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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCGAGCCCGAGAAGGTCACGCCGCACTGCCTCTTCCTCAGCTACCAGCCGGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCGgtacgccattgccccctttgccacgtacctgctcagattctcgtcttgcagcagaactactaagattcaattgcccgattcgctcgtttggttctgcgcatccag

Basic information

species Zea mays
transcript GRMZM2G025977_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G025977_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os07g06080.1 (Oryza sativa), 5'ss of exon 1
CGCGAGCCCGAGAAGGTCACGCCGCACTGCCTCTTCCTCAGCTACCAGCCGGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCGgtacgccattgccccctttg--ccacgtacctg--ctcagattctcgtcttgcagcagaactactaagattcaattgcccgattcgctcgtttggttctgcgcatccag
|| |||||||| ||  |||||||||||  ||| ||||||||||||||||| |||||||||||||||||||||||||| ||||| |||||||||||||||||| |||||||||| ||       || | | ||   | || |||| |   ||||| |    ||| | |    | ||||   | ||   | |    |              
CGTGAGCCCGAAAACATCACGCCGCACGCCCTGTTCCTCAGCTACCAGCCAGAGCCCGGCGCCAAGATGCTCGACCCGGAGGTCTACCCGCGGCCCACCGgtgcgccattgccgccgcccactcaagcaactaaccccaaattcccaa-ttgcatcttgcctatttacccaccattgat-gtttgtgttgcacag--------------
















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|71419916|gb|DR804939.1|DR804939
EST:     GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCG                         GGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
genomic: GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCGgtacgccatt ... gcgcatccagGGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
EST: gi|149107340|gb|EE189220.2|EE189220
EST:     GGAGCCGGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCG                         GGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
genomic: GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCGgtacgccatt ... gcgcatccagGGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
EST: gi|71299092|gb|DR785541.1|DR785541
EST:     GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCCCCG                         GGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
genomic: GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCGgtacgccatt ... gcgcatccagGGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
EST: gi|71326389|gb|DR799878.1|DR799878
EST:     GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCG                         GGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
genomic: GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCGgtacgccatt ... gcgcatccagGGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
EST: gi|71756532|gb|DR954469.1|DR954469
EST:     GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCG                         GGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
genomic: GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCGgtacgccatt ... gcgcatccagGGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
EST: gi|76914008|gb|DV165370.1|DV165370
EST:     GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGGGTACCCGCGGCCCACCG                         GGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
genomic: GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCGgtacgccatt ... gcgcatccagGGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
EST: gi|6021435|gb|AW066363.1|AW066363
EST:     GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCG                         GGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
genomic: GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCGgtacgccatt ... gcgcatccagGGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
EST: gi|78075379|gb|DV503813.1|DV503813
EST:     GGCGCCAAGATGCTTGACCCCGAGGTGTACCCGCGGCCCACCG                         GGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
genomic: GGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCGgtacgccatt ... gcgcatccagGGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
EST: gi|149061110|gb|EE157371.2|EE157371
EST:     GAGCCCGGGCGCCAAGATGCTGGACCCCGAGGTGTACCCGCGGCCCACCG                         GGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
genomic: GAGCCC-GGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCGgtacgccatt ... gcgcatccagGGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
EST: gi|76916475|gb|DV166404.1|DV166404
EST:     GGAGCCGGGCGCCAAGATGCTCGACCCCGAGGGGTCCCCGCGGCCCACCG                         GGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
genomic: GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCGgtacgccatt ... gcgcatccagGGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
EST: gi|71760476|gb|DR958413.1|DR958413
EST:     GAGCCCGGCGCCAAGATGCTCGTCCCCGAGGTGTACCCGCGGCCCACCG                         GGGAGGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGAC
genomic: GAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCGgtacgccatt ... gcgcatccagGGGA-GGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGAC
EST: gi|149107341|gb|EE189221.2|EE189221
EST:     GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCG                         GGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
genomic: GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCGgtacgccatt ... gcgcatccagGGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
EST: gi|71445147|gb|DR826197.1|DR826197
EST:     GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCG                         GGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
genomic: GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCGgtacgccatt ... gcgcatccagGGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
EST: gi|149105156|gb|EE290639.2|EE290639
EST:     CCGCGGCCCCCCG                         GGGAGGTGTACATTATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGAC
genomic: CCGCGGCCCACCGgtacgccatt ... gcgcatccagGGGAGGTGTACA-TATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGAC
EST: gi|149096139|gb|EE181829.2|EE181829
EST:     CCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGNNNNNNNG                         GGGAGGTGTACATATGTGGGATGAGCAAGGGACGAGAACCCGCCAGATGA
genomic: CCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGG-CCCACCGgtacgccatt ... gcgcatccagGGGAGGTGTACATATGTGGGATGAGCAA-GGACGAGAACCCGCCAGATGA
EST: gi|76018402|gb|DT945572.1|DT945572
EST:     GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCG                         GGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
genomic: GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCGgtacgccatt ... gcgcatccagGGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
EST: gi|71445641|gb|DR826691.1|DR826691
EST:     GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCG                         GGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
genomic: GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCGgtacgccatt ... gcgcatccagGGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
EST: gi|71428314|gb|DR809364.1|DR809364
EST:     GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCG                         GGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
genomic: GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCGgtacgccatt ... gcgcatccagGGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
EST: gi|71416522|gb|DR803736.1|DR803736
EST:     GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCG                         GGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
genomic: GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCGgtacgccatt ... gcgcatccagGGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
EST: gi|93281616|gb|EB673880.1|EB673880
EST:     GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCG                         GGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
genomic: GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCGgtacgccatt ... gcgcatccagGGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
EST: gi|78109403|gb|DV527819.1|DV527819
EST:     GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCG                         GGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
genomic: GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCGgtacgccatt ... gcgcatccagGGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
EST: gi|13150101|gb|BG320423.1|BG320423
EST:     GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCG                         GGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
genomic: GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCGgtacgccatt ... gcgcatccagGGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
EST: gi|88752615|gb|DY536756.1|DY536756
EST:     GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCCCCG                         GGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
genomic: GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCGgtacgccatt ... gcgcatccagGGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
EST: gi|71757958|gb|DR955895.1|DR955895
EST:     GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCCCCG                         GGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
genomic: GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCGgtacgccatt ... gcgcatccagGGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
EST: gi|94476402|gb|EB705360.1|EB705360
EST:     GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCG                         GGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
genomic: GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCGgtacgccatt ... gcgcatccagGGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
EST: gi|76013723|gb|DT940893.1|DT940893
EST:     GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCG                         GGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
genomic: GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCGgtacgccatt ... gcgcatccagGGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
EST: gi|78079918|gb|DV508330.1|DV508330
EST:     GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCG                         GGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
genomic: GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCGgtacgccatt ... gcgcatccagGGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
EST: gi|76914004|gb|DV165368.1|DV165368
EST:     GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCG                         GGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
genomic: GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCGgtacgccatt ... gcgcatccagGGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
EST: gi|91053995|gb|EB164413.1|EB164413
EST:     GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCG                         GGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
genomic: GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCGgtacgccatt ... gcgcatccagGGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
EST: gi|78084221|gb|DV512614.1|DV512614
EST:     GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCG                         GGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC
genomic: GGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCGgtacgccatt ... gcgcatccagGGGAGGTGTACATATGTGGGATGAGCAAGGACGAGAACCCGCCAGATGACC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCGAGCCCGAGAAGGTCACGCCGCACTGCCTCTTCCTCAGCTACCAGCCGGAGCCCGGCGCCAAGATGCTCGACCCCGAGGTGTACCCGCGGCCCACCGgtacgccattgccccctttgccacgtacctgctcagattctcgtcttgcagcagaactactaagattcaattgcccgattcgctcgtttggttctgcgcatccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG