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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaggatatagtttgagaagtttcctggccaattcagtgtcgtagtgttttttatttgacatctgtgtacctaaatcttacaccatttctcaaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT

Basic information

species Zea mays
transcript GRMZM2G068586_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068586_T04 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g48370.1 (Oryza sativa), 3'ss of exon 1
-ttaggatatagtttgagaagtttcctggccaattcagtgtcgtagtgttttttatttg-acatctgtgtacctaaat-cttacaccatttctcaaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT
  |||||| |   |||     || |   |     ||   ||  |  |      |||||| |      |  | |  | | |||||||| ||| ||||    ||||||||||||||||||   |||||||| || || || ||| |||||||||| |||||||| ||||||||||||||||| || |||| | 
cgtaggattttagttgcagtcttgcagaggagtgtcgtagttttgatacacagtatttgtatgcaaattaatcggagttcttacaccttttgtcaag---cagCCAGGGCCAAGGGAGTTCCCAATGCAATGTTTCATTAAGCGGAATAAGAAGAACTCTACGTTCTACCTCTACCTTGGTTTGACAAATG
















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|26456630|gb|CA828213.1|CA828213
EST:     GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
EST: gi|211227913|gb|FL059245.1|FL059245
EST:     GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
EST: gi|211227917|gb|FL059249.1|FL059249
EST:     TCCGCCGGCGGAGTCC-GCAAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
genomic: TCCGCCGGCGGAGTCCGGC-AAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
EST: gi|211227907|gb|FL059239.1|FL059239
EST:     GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAA
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGA-GAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAA
EST: gi|71772807|gb|DR970732.1|DR970732
EST:     GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
EST: gi|211227904|gb|FL059236.1|FL059236
EST:     GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
EST: gi|211227909|gb|FL059241.1|FL059241
EST:     GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAA
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGG-AGAGACCAATGCAGTGCTTTATCAAGAGGAA
EST: gi|148950368|gb|EC895931.2|EC895931
EST:     GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
EST: gi|211225858|gb|FL059235.1|FL059235
EST:     GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
EST: gi|211227911|gb|FL059243.1|FL059243
EST:     GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
EST: gi|211227905|gb|FL059237.1|FL059237
EST:     GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
EST: gi|78078970|gb|DV507382.1|DV507382
EST:     GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
EST: gi|149111829|gb|EE190984.2|EE190984
EST:     GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
EST: gi|71310923|gb|DR791764.1|DR791764
EST:     GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
EST: gi|76914172|gb|DV165433.1|DV165433
EST:     GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
EST: gi|211227916|gb|FL059248.1|FL059248
EST:     GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
EST: gi|20803223|gb|BQ294273.1|BQ294273
EST:     TCCGCCGGCTGATGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGTAATAAGAA
genomic: TCCGCCGGCGGA-GTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGG-AATAAGAA
EST: gi|211227912|gb|FL059244.1|FL059244
EST:     GTCCGCCGGCGGAKTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
EST: gi|211227908|gb|FL059240.1|FL059240
EST:     GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
EST: gi|211227918|gb|FL059250.1|FL059250
EST:     GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
EST: gi|211229972|gb|FL059251.1|FL059251
EST:     GCCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
EST: gi|78109424|gb|DV527840.1|DV527840
EST:     GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTT
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTT
EST: gi|211225857|gb|FL059234.1|FL059234
EST:     GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAG                         CCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC
genomic: GTCCGCCGGCGGAGTCCGGCAAGATCACCTTCCCCTCCTCGCTCAAGCAGgtgaggacgg ... caaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttttatttgacatctgtgtacctaaatcttacaccatttctcaaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT
                             atcttac  putative branch site (score: 3)
                                     ccatttctc  CT-rich tract
     tttatttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaggatatagtttgagaagtttcctggccaattcagtgtcgtagtgttttttatttgacatctgtgtacctaaatcttacaccatttctcaaaacacagCCAGGGCCAAGGGAGAGACCAATGCAGTGCTTTATCAAGAGGAATAAGAACAACTCTACATTCTACCTCTACCTTGGCTTCACAAGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - tcctggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tacacca