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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAGCCCTGGGAGCAGCGCCTTGACACCTCGGGGgtatgtaccaatgcctcctcatgtccacgttgccttagtttattttttaatggaagctagggttcaccggctcagttaggagatgcagaatgtgtacatc...

Basic information

species Zea mays
transcript GRMZM2G090647_T04
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G090647_T04 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g37832.1 (Oryza sativa), 5'ss of exon 2
GTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAGCCCTGGGAGCAGCGCCTTGACACCTCGGGGgtatgtaccaatgcctcctcatgtccacgttgccttagtttattttttaatggaagctagggttcaccggctcagttaggagatgcagaatgtgtacatc-
||||||||||| |||||||| ||| | |||||||||||||| |||||||||||||||||||||||||| |||||||| ||||||||||  ||||   |   |        |   | ||      |    | |    |     |   |  |  |||  || ||||||| | |  || | |   
GTGGTGGCTCTGAACGAATCTGTGGCGGGGAGCGTCAAGTCGGTCTTCAAGCCCTGGGAGCAGCGCCTCGACACCTCTGGGgtatgtagtaatgtagcagtagcaatgtctctgcctacccatgtcagcagtaatcggcgaagcgtagggtttca-ctaagagatgcgggagatgaagaatc
















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|211391416|gb|FL107759.1|FL107759
EST:     GCGTCAAGTCCGTCTTCAAGCCCTGGGAGCAGCGCCTTGACACCTCGGGG                         GGTTTTCTGGAGAGTAATGAGGGTGACCCTGAGCTACTTATTTTCATCCCG
genomic: GCGTCAAGTCCGTCTTCAAGCCCTGGGAGCAGCGCCTTGACACCTCGGGGgtatgtacca ... gctgcaccagGGTTTTCTGGAGAGTAATGAGGGTGACCCTGAGCTACTTATTTTCATCCCG
EST: gi|211394035|gb|FL107766.1|FL107766
EST:     GCGTCAAGTCCGTCTTCAAGCCCTGGGAGCAGCGCCTTGACACCTCGGGG                         GGTTTTCTGGAGAGTAATGAGGGTGACCCTGAGCTACTTATTTTCATCCCG
genomic: GCGTCAAGTCCGTCTTCAAGCCCTGGGAGCAGCGCCTTGACACCTCGGGGgtatgtacca ... gctgcaccagGGTTTTCTGGAGAGTAATGAGGGTGACCCTGAGCTACTTATTTTCATCCCG
EST: gi|20301430|gb|BQ164373.1|BQ164373
EST:     GCGTCAAGTCCGTCTTCAAGCCCTGGGAGCAGCGCCTTGACACCTCGGGG                         GGTTTTCTGGAG
genomic: GCGTCAAGTCCGTCTTCAAGCCCTGGGAGCAGCGCCTTGACACCTCGGGGgtatgtacca ... gctgcaccagGGTTTTCTGGAG
EST: gi|211396668|gb|FL107792.1|FL107792
EST:     GCGTCAAGTCCGTCTTCAAGCCCTGGGAGCAGCGCCTTGACACCTCGGGG                         GGTTTTCTGGAGAGTAATGAGGGTGA
genomic: GCGTCAAGTCCGTCTTCAAGCCCTGGGAGCAGCGCCTTGACACCTCGGGGgtatgtacca ... gctgcaccagGGTTTTCTGGAGAGTAATGAGGGTGA
EST: gi|211391414|gb|FL107757.1|FL107757
EST:     CGTCAAGTCCGTCTTCAAGCCCTGGGAGCAGCGCCTTGACNACCTCGGGG                         GGTTTTCTGGAGAGTAAATGAGGGTGACCCTGAGCTACTTATTTTCATCC
genomic: CGTCAAGTCCGTCTTCAAGCCCTGGGAGCAGCGCCTTGAC-ACCTCGGGGgtatgtacca ... gctgcaccagGGTTTTCTGGAGAGTAA-TGAGGGTGACCCTGAGCTACTTATTTTCATCC
EST: gi|211391419|gb|FL107762.1|FL107762
EST:     GCGTCAAGTCCGTCTTCAAGCCCTGGGAGCAGCGCCTTGACACCTCGGGG                         GGTTTTCTGGAGAGTAATGAGGGTGACCCTGAGCTACTTATTTTCATCCCG
genomic: GCGTCAAGTCCGTCTTCAAGCCCTGGGAGCAGCGCCTTGACACCTCGGGGgtatgtacca ... gctgcaccagGGTTTTCTGGAGAGTAATGAGGGTGACCCTGAGCTACTTATTTTCATCCCG
EST: gi|71770110|gb|DR968047.1|DR968047
EST:     GCGTCAAGTCCGTCTTCAAGCCCTGGGAGCAGCGCCTTGACACCTCGGGG                         GGTTTTCTGGAGAGTAATGAGGGTGACCCTGAGCTACTTATTTTCATCCCG
genomic: GCGTCAAGTCCGTCTTCAAGCCCTGGGAGCAGCGCCTTGACACCTCGGGGgtatgtacca ... gctgcaccagGGTTTTCTGGAGAGTAATGAGGGTGACCCTGAGCTACTTATTTTCATCCCG
EST: gi|211396658|gb|FL107782.1|FL107782
EST:     GCGTCAAGTCCGTCTTCAAGCCCTGGGAGCAGCGCCTTGACACCTCGGGG                         GGTTTTCTGGAGAGTAATGAGGGTGACCCTGAGCTACTTATTTTTATCCCG
genomic: GCGTCAAGTCCGTCTTCAAGCCCTGGGAGCAGCGCCTTGACACCTCGGGGgtatgtacca ... gctgcaccagGGTTTTCTGGAGAGTAATGAGGGTGACCCTGAGCTACTTATTTTCATCCCG
EST: gi|211394048|gb|FL107779.1|FL107779
EST:     GCGTCAAGTCCGTCTTCAAGCCCTGGGAGCAGCGCCTTGACACCTCGGGG                         GGTTTTCTGGAGAGTAATGAGGGTGACCCTGAGCKACTTATTTTSATCCCG
genomic: GCGTCAAGTCCGTCTTCAAGCCCTGGGAGCAGCGCCTTGACACCTCGGGGgtatgtacca ... gctgcaccagGGTTTTCTGGAGAGTAATGAGGGTGACCCTGAGCTACTTATTTTCATCCCG
EST: gi|211396659|gb|FL107783.1|FL107783
EST:     GCGTCAAGTCCGTCTTCAAGCCCTGGGAGCAGCGCCTTGACACCTCGGGG                         GGTTTTCTGGAGAGTAATGAGGGTGACC-TGAGCTACTTATTTTCATCCCG
genomic: GCGTCAAGTCCGTCTTCAAGCCCTGGGAGCAGCGCCTTGACACCTCGGGGgtatgtacca ... gctgcaccagGGTTTTCTGGAGAGTAATGAGGGTGACCCTGAGCTACTTATTTTCATCCCG
EST: gi|20507306|gb|BQ279572.1|BQ279572
EST:     GCGTCAAGTCCGTCTTCAAGCCCTGGGAGCAGCGCCTTGACACCTCGGGG                         GGTTTTCTGGAGAGTAATGAGGGTGACCCTGAGCTACTTATTTTCATCCCG
genomic: GCGTCAAGTCCGTCTTCAAGCCCTGGGAGCAGCGCCTTGACACCTCGGGGgtatgtacca ... gctgcaccagGGTTTTCTGGAGAGTAATGAGGGTGACCCTGAGCTACTTATTTTCATCCCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGTGGCTCTCAACGAATCGGTGCCCGGGAGCGTCAAGTCCGTCTTCAAGCCCTGGGAGCAGCGCCTTGACACCTCGGGGgtatgtaccaatgcctcctcatgtccacgttgccttagtttattttttaatggaagctagggttcaccggctcagttaggagatgcagaatgtgtacatc

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