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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAGgcaagttgctcatcgtttttaatggttgcaaatttgcaatctcgtggcggtgaagtgctcttgttttcttatactatctctgaaactcttgagtctggtggtaatgtcactgacagcgttactgttgcatctcag

Basic information

species Zea mays
transcript GRMZM2G019260_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G019260_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g14830.1 (Oryza sativa), 5'ss of exon 3
GCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAGgcaagttgctcatcgtttttaatggttgcaaatttgcaatctcgtggcggtgaagtgctcttgttttcttatactatctctgaaactcttgagtctggtggtaatgtcactgacagcgttactgttgcatctcag
|||||||||||||| |||||||| || ||||||||||| ||||||||||| |||||||| ||||| | ||| || ||||| || ||||||||| | ||||||||   | ||| |||      | ||  |          | ||||| |   || ||||| || |        | | |  | || ||     | ||||| || ||| |   ||    ||| |||||||      
GCGTGGACGGATGTGAAAGTGACCTCTCCTCAGCTCTCCCGGGAGGCCACCTACAAGCTCTCCCTGAAGAAATCAACGCTCCAGTTGACGTCTTCAAGgcaagtcattgatcattt------gctggga----------ttgtggcagc--agcgctctggtctgta---gttgttttcggaattcact--tttggtgatagtgttaacaac----ttaatgttgcag-----

upper sequence: GRMZM2G019260_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g48160.1 (Oryza sativa), 5'ss of exon 4
GCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAGgcaagttgctcatcgtttttaatggttgcaaatttgcaatct-cgtggcggtgaagtgctcttgttttcttatactatctctgaaactcttgagtctggtggtaatgtcactgacagcgttactgttgcatctcag
||||||||| |||| |||||||| || ||||||||||| ||||||||||| |||||||| ||||  | ||| ||||||            ||  | ||| |||| |  |||  |  ||    | ||  | | | | || | ||  |                                                                                        
GCGTGGACGAATGTGAAAGTGACATCTCCTCAGCTCTCCCGGGAGGCCACCTACAAGCTCTCCCCGAAGAAATCGACG------------TCCTCAAGgtaagtagtccatgatcattt---gctgggattgtaccatttgcgcag----------------------------------------------------------------------------------------
















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|211063636|gb|FL185551.1|FL185551
EST:     ACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAG                         GGAATCTACAAACCCTTTTGTGGAGCAGGCCATACAATTCTCGGTAGCAGC
genomic: ACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAGgcaagttgct ... tgcatctcagGGAATCTACAAACCCTTTTGTGGAGCAGGCCATACAATTCTCGGTAGCAGC
EST: gi|78089475|gb|DV517849.1|DV517849
EST:     ACATACAAGCTGTCCCTAACGAAGTCGACGCTGCGATTGACGTCTGCGAC                         GGAATCTACAAACCCTTTT
genomic: ACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAGgcaagttgct ... tgcatctcagGGAATCTACAAACCCTTTT
EST: gi|78093392|gb|DV521766.1|DV521766
EST:     ACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAG                         GGAATCTACAAACCCTTTTGTGGAGCAGGCCATACAATTCTCGGTAGCAGC
genomic: ACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAGgcaagttgct ... tgcatctcagGGAATCTACAAACCCTTTTGTGGAGCAGGCCATACAATTCTCGGTAGCAGC
EST: gi|101392374|gb|EB818116.1|EB818116
EST:     ACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAG                         GGAATCTACAAACCCTTTTGTGGAGCAGGCCATACAATTCTCGGTAGCAGC
genomic: ACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAGgcaagttgct ... tgcatctcagGGAATCTACAAACCCTTTTGTGGAGCAGGCCATACAATTCTCGGTAGCAGC
EST: gi|76285163|gb|DV024731.1|DV024731
EST:     ACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAG                         GGAATCTACAAACCCTTTTGTGGAGCAGGCCATACAATTCTCGGTAGCAGC
genomic: ACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAGgcaagttgct ... tgcatctcagGGAATCTACAAACCCTTTTGTGGAGCAGGCCATACAATTCTCGGTAGCAGC
EST: gi|211060651|gb|FL185544.1|FL185544
EST:     ACATACAAGCTGTCCCTAACGAAGTCGGCGCTGCAATTGACATCTGCGAG                         GGAATCTACAAACCCTTTTGTGGAGCAGGCCATACAATTCTCGGTAGCAGC
genomic: ACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAGgcaagttgct ... tgcatctcagGGAATCTACAAACCCTTTTGTGGAGCAGGCCATACAATTCTCGGTAGCAGC
EST: gi|211063635|gb|FL185550.1|FL185550
EST:     ACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAG                         GGAATCTACAAACCCTTTTGTGGAGCAGGCCATACAATTCTCGGTAGCAGC
genomic: ACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAGgcaagttgct ... tgcatctcagGGAATCTACAAACCCTTTTGTGGAGCAGGCCATACAATTCTCGGTAGCAGC
EST: gi|211060654|gb|FL185547.1|FL185547
EST:     ACATACAAGCTGTCCCTAACGAAGTCGGCGCTGCAATTGACATCTGCGAG                         GGAATCTACAAACCCTTTTGTGGAGCAGGCCATACAATTCTCGGTAGCAGC
genomic: ACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAGgcaagttgct ... tgcatctcagGGAATCTACAAACCCTTTTGTGGAGCAGGCCATACAATTCTCGGTAGCAGC
EST: gi|74234775|gb|DT642689.1|DT642689
EST:     ACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAG                         GGAATCTACAAACCCTTTTGTGGAGCAGGCCATACAATTCTCGGTAGCAGC
genomic: ACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAGgcaagttgct ... tgcatctcagGGAATCTACAAACCCTTTTGTGGAGCAGGCCATACAATTCTCGGTAGCAGC
EST: gi|211060650|gb|FL185543.1|FL185543
EST:     ACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAG                         GGAATCTACAAACCCTTTTGTGGAGCAGGCCATACAATTCTCGGTA
genomic: ACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAGgcaagttgct ... tgcatctcagGGAATCTACAAACCCTTTTGTGGAGCAGGCCATACAATTCTCGGTA
EST: gi|71447563|gb|DR828613.1|DR828613
EST:     ACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAG                         GGAATCTACAAACCCTTTTGTGGAGCAGGCCATACAATTCTCGGTAGCAGC
genomic: ACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAGgcaagttgct ... tgcatctcagGGAATCTACAAACCCTTTTGTGGAGCAGGCCATACAATTCTCGGTAGCAGC
EST: gi|148978577|gb|EE026218.2|EE026218
EST:     ACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAG                         GGAATCTACAAACCCTTTTGTGGAGCAGGCCATACAATTCTCGGTAGCAGC
genomic: ACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAGgcaagttgct ... tgcatctcagGGAATCTACAAACCCTTTTGTGGAGCAGGCCATACAATTCTCGGTAGCAGC
EST: gi|211060652|gb|FL185545.1|FL185545
EST:     ACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAG                         GGAATCTACAAACCCTTTTGTGGAGCAGGCCATACAATTCTCGGTAGCAGC
genomic: ACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAGgcaagttgct ... tgcatctcagGGAATCTACAAACCCTTTTGTGGAGCAGGCCATACAATTCTCGGTAGCAGC
EST: gi|91867695|gb|EB399758.1|EB399758
EST:     ACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAG                         GGAATCTACAAACCCTTTTGTGGAGCAGGCCATACAATTCTCGGTAGCAGC
genomic: ACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAGgcaagttgct ... tgcatctcagGGAATCTACAAACCCTTTTGTGGAGCAGGCCATACAATTCTCGGTAGCAGC
EST: gi|76017987|gb|DT945157.1|DT945157
EST:     ACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAG                         GGAATCTACAAACCCTTTTGTGGAGCAGGCCATACAATTCTCGGTAGCAGC
genomic: ACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAGgcaagttgct ... tgcatctcagGGAATCTACAAACCCTTTTGTGGAGCAGGCCATACAATTCTCGGTAGCAGC
EST: gi|101390541|gb|EB817205.1|EB817205
EST:     ACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACATCTGCGAG                         GGAATCTACAAACCCTTTTGTGGAGCAGGCCATACAATTCTCGGTAGCAGC
genomic: ACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAGgcaagttgct ... tgcatctcagGGAATCTACAAACCCTTTTGTGGAGCAGGCCATACAATTCTCGGTAGCAGC
EST: gi|71308540|gb|DR790509.1|DR790509
EST:     ACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAG                         GGAATCTACAAACCCTTTTGTGGAGCAGGCCATACAATTCTCGGTAGCAGC
genomic: ACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAGgcaagttgct ... tgcatctcagGGAATCTACAAACCCTTTTGTGGAGCAGGCCATACAATTCTCGGTAGCAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGTGGACGGATGTCAAAGTGACTTCCCCTCAGCTCTCACGGGAGGCCACATACAAGCTGTCCCTAACGAAGTCGACGCTGCAATTGACGTCTGCGAGgcaagttgctcatcgtttttaatggttgcaaatttgcaatctcgtggcggtgaagtgctcttgttttcttatactatctctgaaactcttgagtctggtggtaatgtcactgacagcgttactgttgcatctcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG