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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATGGGAAATGGTGGACCTGCCCCTGAATCCGTTACCGACAAGATTTTCTCTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGATgtatgattcagtgccaacctgccaagtattttctctgtttctttgacaggttagtggaatattcattttctctcactttactactgcag

Basic information

species Zea mays
transcript GRMZM2G023289_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G023289_T03 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g50480.1 (Oryza sativa), 5'ss of exon 6
TATGGGAAATGGTGGACCTGCCCCTGAATCCGTTACCGACAAGATTTTCTCTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGATgtatgattcagtgccaacctgccaagtatt-ttctctgtttctttgacaggttagtggaatattcattttctctcactttactactgcag---------
 |||| |||||||||||||||||||||||| ||||| || ||||| ||||||||||||||||||||  ||||||| |||||| | |||||||||||||||||| || |    ||  || ||  |  | || || | |||||   |  |||| || || |||||   ||| | ||| ||||| |  |||           
CATGGAAAATGGTGGACCTGCCCCTGAATCGGTTACTGATAAGATCTTCTCTAATACAACGACAATTACTGAATATCTCATCGCGGAAGACCTTCCAGATgtaagagttgacgctgacttgttagtttttgttgtttgttttgctcccagggtattgaaatatatgttt-cactc-ctttattcttgcccacatcgcag
















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|31353596|gb|CD437953.1|CD437953
EST:     CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGAT                         GTTGATATTTCTGTTGTCGGTGTCACCAGCTTCAGTGGACCCGAAGGCCCC
genomic: CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGATgtatgattca ... actactgcagGTTGATATTTCTGTTGTCGGTGTCACCAGCTTCAGTGGACCCGAAGGCCCC
EST: gi|211538908|gb|FL379332.1|FL379332
EST:     TAATACAACGAGCAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGAT                         GTTGATATTTCTGTTGTCGGTGTCACCAGCTTCAGTGGACCCGAAGGCCCT
genomic: TAATACAACGA-CAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGATgtatgattca ... actactgcagGTTGATATTTCTGTTGTCGGTGTCACCAGCTTCAGTGGACCCGAAGGCCCC
EST: gi|211092187|gb|FL375383.1|FL375383
EST:     CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCT-CCAGAT                         GTTGATANTTCTGTTGTCGGTGTCACCAGCTTCAGTGGACCCCGA-GGCCC
genomic: CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGATgtatgattca ... actactgcagGTTGATATTTCTGTTGTCGGTGTCACCAGCTTCAGTGGACCC-GAAGGCCC
EST: gi|149106401|gb|EE292127.2|EE292127
EST:     CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGAT                         GTTGATATTTCTGTTGTCGGTGTCACCAGCTTCAGTGGACCCGAAGGCCCC
genomic: CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGATgtatgattca ... actactgcagGTTGATATTTCTGTTGTCGGTGTCACCAGCTTCAGTGGACCCGAAGGCCCC
EST: gi|211445897|gb|FL403744.1|FL403744
EST:     CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGAT                         GTTGATATTTCTGGGTGTCGGTGTCACCAGCTTCAGTGGACCCCGAAG-CC
genomic: CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGATgtatgattca ... actactgcagGTTGATATTTCTGT-TGTCGGTGTCACCAGCTTCAGTGGACCC-GAAGGCC
EST: gi|211217606|gb|FL408377.1|FL408377
EST:     CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGAT                         GTTGATATTTNCTGTTGTCGGTGTCACCAGCTTCAGTGGACCCGAAAGGCC
genomic: CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGATgtatgattca ... actactgcagGTTGATATTT-CTGTTGTCGGTGTCACCAGCTTCAGTGGACCCGAA-GGCC
EST: gi|211012104|gb|FL418130.1|FL418130
EST:     CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGAA                         GTTGAATATTTCTGGTTGTCGG
genomic: CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGATgtatgattca ... actactgcagGTTGA-TATTTCTG-TTGTCGG
EST: gi|211079915|gb|FL412204.1|FL412204
EST:     CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTC-AGAT                         N
genomic: CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGATgtatgattca ... actactgcag-
EST: gi|211079915|gb|FL412204.1|FL412204
EST:     CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTC-AGAT                         N
genomic: CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGATgtatgattca ... actactgcag-
EST: gi|67021929|gb|CO450678.1|CO450678
EST:     CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGAT                         GTTGATATTTCTGTTGTCGGTGTCACCAGCTTCAGTGGACCCGAAGGCCCC
genomic: CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGATgtatgattca ... actactgcagGTTGATATTTCTGTTGTCGGTGTCACCAGCTTCAGTGGACCCGAAGGCCCC
EST: gi|211111130|gb|FL394545.1|FL394545
EST:     CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGAT                         GTTGATATTTCTGTTGTCGGTGTCACCAGCTTCAGTGGACCCGAAAGCCCC
genomic: CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGATgtatgattca ... actactgcagGTTGATATTTCTGTTGTCGGTGTCACCAGCTTCAGTGGACCCGAAGGCCCC
EST: gi|211503690|gb|FL022245.1|FL022245
EST:     CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGAT                         GTTGATATTTCTGTTGTCGGNGTCACCAGCTTCAGTGGACCCGAAGGCCCC
genomic: CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGATgtatgattca ... actactgcagGTTGATATTTCTGTTGTCGGTGTCACCAGCTTCAGTGGACCCGAAGGCCCC
EST: gi|211394811|gb|FL369335.1|FL369335
EST:     CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGAT                         GTTGATATTTCTGTTGTCGGTGTCACCAGCTTCAGTGGACCCGAAG-CCCC
genomic: CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGATgtatgattca ... actactgcagGTTGATATTTCTGTTGTCGGTGTCACCAGCTTCAGTGGACCCGAAGGCCCC
EST: gi|31356531|gb|CD440888.1|CD440888
EST:     CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGAT                         GTTGATATTTCTGTTGTCGGTGTCACCAGCTTCAGTGGACCCGAAGGCTCC
genomic: CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGATgtatgattca ... actactgcagGTTGATATTTCTGTTGTCGGTGTCACCAGCTTCAGTGGACCCGAAGGCCCC
EST: gi|211099119|gb|FL353128.1|FL353128
EST:     CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGAT                         GTTGATATTTCTGTTGTCGGTGTCACCAGCTTCAG
genomic: CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGATgtatgattca ... actactgcagGTTGATATTTCTGTTGTCGGTGTCACCAGCTTCAG
EST: gi|31354050|gb|CD438407.1|CD438407
EST:     CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGAT                         GTTGATATTTCTGTTGTCGGTGTCACCAGCTTCAGTGGACCCGAAGGCCCC
genomic: CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGATgtatgattca ... actactgcagGTTGATATTTCTGTTGTCGGTGTCACCAGCTTCAGTGGACCCGAAGGCCCC
EST: gi|211445226|gb|FL373040.1|FL373040
EST:     CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGAT                         GTTGATATTTCTGTTGTCGGTGTCACCAGCTTCAGTGGACCCGAAGGCCCC
genomic: CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGATgtatgattca ... actactgcagGTTGATATTTCTGTTGTCGGTGTCACCAGCTTCAGTGGACCCGAAGGCCCC
EST: gi|31351485|gb|CD435842.1|CD435842
EST:     CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGAT                         GTTGATATTTCTGTTGTCGGTGTCACCAGCTTCAGTGGACCCGAAGGCCCC
genomic: CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGATgtatgattca ... actactgcagGTTGATATTTCTGTTGTCGGTGTCACCAGCTTCAGTGGACCCGAAGGCCCC
EST: gi|149060809|gb|EE157261.2|EE157261
EST:     CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGAT                         GTTGATATTTCTGTTGTCGGTGTCACCAGCTTCAGTGGACCCGAAGGCCCC
genomic: CTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGATgtatgattca ... actactgcagGTTGATATTTCTGTTGTCGGTGTCACCAGCTTCAGTGGACCCGAAGGCCCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATGGGAAATGGTGGACCTGCCCCTGAATCCGTTACCGACAAGATTTTCTCTAATACAACGACAATCTCTGAATACCTCATCTCTGAAGACCTTCCAGATgtatgattcagtgccaacctgccaagtattttctctgtttctttgacaggttagtggaatattcattttctctcactttactactgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA