCGAGGACCTCCTCATCAACAAGTACAAGAAGAACGACCCATCCGACCAG                         ATATATGTCTTCTTCCCCAACGATGACAAGGTAGGGATGAAGCACATCAAG
genomic: GCGAGGACCTCCTCATCAACAAGTACAAGAAGAACGACCCATCCGACCAGgtcagtccag ... cttggatcagATATATGTCTTCTTCCCCAACGATGACAAGGTAGGGATGAAGCACATCAAG
EST: gi|13316033|gb|BG410480.1|BG410480
EST:     GCGAGGACCTCCTCATCAACAAGTACAAGAAGAACGACCCATCCGACCAG                         ATATATGTCTTCTTCCCCAACGATGACAAGGTAGGGATGAAGCACATCAAG
genomic: GCGAGGACCTCCTCATCAACAAGTACAAGAAGAACGACCCATCCGACCAGgtcagtccag ... cttggatcagATATATGTCTTCTTCCCCAACGATGACAAGGTAGGGATGAAGCACATCAAG
EST: gi|78124667|gb|DV543051.1|DV543051
EST:     GACCCATCCGACCAG                         ATATATGTC-TCTTCCCCAACGATGACAAGGTAGGGATGAAGCACATCAAG
genomic: GACCCATCCGACCAGgtcagtccag ... cttggatcagATATATGTCTTCTTCCCCAACGATGACAAGGTAGGGATGAAGCACATCAAG
EST: gi|16925901|gb|BM078969.1|BM078969
EST:     GACCCATCCGACCAG                         ATATATGTCTTCTTCCCCAACGATGACAAGGTAGGGATGAAGCACATCAAG
genomic: GACCCATCCGACCAGgtcagtccag ... cttggatcagATATATGTCTTCTTCCCCAACGATGACAAGGTAGGGATGAAGCACATCAAG
EST: gi|37388912|gb|CF631671.1|CF631671
EST:     GCGAGGACCTCCTCATCAACAAGTACAAGAAGAACGACCCATCCGACCAG                         ATATATGTCTTCTTCCCCAACGATGACAAGGTAGGGATGAAGCACATCAAG
genomic: GCGAGGACCTCCTCATCAACAAGTACAAGAAGAACGACCCATCCGACCAGgtcagtccag ... cttggatcagATATATGTCTTCTTCCCCAACGATGACAAGGTAGGGATGAAGCACATCAAG
EST: gi|120480234|gb|EH210778.1|EH210778
EST:     GCGAGGACCTCCTCATCAACAAGTACAAGAAGAACGACCCATCCGACCAG                         ATATATGTCTTCTTCCCCAACGATGACAAGGTAGGGATGAAGCACATCAAG
genomic: GCGAGGACCTCCTCATCAACAAGTACAAGAAGAACGACCCATCCGACCAGgtcagtccag ... cttggatcagATATATGTCTTCTTCCCCAACGATGACAAGGTAGGGATGAAGCACATCAAG
EST: gi|71762794|gb|DR960731.1|DR960731
EST:     GTACAAGAAGAACGACCCATCCGACCAG                         ATATATGTCTTCTTCCCCAACGATGACAAGGTAGGGATGAAGCACATCAAG
genomic: GTACAAGAAGAACGACCCATCCGACCAGgtcagtccag ... cttggatcagATATATGTCTTCTTCCCCAACGATGACAAGGTAGGGATGAAGCACATCAAG
EST: gi|5871454|gb|AW017925.1|AW017925
EST:     GCGAGGACCTCCTCATCAACAAGTACAAGAAGAACGACCCATCCGACCAG                         ATATATGTCTTCTTCCCCAACGATGACAAGGTAGGGATGAAGCACATCAAG
genomic: GCGAGGACCTCCTCATCAACAAGTACAAGAAGAACGACCCATCCGACCAGgtcagtccag ... cttggatcagATATATGTCTTCTTCCCCAACGATGACAAGGTAGGGATGAAGCACATCAAG
EST: gi|211038261|gb|FL216363.1|FL216363
EST:     CGAGGACTCTCCTCATCAACAAGTACAAGAAGAACGACCCATCCGACCAG                         ATATATGTCTTCTTCCCCAACGATGACAAGGTAGGGATGAAGCACATCAAG
genomic: CGAGGAC-CTCCTCATCAACAAGTACAAGAAGAACGACCCATCCGACCAGgtcagtccag ... cttggatcagATATATGTCTTCTTCCCCAACGATGACAAGGTAGGGATGAAGCACATCAAG
EST: gi|13490733|gb|BG517497.1|BG517497
EST:     GCGAGGACCTCCTCATCAACAAGTACAAGAAGAACGACCCATCCGACCAG                         ATATATGTCTTCTTCCCCAACGATGACAAGGTAGGGATGAAGCACATCAAG
genomic: GCGAGGACCTCCTCATCAACAAGTACAAGAAGAACGACCCATCCGACCAGgtcagtccag ... cttggatcagATATATGTCTTCTTCCCCAACGATGACAAGGTAGGGATGAAGCACATCAAG
EST: gi|149001168|gb|EE038433.2|EE038433
EST:     GCGAGGACCTCCTCATCAACAAGTACAAGAAGAACGACCCATCCGACCAG                         ATATATGTCTTCTTCCCCAACGATGACAAGGTAGGGATGAAGCACATCAAG
genomic: GCGAGGACCTCCTCATCAACAAGTACAAGAAGAACGACCCATCCGACCAGgtcagtccag ... cttggatcagATATATGTCTTCTTCCCCAACGATGACAAGGTAGGGATGAAGCACATCAAG
EST: gi|13316032|gb|BG410479.1|BG410479
EST:     GCGAGGACCTCCTCATCAACAAGTACAAGAAGAACGACCCATCCGACCAG                         ATATATGTCTTCTTCCCCAACGATGACAAGGTAGGGATGAAGCACATCAAG
genomic: GCGAGGACCTCCTCATCAACAAGTACAAGAAGAACGACCCATCCGACCAGgtcagtccag ... cttggatcagATATATGTCTTCTTCCCCAACGATGACAAGGTAGGGATGAAGCACATCAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCCACCAGCCGCCGCGACTTCCTCCGCAAGTTCGGCGAGTCCTTCCACCGCGAGGACCTCCTCATCAACAAGTACAAGAAGAACGACCCATCCGACCAGgtcagtccaggctcagctcccgatccaatccgaatccactccgccgcgggtcaacggcctcccctgctttgcttcctgccgctcctgatcggatcggaca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccgccgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctcccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccgctcc