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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCCTGAAGGTTCAGAAGAATGGTACGGGCGAGCATCTGCCCCCACCCAGGCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATGgtttgtattattcaagtacctagctatttgggactttttttttctagtttacgagtgatgactagacctatttagctcctgcag

Basic information

species Zea mays
transcript GRMZM2G057408_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057408_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os06g45840.2 (Oryza sativa), 5'ss of exon 3
TTCCTGAAGGTTCAGAAGAATGGTACGGGCGAGCATCTGCCCCCACCCAGGCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATGgtttgtattattcaagtacct-agctatttgggacttttt----------ttttctagtttacgagtgatgactagacctatttagctcctgcag
||  ||||||||||||| |||||||| || || |||||||| |||||||||||||| || ||||||||||||||||||||||||||||| ||||||||||||||||| |  |||    ||| ||   | |   | |||||           |||||||||    |||  | |   ||  |||||||         
TTTTTGAAGGTTCAGAAAAATGGTACAGGTGAACATCTGCCTCCACCCAGGCCAAAGCGGAAGGCAGCTCATCCATATCCACAGAAGGCCTCTAAAAATGgtttgtactgctcagcagcctcagtcttgtaatattttttgccatcaactatttctagttgggaagtagtaatcggaattatttag---------

upper sequence: GRMZM2G057408_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA10G37520.1 (Glycine max), 5'ss of exon 3
TTCCTGAAGGTTCAGAAGAATGGTACGGGCGAGCATCTGCCCCCACCCAGGCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATGgtttgtattattcaagtacctagctatttgggactttttttttctagtttacgagtgatgactagacctatttagctcctgcag
|| || || |||||||||| ||| ||  | || ||||| || |||||||| |||||| |||| || | |||||||||||| ||||| || || |||||||||| | ||  |     ||  |   |  |    | |||  |    | || | | | | ||   |||   ||||| ||        
TTTCTAAAAGTTCAGAAGAGTGGGACAAGTGAACATCTTCCTCCACCCAGACCAAAAAGAAAAGCTGTTCATCCATATCCTCAGAAAGCTTCAAAAAATGgttagaatcttcactatatttt-ttgctacacaatttagtgcatttgtat-ctaataattgttagtgatatttggcag------

upper sequence: GRMZM2G057408_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA20G30250.1 (Glycine max), 5'ss of exon 3
TTCCTGAAGGTTCAGAAGAATGGTACGGGCGAGCATCTGCCCCCACCCAGGCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATGgtttgtattattca--agtacctagctatttgggactttttttttctagtttacgagtgatgactagacctatttagctcctgcag
|| || || |||||||||| ||| ||    || ||||| || |||||||| |||||| |||| || |||||||||||||| ||||| || || |||| |||||  || | ||||  |     |   | ||||  ||    |||      |||     | || | |     |  | || |   ||||
TTTCTAAAAGTTCAGAAGAGTGGGACAAATGAACATCTTCCTCCACCCAGACCAAAAAGAAAAGCTGCTCATCCATATCCTCAGAAAGCTTCAAAAACTGgtt-atagtcttcactatattttttttttttgctacacaatttagtgcatttgtctctaataattg---ttggtgagatttggcag

