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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATCATCAAGGACAAGGACAACGTCACTCTGGAGGACGTGCTGCAACCTGGCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACGgtaataaccaattaattctcttgaacccatcttctccgaaggtaatcatctgtaacgaaatataattgacatgcgcaaccaatctgatgcag

Basic information

species Zea mays
transcript GRMZM5G836250_T02
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G836250_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g64660.1 (Oryza sativa), 5'ss of exon 6
CATCATCAAGGACAAGGACAACGTCACTCTGGAGGACGTGCTGCAACCTGGCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACGgtaat-aaccaattaattctcttgaacccatcttctccgaaggtaatcatctgtaacgaaatataattgacatgcgcaaccaatctgatgcag
||| ||||| || ||||| || || ||||| ||||||||| | || ||||| || |||||| | || || |||||||||||||||||||||||||||||||||||  |||   |||| |     | || |   |||   || || || ||    | |  |||||||      || | ||| ||| ||||||||
CATGATCAAAGATAAGGAGAATGTGACTCTTGAGGACGTGTTACAGCCTGGAAAAAACATGGTTGCTGCTGGATACTGCATGTACGGCAGTTCCTGCACGgtaatcgacctcctaatcc-----atcctac--tctataaatgtcataattctcacctgaatataacc----tgtgtaactaatttgatgcag
















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|149064613|gb|EE286484.2|EE286484
EST:     GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACG                         CTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCA
genomic: GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACGgtaataacca ... tctgatgcagCTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCA
EST: gi|149085230|gb|EE174737.2|EE174737
EST:     GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACG                         CTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCA
genomic: GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACGgtaataacca ... tctgatgcagCTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCA
EST: gi|149056940|gb|EE156494.2|EE156494
EST:     GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACG                         CTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCA
genomic: GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACGgtaataacca ... tctgatgcagCTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCA
EST: gi|50327741|gb|CO522867.1|CO522867
EST:     GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACG                         CTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCA
genomic: GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACGgtaataacca ... tctgatgcagCTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCA
EST: gi|89759142|gb|DY688055.1|DY688055
EST:     GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACG                         CTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCA
genomic: GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACGgtaataacca ... tctgatgcagCTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCA
EST: gi|211007786|gb|FL012051.1|FL012051
EST:     GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACG                         CTCGTTCTGAGCACTGGAACTGGGTGTCA-TGGCTTCACG
genomic: GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACGgtaataacca ... tctgatgcagCTCGTTCTGAGCACTGGAACTGG-TGTCAATGGCTTCACG
EST: gi|149088446|gb|EE177549.2|EE177549
EST:     GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACG                         CTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCA
genomic: GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACGgtaataacca ... tctgatgcagCTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCA
EST: gi|149095912|gb|EE181574.2|EE181574
EST:     GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACG                         CTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCA
genomic: GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACGgtaataacca ... tctgatgcagCTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCA
EST: gi|32838746|gb|CD978427.1|CD978427
EST:     ACGGCAGTTCCTGCACG                         CTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCA
genomic: ACGGCAGTTCCTGCACGgtaataacca ... tctgatgcagCTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCA
EST: gi|148983226|gb|EE029190.2|EE029190
EST:     NCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACG                         CTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTT
genomic: GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACGgtaataacca ... tctgatgcagCTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTT
EST: gi|71768089|gb|DR966026.1|DR966026
EST:     GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACG                         CTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCCTCA
genomic: GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACGgtaataacca ... tctgatgcagCTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCA
EST: gi|71770843|gb|DR968780.1|DR968780
EST:     GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACG                         CTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCA
genomic: GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACGgtaataacca ... tctgatgcagCTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCA
EST: gi|148932776|gb|EE285437.2|EE285437
EST:     GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACG                         CTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCA
genomic: GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACGgtaataacca ... tctgatgcagCTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCA
EST: gi|71317308|gb|DR795339.1|DR795339
EST:     GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACG                         CTCGTTCTGAGCACTGGAACT
genomic: GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACGgtaataacca ... tctgatgcagCTCGTTCTGAGCACTGGAACT
EST: gi|211005021|gb|FL012048.1|FL012048
EST:     GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACG                         CTCGTTCTGAGCACTGGAACTGGTGTC
genomic: GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACGgtaataacca ... tctgatgcagCTCGTTCTGAGCACTGGAACTGGTGTC
EST: gi|78106829|gb|DV525247.1|DV525247
EST:     GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACG                         CTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCA
genomic: GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACGgtaataacca ... tctgatgcagCTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCA
EST: gi|32920564|gb|CF025376.1|CF025376
EST:     ACGGCAGTTCCTGCACG                         CTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCA
genomic: ACGGCAGTTCCTGCACGgtaataacca ... tctgatgcagCTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCA
EST: gi|91055488|gb|EB165906.1|EB165906
EST:     CCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACG                         CTCGCTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCA
genomic: GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACGgtaataacca ... tctgatgcagCTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCA
EST: gi|74244032|gb|DT651946.1|DT651946
EST:     GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACG                         CTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCA
genomic: GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACGgtaataacca ... tctgatgcagCTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCA
EST: gi|71757120|gb|DR955057.1|DR955057
EST:     GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACG                         CTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCA
genomic: GCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACGgtaataacca ... tctgatgcagCTCGTTCTGAGCACTGGAACTGGTGTCAATGGCTTCACGCTCGACCCTTCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATCATCAAGGACAAGGACAACGTCACTCTGGAGGACGTGCTGCAACCTGGCAAGAACATGCTCGCCGCCGGATACTGCATGTACGGCAGTTCCTGCACGgtaataaccaattaattctcttgaacccatcttctccgaaggtaatcatctgtaacgaaatataattgacatgcgcaaccaatctgatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC