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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgttgcataattgtgtgcttaaattcttcctttccccatgaattcattttctcttttacgtttataaacctgccgatatag

Basic information

species Zea mays
transcript GRMZM2G070422_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G070422_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os08g23810.2 (Oryza sativa), 5'ss of exon 10
GTATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgttgcataat-tgtgtgc----ttaaattcttcctttcccc----atgaattca-ttttctcttttacgtt-----tataaacctgccgatatag---------------------------------------------------------------
 ||||||||||| |||||||| ||||||||||||||||||||||| |||   ||||||| ||  | ||| | | ||     || ||  || |||    ||    || | | ||    |||  || |  ||     || ||  ||||   |||                                                                 
ATATGGTGGTGGCATGAGTTCAGCTAAAGCAGCTCTTGAGAGTGACACAAAAgtatggtcttctagaatatatatgttattttcaacactccctccatcccaaaataagtgcaaccctctagttcaaatttgaactacaaggctgcacttattttgggacggagggagtatgtaccatgaatgtacttttttaatctttttctgcaaatctttgtag

upper sequence: GRMZM2G070422_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA12G03060.1 (Glycine max), 5'ss of exon 11
GTATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgttgca--taattgtgtgcttaaattcttcctttccccatga---attcattttctctt-ttacgtttataaacctgccgatatag----------------------------
 ||||||||||| ||||||||||| ||||| || || |||||||||||||| ||| | |    |   ||           |||      ||  ||  || |   | | | ||   | |  | | ||| ||   ||  |  | |                              
ATATGGTGGTGGTATGAGTTCTGCAAAAGCTGCACTGGAGAGTGATACACGAgtaagcttcaactcctacccacaccaccaaaaaaaaactcaccagattacatactgacttagacgtgcttcatttttacttctctctcttttaaattacatcatatgtcatgccttttcag

upper sequence: GRMZM2G070422_T01 (Zea mays), 5'ss of exon 10
lower sequence: GLYMA11G10770.1 (Glycine max), 5'ss of exon 10
GTATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtg----ttgcataattgtgtgcttaaattcttcc-tttccccatgaattcattttctctt---ttacgtttataaacctgccgatatag
 ||||||||||| ||||||||||| ||||| || || |||||||||||||| ||| | |     |  |          ||| | ||   |   ||||    | | |||  | ||| ||   |||| |       | |||   |  ||
ATATGGTGGTGGTATGAGTTCTGCCAAAGCTGCACTGGAGAGTGATACACGAgtaagcttcaactcccccccccccccgctgacatagatgtgtttcatttttacttctctctcttttaaattacatcatatttcatgctatttcag

upper sequence: GRMZM2G070422_T01 (Zea mays), 5'ss of exon 10
lower sequence: AT2G05990.2 (Arabidopsis thaliana), 5'ss of exon 9
GTATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgttgcataattgtgtgct-taaattcttcctttccccatgaattcattttctcttttacgtttataaacctgccgatatag
||||||||| || ||||||||||| ||||| || || |||||||| ||||||||  | |     | |||| |||    |||| ||     |    |    |    | |  |  |  |   |        |  | | ||||
GTATGGTGGAGGTATGAGTTCTGCCAAAGCTGCACTAGAGAGTGACACACGGgtgagtt----tacaattctgtttcgtaaactcaaagatgtatcggttagaagtctcttagtccaaact----gtgttttcaacatag

upper sequence: GRMZM2G070422_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S99_59V6.3 (Physcomitrella patens), 5'ss of exon 9
GTATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgtt-----gcataattgtgtgcttaaat--tcttcctttccccatgaattcattttct--cttttacgtttataaacctgccgatatag-----
 |||||||| |||||||| ||||| ||||| || ||||||||||| ||||| ||| | |  |     || |||   | |  |  | |  || || ||| |  || ||  ||| |      | || ||  ||      |      |        
ATATGGTGGAGGGATGAGCTCTGCCAAAGCTGCACTTGAGAGTGACACACGTgtaagttccttatctgcgtaagaatctcttgtagtaatcgtcatttgcgaat-aacccatctctaggttattccgactacttgattagtagcaagtttggt

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|67015153|gb|CO443902.1|CO443902
EST:     ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGG                         GTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
genomic: ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgtt ... gccgatatagGTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
EST: gi|211267881|gb|FL003946.1|FL003946
EST:     ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGG                         GTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
genomic: ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgtt ... gccgatatagGTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
EST: gi|31364152|gb|CD448507.1|CD448507
EST:     ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGG                         GTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
genomic: ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgtt ... gccgatatagGTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
EST: gi|67015181|gb|CO443930.1|CO443930
EST:     ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGG                         GTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
genomic: ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgtt ... gccgatatagGTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
EST: gi|31357208|gb|CD441565.1|CD441565
EST:     ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGG                         GTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
genomic: ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgtt ... gccgatatagGTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
EST: gi|24768563|gb|CA403692.1|CA403692
EST:     ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGG                         GTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
genomic: ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgtt ... gccgatatagGTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
EST: gi|32907864|gb|CF012677.1|CF012677
EST:     ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGG                         GTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACCCCATA
genomic: ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgtt ... gccgatatagGTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
EST: gi|31362224|gb|CD446581.1|CD446581
EST:     ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGG                         GTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
genomic: ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgtt ... gccgatatagGTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
EST: gi|67042246|gb|CO468501.1|CO468501
EST:     ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGG                         GTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
genomic: ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgtt ... gccgatatagGTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
EST: gi|84980240|gb|DW530589.1|DW530589
EST:     ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGG                         GTGCTTGCATTCGAAGCTGNGCGAAAAGGCAAAATCAGAGTTAACACCATA
genomic: ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgtt ... gccgatatagGTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
EST: gi|9952049|gb|BE638632.1|BE638632
EST:     ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGG                         GTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
genomic: ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgtt ... gccgatatagGTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
EST: gi|9254230|gb|BE344698.1|BE344698
EST:     ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGG                         GTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
genomic: ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgtt ... gccgatatagGTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
EST: gi|31355683|gb|CD440040.1|CD440040
EST:     ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGG                         GTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
genomic: ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgtt ... gccgatatagGTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
EST: gi|31364652|gb|CD449007.1|CD449007
EST:     ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGG                         GTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTGAACACCATA
genomic: ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgtt ... gccgatatagGTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
EST: gi|32908049|gb|CF012862.1|CF012862
EST:     ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGG                         GTACTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACCCCATA
genomic: ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgtt ... gccgatatagGTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
EST: gi|211497962|gb|FL450082.1|FL450082
EST:     ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGG                         GTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
genomic: ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgtt ... gccgatatagGTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
EST: gi|211375763|gb|FL457930.1|FL457930
EST:     ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGG                         GTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACTCCATA
genomic: ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgtt ... gccgatatagGTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
EST: gi|71766308|gb|DR964245.1|DR964245
EST:     ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGG                         GTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
genomic: ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgtt ... gccgatatagGTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
EST: gi|166665694|gb|EG087295.1|EG087295
EST:     GATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGG                         GTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
genomic: GATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgtt ... gccgatatagGTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
EST: gi|60399474|gb|DN232286.1|DN232286
EST:     ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGG                         GTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
genomic: ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgtt ... gccgatatagGTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
EST: gi|67022814|gb|CO451563.1|CO451563
EST:     ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGG                         GTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
genomic: ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgtt ... gccgatatagGTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
EST: gi|13150169|gb|BG320491.1|BG320491
EST:     ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGG                         GTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
genomic: ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgtt ... gccgatatagGTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
EST: gi|211497961|gb|FL450081.1|FL450081
EST:     ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGG                         GTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
genomic: ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgtt ... gccgatatagGTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
EST: gi|6466754|gb|AW191414.1|AW191414
EST:     CTGCTAAACCAGCTCTTGAGAGTGATCCNCGG                         GTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTACCCCCATA
genomic: CTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgtt ... gccgatatagGTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
EST: gi|31353471|gb|CD437828.1|CD437828
EST:     ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGG                         GTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
genomic: ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgtt ... gccgatatagGTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
EST: gi|6526806|gb|AW216075.1|AW216075
EST:     ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACCCGG                         GTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTACCCCCATA
genomic: ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgtt ... gccgatatagGTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
EST: gi|111990916|gb|EE332354.1|EE332354
EST:     ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGG                         GTGCTTGCATNCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
genomic: ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgtt ... gccgatatagGTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
EST: gi|29544932|gb|CB605540.1|CB605540
EST:     ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGG                         GTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
genomic: ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgtt ... gccgatatagGTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
EST: gi|32908050|gb|CF012863.1|CF012863
EST:     ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGG                         GTACTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
genomic: ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgtt ... gccgatatagGTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
EST: gi|32907865|gb|CF012678.1|CF012678
EST:     ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGG                         GTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
genomic: ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgtt ... gccgatatagGTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
EST: gi|211297571|gb|FL439288.1|FL439288
EST:     ATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGG                         GTGCTTGCATTCGAAGCTGGGCGWAAAGGCAAAATCAGAGTTAACACCATA
genomic: ATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgtt ... gccgatatagGTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
EST: gi|6564253|gb|AW231875.1|AW231875
EST:     ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGG                         GTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA
genomic: ATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgtt ... gccgatatagGTGCTTGCATTCGAAGCTGGGCGAAAAGGCAAAATCAGAGTTAACACCATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATGGTGGTGGGATGAGTTCTGCTAAAGCAGCTCTTGAGAGTGATACACGGgtatggtgttgcataattgtgtgcttaaattcttcctttccccatgaattcattttctcttttacgtttataaacctgccgatatag

-  TGGTGG
- - - TGGTGG
- - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - -  CAGCTC