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|78076508|gb|DV504942.1|DV504942
EST:     GCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATG                         TTTCTCAAGCTATTTTATCACAAGAACAACCTACCCAGAGGGAGCAAGGTT
genomic: GCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATGgtttgtatta ... gctcctgcagTTTCTCAAGCTATTTTATCACAAGAACAACCTACCCAGAGGGAGCAAGGTT
EST: gi|211503280|gb|FL119721.1|FL119721
EST:     GCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATG                         TTTCTCAAGCTATTT
genomic: GCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATGgtttgtatta ... gctcctgcagTTTCTCAAGCTATTT
EST: gi|148956892|gb|EC902815.2|EC902815
EST:     GCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATG                         TTTCTCAAGCTATTTTATCACAAGAACAACCTACCCAGAGGGAGCAAGGTT
genomic: GCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATGgtttgtatta ... gctcctgcagTTTCTCAAGCTATTTTATCACAAGAACAACCTACCCAGAGGGAGCAAGGTT
EST: gi|89755460|gb|DY685870.1|DY685870
EST:     GCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATG                         TTTCTCAAGCTATTTTATCACAAGAACAACCTACCCAGAGGGAGCAAGGTT
genomic: GCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATGgtttgtatta ... gctcctgcagTTTCTCAAGCTATTTTATCACAAGAACAACCTACCCAGAGGGAGCAAGGTT
EST: gi|71428977|gb|DR810027.1|DR810027
EST:     GCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATG                         TTTCTCAAGCTATTTTATCACAAGAACAACCTACCCAGAGGGAGCAAGGTT
genomic: GCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATGgtttgtatta ... gctcctgcagTTTCTCAAGCTATTTTATCACAAGAACAACCTACCCAGAGGGAGCAAGGTT
EST: gi|89757689|gb|DY687184.1|DY687184
EST:     GCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATG                         TTTCTCAAGCTATTTTATCACAAGAACAACCTACCCAGAGGGAGCAAGGTT
genomic: GCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATGgtttgtatta ... gctcctgcagTTTCTCAAGCTATTTTATCACAAGAACAACCTACCCAGAGGGAGCAAGGTT
EST: gi|50336085|gb|CO531211.1|CO531211
EST:     GCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATG                         TTTCTCAAGCTATTTTATCACAAGAACAACCTACCCAGAGGGAGCAAGGTT
genomic: GCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATGgtttgtatta ... gctcctgcagTTTCTCAAGCTATTTTATCACAAGAACAACCTACCCAGAGGGAGCAAGGTT
EST: gi|211503279|gb|FL119720.1|FL119720
EST:     CCAAAACGAAAGGCAGCTCATCCATATCCACAGAAAGGCATCTAAAAATG                         TTTCTCAAGCTATTTTATCACAAG
genomic: CCAAAACGAAAGGCAGCTCATCCATATCCACAGAA-GGCATCTAAAAATGgtttgtatta ... gctcctgcagTTTCTCAAGCTATTTTATCACAAG
EST: gi|211503272|gb|FL119713.1|FL119713
EST:     GCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCCAAAAATG                         TTTCTCAAGCTATTTTATCACAAGAACAACCTACCCAGAAGGGA-CAAGGT
genomic: GCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATGgtttgtatta ... gctcctgcagTTTCTCAAGCTATTTTATCACAAGAACAACCTACCCAGA-GGGAGCAAGGT
EST: gi|71441161|gb|DR822211.1|DR822211
EST:     GCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATG                         TTTCTCAAGCTATTTTATCACAAGAACAACCTACCCAGAGGGAGCAAGGTT
genomic: GCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATGgtttgtatta ... gctcctgcagTTTCTCAAGCTATTTTATCACAAGAACAACCTACCCAGAGGGAGCAAGGTT
EST: gi|91876492|gb|EB406449.1|EB406449
EST:     GCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATG                         TTTCTCAAGCTATTTTATCACAAGAACAACCTACCCAGAGGGAGCAAGGTT
genomic: GCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATGgtttgtatta ... gctcctgcagTTTCTCAAGCTATTTTATCACAAGAACAACCTACCCAGAGGGAGCAAGGTT
EST: gi|211500935|gb|FL119704.1|FL119704
EST:     GC-AAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATG                         TTTCTCAAGCTATTTTATCACAAGAACAACCTACC
genomic: GCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATGgtttgtatta ... gctcctgcagTTTCTCAAGCTATTTTATCACAAGAACAACCTACC
EST: gi|211503276|gb|FL119717.1|FL119717
EST:     -CCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATG                         TTTCTCAAGCTATTTTATCACAAGAACAACCTACCCAGAG
genomic: GCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATGgtttgtatta ... gctcctgcagTTTCTCAAGCTATTTTATCACAAGAACAACCTACCCAGAG
EST: gi|78118283|gb|DV536669.1|DV536669
EST:     GCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATG                         C
genomic: GCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATGgtttgtatta ... gctcctgcag-
EST: gi|78118283|gb|DV536669.1|DV536669
EST:     GCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATG                         C
genomic: GCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATGgtttgtatta ... gctcctgcag-
EST: gi|101392321|gb|EB818090.1|EB818090
EST:     GCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATG                         TTTCTCAAGCTATCTTATCACAAGAACAACCTACCCAGAGGGAGCAAGGTT
genomic: GCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATGgtttgtatta ... gctcctgcagTTTCTCAAGCTATTTTATCACAAGAACAACCTACCCAGAGGGAGCAAGGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCCTGAAGGTTCAGAAGAATGGTACGGGCGAGCATCTGCCCCCACCCAGGCCAAAACGAAAGGCAGCTCATCCATATCCACAGAAGGCATCTAAAAATGgtttgtattattcaagtacctagctatttgggactttttttttctagtttacgagtgatgactagacctatttagctcctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA