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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcccagcgctcccagattggcactttgccctcccattttcaagtattgcgtgggatttattcgtgctattttggaggctgggactgatggattagggtttgtcgattgtttgggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCGGCTGGGTCCGTACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCA

Basic information

species Zea mays
transcript GRMZM2G064695_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G064695_T03 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g40830.1 (Oryza sativa), 3'ss of exon 1
--------gtgcccagcgctcccagattg-gcactttgccctcccat-----tttcaagtattgcgtgggatttattcgtgctat---tttggaggctgggactgatggattagggtttgtcgattgtttgggtct-gcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCGGCTGGGTCCGTACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCA
        |   ||  | |  ||||||   |||  || ||   ||||      ||| | | ||||| |   ||| || | |   |   ||| | |||  || || | |   ||||||| || ||| || ||||| | ||||||||||||| ||||||| || |||||||||||||||||||||||||||||||| || || ||  | ||||||||  || ||||||||||| | ||||| |
gtgctcttgcaaccccctccaccagatcccgcagattcccgcaccatattccgttcgatttttgcgggtttttttttggagtcttcgatttaggggcctgggctaacgcgctagggttcgtggat-gtgtgggtatcgcagGGCGCGGAGCTGATGGGGAAGTACGGGATCAACGTGCCCAGGGGCGCGGCGGCGGGATCGGTGGAGGAGGTCAAAAACACCTTGAAGAACGTCTTCCCTA
















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|211374289|gb|FL290759.1|FL290759
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
EST: gi|71760334|gb|DR958271.1|DR958271
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
EST: gi|149076126|gb|EE164711.2|EE164711
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
EST: gi|211376944|gb|FL290772.1|FL290772
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
EST: gi|149094704|gb|EE180255.2|EE180255
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
EST: gi|211374290|gb|FL290760.1|FL290760
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
EST: gi|211374286|gb|FL290756.1|FL290756
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
EST: gi|211003343|gb|FL290782.1|FL290782
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
EST: gi|211376939|gb|FL290767.1|FL290767
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
EST: gi|211374284|gb|FL290754.1|FL290754
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
EST: gi|148935326|gb|EC879367.2|EC879367
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
EST: gi|211376941|gb|FL290769.1|FL290769
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
EST: gi|211376947|gb|FL290775.1|FL290775
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTWCCAG                         GGCGCGGWGTTGATGGGTTAATACGGGATCAACGTGCCCAGGGGCGCGGCG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
EST: gi|211003342|gb|FL290781.1|FL290781
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGARTTGATGGGTAAATACGGGATCAACGTGCC-AGGGGCGCGGCG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
EST: gi|67017499|gb|CO446248.1|CO446248
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
EST: gi|91872808|gb|EB402765.1|EB402765
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
EST: gi|211374293|gb|FL290763.1|FL290763
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
EST: gi|211374280|gb|FL290750.1|FL290750
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGGC
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGG-C
EST: gi|211376938|gb|FL290766.1|FL290766
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTT
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTT
EST: gi|211374285|gb|FL290755.1|FL290755
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
EST: gi|211374291|gb|FL290761.1|FL290761
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
EST: gi|211374288|gb|FL290758.1|FL290758
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCKCGGCG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
EST: gi|211376945|gb|FL290773.1|FL290773
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
EST: gi|211374292|gb|FL290762.1|FL290762
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
EST: gi|211376937|gb|FL290765.1|FL290765
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
EST: gi|211374287|gb|FL290757.1|FL290757
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
EST: gi|211376951|gb|FL290779.1|FL290779
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
EST: gi|148951069|gb|EC896728.2|EC896728
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
EST: gi|211376949|gb|FL290777.1|FL290777
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCTAGGGGCGCGGCG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
EST: gi|149017003|gb|EE154318.2|EE154318
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
EST: gi|211376948|gb|FL290776.1|FL290776
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
EST: gi|76282776|gb|DV022344.1|DV022344
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
EST: gi|211374282|gb|FL290752.1|FL290752
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGG
EST: gi|88754000|gb|DY538141.1|DY538141
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
EST: gi|211374283|gb|FL290753.1|FL290753
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
EST: gi|211376940|gb|FL290768.1|FL290768
EST:     GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAG                         GGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG
genomic: GGAGATGGCAGCACCAGCAGCTCCGCCGCCTCAACATCCACGAGTACCAGgtgcccagcg ... gggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttggaggctgggactgatggattagggtttgtcgattgtttgggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCGGCTGGGTCCGTACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCA
               gactgat  putative branch site (score: 3)
                                      attgttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcccagcgctcccagattggcactttgccctcccattttcaagtattgcgtgggatttattcgtgctattttggaggctgggactgatggattagggtttgtcgattgtttgggtctgcagGGCGCGGAGTTGATGGGTAAATACGGGATCAACGTGCCCAGGGGCGCGGCGGCTGGGTCCGTACACGAGGTCAAGGACGCCTTGAAGAACATGTTCCCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC