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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAGCAGTCTACCTGGAGCCGGTGCCTTTCAGCATCGAGAAGGACCTCGTCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAGgtctgatggaaccatgcagaattattcacacaaaagtttttacaatgtcgtcgcgatgatttctttaagtaaaacggaaaattttgtagtttcattttattcaaatttgtcgtag

Basic information

species Zea mays
transcript GRMZM2G104847_T01
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104847_T01 (Zea mays), 5'ss of exon 18
lower sequence: LOC_Os11g35400.2 (Oryza sativa), 5'ss of exon 18
GAAAGCAGTCTACCTGGAGCCGGTGCCTTTCAGCATCGAGAAGGACCTCGTCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAGgtctgatggaacca--tgcagaattat----tcacacaaaagtttttacaatgtcgtcgcgatgatttctttaagtaaaacggaaaattttgtagtttcattttattcaaatttgtcgtag---------------------------------------
 || ||| |  |||| ||| |   ||| |||||||| ||||||||||| || |||||||| ||||||||||||||||||||||||||||| |||||||||||  ||  |||| |  |  | ||  ||    ||        ||| |||  || |  |      |||      | || ||  | |    ||  |    | ||| |  | |  ||| |   |                                        
AAAGGCAATTCACCTAGAGACAACGCCATTCAGCATAGAGAAGGACCTGGTGACTCCAACTTTTAAGCTCAAGAGACCCCAGCTGCTCAAATATTACAAGgttagagagaacaaactctataaccatgatttcctggttttgttcttatgat-ttattttacggatgcaaacatgtgaa-tgaagttcttcatgacattattctggtgatctttataagactaagcatgtggataatggtagcacatttttttaatgcag
















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|9254901|gb|BE345369.1|BE345369
EST:     TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAG                         GATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
genomic: TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAGgtctgatgga ... tttgtcgtagGATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
EST: gi|5670866|gb|AI932129.1|AI932129
EST:     TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAG                         GATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
genomic: TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAGgtctgatgga ... tttgtcgtagGATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
EST: gi|76283291|gb|DV022859.1|DV022859
EST:     TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAG                         GATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
genomic: TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAGgtctgatgga ... tttgtcgtagGATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
EST: gi|211099227|gb|FL470676.1|FL470676
EST:     TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAG                         GATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
genomic: TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAGgtctgatgga ... tttgtcgtagGATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
EST: gi|4647598|gb|AI622673.1|AI622673
EST:     TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAG                         GATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
genomic: TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAGgtctgatgga ... tttgtcgtagGATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
EST: gi|32909558|gb|CF014370.1|CF014370
EST:     TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAG                         GATCCGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
genomic: TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAGgtctgatgga ... tttgtcgtagGATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
EST: gi|148958442|gb|EC904676.2|EC904676
EST:     TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAG                         GATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
genomic: TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAGgtctgatgga ... tttgtcgtagGATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
EST: gi|60337173|gb|DN204146.1|DN204146
EST:     TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAG                         GATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
genomic: TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAGgtctgatgga ... tttgtcgtagGATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
EST: gi|4647597|gb|AI622672.1|AI622672
EST:     TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAG                         GATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
genomic: TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAGgtctgatgga ... tttgtcgtagGATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
EST: gi|86473157|gb|DY239527.1|DY239527
EST:     TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAG                         GATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
genomic: TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAGgtctgatgga ... tttgtcgtagGATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
EST: gi|32836844|gb|CD976522.1|CD976522
EST:     TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAG                         GATCCGGTCGACCAAATGT
genomic: TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAGgtctgatgga ... tttgtcgtagGATCGGGTCGACCAAATGT
EST: gi|9254900|gb|BE345368.1|BE345368
EST:     TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAG                         GATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
genomic: TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAGgtctgatgga ... tttgtcgtagGATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
EST: gi|20315387|gb|BQ169253.1|BQ169253
EST:     TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAG                         GATCGGGTCGACCATATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
genomic: TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAGgtctgatgga ... tttgtcgtagGATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
EST: gi|83279443|gb|DV943451.1|DV943451
EST:     TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAG                         GATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
genomic: TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAGgtctgatgga ... tttgtcgtagGATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
EST: gi|32837781|gb|CD977459.1|CD977459
EST:     TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAG                         GATCCGGTCGACCAAATGT
genomic: TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAGgtctgatgga ... tttgtcgtagGATCGGGTCGACCAAATGT
EST: gi|71430908|gb|DR811958.1|DR811958
EST:     TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAG                         GATGGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
genomic: TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAGgtctgatgga ... tttgtcgtagGATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
EST: gi|13150470|gb|BG320792.1|BG320792
EST:     TCACTCCAACCTTTAAGCTCAAGAGACYCCAGCTGCTCAAGTATTACAAG                         GATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
genomic: TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAGgtctgatgga ... tttgtcgtagGATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
EST: gi|148999539|gb|EE036510.2|EE036510
EST:     TCCCTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAG                         GATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGGTGCGCCA
genomic: TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAGgtctgatgga ... tttgtcgtagGATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
EST: gi|149086278|gb|EE175819.2|EE175819
EST:     TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAG                         GATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGGTGCGCCA
genomic: TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAGgtctgatgga ... tttgtcgtagGATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
EST: gi|211174079|gb|FL129194.1|FL129194
EST:     TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAG                         GATCCGGTCGACCAAATGTACAAGGATGCCAAAGGAGGGGAGAGCTGCGCC
genomic: TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAGgtctgatgga ... tttgtcgtagGATCGGGTCGACCAAATGTACAAGGATGCCAA-GGAGGGGAGAGCTGCGCC
EST: gi|32837912|gb|CD977590.1|CD977590
EST:     TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAG                         GATCCGGTCGACCAAATGT
genomic: TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAGgtctgatgga ... tttgtcgtagGATCGGGTCGACCAAATGT
EST: gi|12972551|gb|BG268038.1|BG268038
EST:     TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAG                         GATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
genomic: TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAGgtctgatgga ... tttgtcgtagGATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
EST: gi|7145452|gb|AW506933.1|AW506933
EST:     TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAG                         GATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
genomic: TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAGgtctgatgga ... tttgtcgtagGATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
EST: gi|149098381|gb|EE184357.2|EE184357
EST:     TCACTCCACCCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAG                         GATCGGGTCGCCCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
genomic: TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAGgtctgatgga ... tttgtcgtagGATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
EST: gi|32867314|gb|CF006996.1|CF006996
EST:     TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAG                         GATCCGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
genomic: TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAGgtctgatgga ... tttgtcgtagGATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
EST: gi|213187833|gb|FM185065.1|FM185065
EST:     TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAG                         GATCCGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
genomic: TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAGgtctgatgga ... tttgtcgtagGATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
EST: gi|78544549|gb|DV622047.1|DV622047
EST:     TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAG                         GATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
genomic: TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAGgtctgatgga ... tttgtcgtagGATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
EST: gi|149076510|gb|EE165136.2|EE165136
EST:     TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAG                         GATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
genomic: TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAGgtctgatgga ... tttgtcgtagGATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
EST: gi|149085815|gb|EE175337.2|EE175337
EST:     TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAG                         GATCGGGTCGGCCAAATGTACAAGGATGCCAAGGAGGGGAGAGGTGCGCCA
genomic: TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAGgtctgatgga ... tttgtcgtagGATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
EST: gi|94479493|gb|EB708451.1|EB708451
EST:     TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAG                         GATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA
genomic: TCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAGgtctgatgga ... tttgtcgtagGATCGGGTCGACCAAATGTACAAGGATGCCAAGGAGGGGAGAGCTGCGCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAGCAGTCTACCTGGAGCCGGTGCCTTTCAGCATCGAGAAGGACCTCGTCACTCCAACCTTTAAGCTCAAGAGACCCCAGCTGCTCAAGTATTACAAGgtctgatggaaccatgcagaattattcacacaaaagtttttacaatgtcgtcgcgatgatttctttaagtaaaacggaaaattttgtagtttcattttattcaaatttgtcgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT