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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgcttatttaaggaatatttctacatccagtaaatgtgcatgcgtgtttaatacaactttacttcctaaaaatgtgaatgcttgtttctgtat...

Basic information

species Zea mays
transcript GRMZM2G171745_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G171745_T05 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os07g30840.4 (Oryza sativa), 5'ss of exon 6
GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgcttatttaaggaatatttctacatccagtaaatgtgcatgcgtgtttaatacaactttacttcctaaaaatgtgaatgcttgtttct-gtat----
|||||||||||| ||||||| |||||||||||||||||||| || || |||||||| || || ||||| |||||||||   ||| || ||  ||  |  | |||||  |   | |   |   |||| |    |  |||| |   |  |  | |  ||| || |  ||  |||    
GTACAATTTGCAACTGGAAGGGATCTTACACCTGATCAGCTGAACAATATGATAGATACATTATCTGACTGgtgtgtacctttacttgagtgat--tgttgcatcccatccctattttt---tgttcacagaagttttaatgtttgcatttatatatggttctccctcatatctga
















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|74242378|gb|DT650292.1|DT650292
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
EST: gi|60346665|gb|DN213638.1|DN213638
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
EST: gi|78118434|gb|DV536820.1|DV536820
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
EST: gi|211195518|gb|FL100642.1|FL100642
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGAACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
EST: gi|71427328|gb|DR808378.1|DR808378
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
EST: gi|148943925|gb|EC889005.2|EC889005
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
EST: gi|148972927|gb|EE023942.2|EE023942
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
EST: gi|78112152|gb|DV530548.1|DV530548
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
EST: gi|74242379|gb|DT650293.1|DT650293
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
EST: gi|60340320|gb|DN207293.1|DN207293
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
EST: gi|211178525|gb|FK980683.1|FK980683
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGGACATCAGATAGACTGTTGCATCAAATTCANGAGAAAAATCA-GT
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAA-TCAAGT
EST: gi|76931006|gb|DV172592.1|DV172592
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
EST: gi|211192853|gb|FL432744.1|FL432744
EST:     TGATAGAGACTTTGTCTGATTG                         GTTGGGAACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: TGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
EST: gi|78118433|gb|DV536819.1|DV536819
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
EST: gi|32809485|gb|CD961719.1|CD961719
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGAACCATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGT
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGA-CATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGT
EST: gi|76931005|gb|DV172591.1|DV172591
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
EST: gi|71427327|gb|DR808377.1|DR808377
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
EST: gi|32823261|gb|CD962983.1|CD962983
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGAACCATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGT
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGA-CATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGT
EST: gi|78112153|gb|DV530549.1|DV530549
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GGTTGGGGAAATCAGATAGAATGTTGCATCAAATTCAGGAGAAAATCAAGT
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagG-TTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGT
EST: gi|31352916|gb|CD437273.1|CD437273
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
EST: gi|89251568|gb|DY623354.1|DY623354
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
EST: gi|32823432|gb|CD963154.1|CD963154
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GTTGGGAACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
EST: gi|67021495|gb|CO450244.1|CO450244
EST:     GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTG                         GGTGGG-ACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG
genomic: GATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgc ... cattgctcagGTTGGGGACATCAGATAGACTGTTGCATCAAATTCAGGAGAAAATCAAGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTACAATTTGCAGCTGGAAGAGATCTTACACCTGATCAGCTAAAGAACATGATAGAGACTTTGTCTGATTGgtgtgtatgcttatttaaggaatatttctacatccagtaaatgtgcatgcgtgtttaatacaactttacttcctaaaaatgtgaatgcttgtttctgtat

- - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - AAGAAC