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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGAGAAACTTCATGAAGAGGCAGATCAAGAGGGCCAGGATGTTTTTTGAGGAGGCAGAGAGAGGGGTAACTGAGCTCTCACAGGCTAGCAGATGGCCAgtaagtccactcaacttcacatttcccacccagtatagcacagcatcctcacttccttttctttgttaccattgcag

Basic information

species Zea mays
transcript GRMZM2G300348_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G300348_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os06g51290.3 (Oryza sativa), 5'ss of exon 5
GTGGAGAAACTTCATGAAGAGGCAGATCAAGAGGGCCAGGATGTTTTTTGAGGAGGCAGAGAGAGGGGTAACTGAGCTCTCACAGGCTAGCAGATGGCCAgtaagtccactcaacttcacatttcccacccagtatagcacagcatcctcacttccttttctttgttaccattgcag-------------------------------------
 ||||||| |||||||||||| ||||||||||| || |||||||||||||||||||||||||||||||| || ||||||   ||||| ||| | ||||| |||||   | ||| ||| |   |          || |||| |  ||  |         |||| ||  |   |  ||                                      
ATGGAGAAGCTTCATGAAGAGACAGATCAAGAGAGCTAGGATGTTTTTTGAGGAGGCAGAGAGAGGGGTGACCGAGCTCAGCCAGGCAAGCCGGTGGCCGgtaagaagagtca-cttgattctcaaggaaacataaagcagattattattgtcggtgcttctatgccatggtgtcaaaaggaaaataaaatatcattgcattgccccgttgcag

upper sequence: GRMZM2G300348_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA14G39050.1 (Glycine max), 5'ss of exon 6
GTGGAGAAACTTCATGAAGAGGCAGATCAAGAGGGCCAGGATGTTTTTTGAGGAGGCAGAGAGAGGGGTAACTGAGCTCTCACAGGCTAGCAGATGGCCAgtaagtccactcaa---cttcacatttcccacccagtatagcacagcatcctcacttccttttctttgttaccattgcag--------------------
|||||| |||||||||||||| || || || ||||| || ||||||||||| |||||||| |  || || || |||||     | |||||||||||||| |||||      |||    ||  ||||    |   | | |      |       | |        |  ||||   ||| ||                    
GTGGAGGAACTTCATGAAGAGCCAAATTAAAAGGGCAAGAATGTTTTTTGATGAGGCAGAAAAGGGAGTGACGGAGCTTAATGAAGCTAGCAGATGGCCTgtaagaaattccaaacatttatcattatataaaaacttttctgtggttgaaagaataaaaaccatcggttatacttgaagtgttctcttaaatattatta

upper sequence: GRMZM2G300348_T01 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA02G40720.1 (Glycine max), 5'ss of exon 6
GTGGAGAAACTTCATGAAGAGGCAGATCAAGAGGGCCAGGATGTTTTTTGAGGAGGCAGAGAGAGGGGTAACTGAGCTCTCACAGGCTAGCAGATGGCCAgtaag---tccactcaacttcacatttccc----acccagtata-gcacagcatcctcacttccttttctttgtt-accattgcag--------------
|||||| |||||||||||||| || ||||| ||||| || ||||||||||| |||||||| |  || || || |||||     | |||||||||||||| |||||   | |    || ||  || |||      |||   | |  ||     ||  | |          |   || | | ||| ||              
GTGGAGGAACTTCATGAAGAGCCAAATCAAAAGGGCAAGAATGTTTTTTGATGAGGCAGAAAAGGGAGTGACCGAGCTTAATGAAGCTAGCAGATGGCCGgtaagaaattccaaaaatttatcaattctataaaacctcttctgtgcttgaaattttaagaataaaccatcaatttatccttgaagtattttcctctctc

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|60344179|gb|DN211152.1|DN211152
EST:     AGGAGGCAGAGAGAGGGGTAACTGAGCTCTCACAGGCTAGCAGATGGCCA                         GTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCC
genomic: AGGAGGCAGAGAGAGGGGTAACTGAGCTCTCACAGGCTAGCAGATGGCCAgtaagtccac ... accattgcagGTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCC
EST: gi|149073531|gb|EE161834.2|EE161834
EST:     AGGAGGCAGAGAGAGGGGTAACTGAGCTCTCACAGGCTAGCAGATGGCCA                         GTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCC
genomic: AGGAGGCAGAGAGAGGGGTAACTGAGCTCTCACAGGCTAGCAGATGGCCAgtaagtccac ... accattgcagGTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCC
EST: gi|149008705|gb|EE040899.2|EE040899
EST:     AGGAGGCAGAGAGAGGGGTAACTGAGCTCTCACAGGCTAGCAGATGGCCA                         GTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCC
genomic: AGGAGGCAGAGAGAGGGGTAACTGAGCTCTCACAGGCTAGCAGATGGCCAgtaagtccac ... accattgcagGTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCC
EST: gi|93283635|gb|EB675899.1|EB675899
EST:     AGGAGGCAGAGAGAGGGGTAACTGAGCTCTCACAGGCTAGCAGATGGCCA                         GTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCC
genomic: AGGAGGCAGAGAGAGGGGTAACTGAGCTCTCACAGGCTAGCAGATGGCCAgtaagtccac ... accattgcagGTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCC
EST: gi|91054432|gb|EB164850.1|EB164850
EST:     AGGAGGCAGAGAGAGGGGTAACTGAGCTTTCACAGGCTAGCAGATGGCCA                         GTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCC
genomic: AGGAGGCAGAGAGAGGGGTAACTGAGCTCTCACAGGCTAGCAGATGGCCAgtaagtccac ... accattgcagGTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCC
EST: gi|78104639|gb|DV523057.1|DV523057
EST:     AGGAGGCAGAGAGAGGGGTAACTGAGCTTTCACAGGCTAGCAGATGGCCA                         GTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCC
genomic: AGGAGGCAGAGAGAGGGGTAACTGAGCTCTCACAGGCTAGCAGATGGCCAgtaagtccac ... accattgcagGTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCC
EST: gi|148946927|gb|EC892211.2|EC892211
EST:     AGGAGGCAGAGAGAGGGGTAACTGAGCTCTCACAGGCTAGCAGATGGCCA                         GTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCC
genomic: AGGAGGCAGAGAGAGGGGTAACTGAGCTCTCACAGGCTAGCAGATGGCCAgtaagtccac ... accattgcagGTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCC
EST: gi|76916873|gb|DV166585.1|DV166585
EST:     GAGCTCTCACAGGCTAGGCAGAGGGCCA                         GTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATGGAAGCC
genomic: GAGCTCTCACAGGCTA-GCAGATGGCCAgtaagtccac ... accattgcagGTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCC
EST: gi|101401213|gb|EB822285.1|EB822285
EST:     AGGAGGCAGAGAGAGGGGTAACTGAGCTCTCACAGGCTAGCAGATGGCCA                         GTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATGGAAGCC
genomic: AGGAGGCAGAGAGAGGGGTAACTGAGCTCTCACAGGCTAGCAGATGGCCAgtaagtccac ... accattgcagGTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCC
EST: gi|71444099|gb|DR825149.1|DR825149
EST:     AGGAGGCAGAGAGAGGGGTAACTGAGCTCTCACAGGCTAGCAGATGGCCA                         GTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCC
genomic: AGGAGGCAGAGAGAGGGGTAACTGAGCTCTCACAGGCTAGCAGATGGCCAgtaagtccac ... accattgcagGTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCC
EST: gi|71429312|gb|DR810362.1|DR810362
EST:     AGGAGGCAGAGAGAGGGGTAACTGAGCTCTCACAGGCTAGCAGATGGCCA                         GTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCC
genomic: AGGAGGCAGAGAGAGGGGTAACTGAGCTCTCACAGGCTAGCAGATGGCCAgtaagtccac ... accattgcagGTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCC
EST: gi|71775306|gb|DR973184.1|DR973184
EST:     AGGAGGCAGAGAGAGGGGTAAATGAGCTCTCACAGGCTAGCAGATGGCCA                         GTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCC
genomic: AGGAGGCAGAGAGAGGGGTAACTGAGCTCTCACAGGCTAGCAGATGGCCAgtaagtccac ... accattgcagGTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCC
EST: gi|50325755|gb|CO520881.1|CO520881
EST:     AGGAGGCAGAGAGAGGGGTAACTGAGCTCTCACAGGCTAGCAGATGGCCA                         GTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCC
genomic: AGGAGGCAGAGAGAGGGGTAACTGAGCTCTCACAGGCTAGCAGATGGCCAgtaagtccac ... accattgcagGTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCC
EST: gi|22521337|gb|BU080148.1|BU080148
EST:     AGGAGGCAGAGAGAGGGGTAAATGAGCTCTCACAGGCTAGCAGATGGCCA                         GTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCC
genomic: AGGAGGCAGAGAGAGGGGTAACTGAGCTCTCACAGGCTAGCAGATGGCCAgtaagtccac ... accattgcagGTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCC
EST: gi|60338830|gb|DN205803.1|DN205803
EST:     AGGAGGCAGAGAGAGGGGTAACTGAGCTCTCACAGGCTAGCAGATGGCCA                         GTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCC
genomic: AGGAGGCAGAGAGAGGGGTAACTGAGCTCTCACAGGCTAGCAGATGGCCAgtaagtccac ... accattgcagGTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCC
EST: gi|148958127|gb|EC904325.2|EC904325
EST:     AGGAGGCAGAGAGAGGGGTAACTGAGCTCTCACAGGCTAGCAGATGGCCA                         GTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCC
genomic: AGGAGGCAGAGAGAGGGGTAACTGAGCTCTCACAGGCTAGCAGATGGCCAgtaagtccac ... accattgcagGTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCC
EST: gi|149075799|gb|EE164332.2|EE164332
EST:     AGGAGGCAGAGAGAGGGGTAACTGAGCTCTCACAGGCTAGCAGATGGCCA                         GTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCC
genomic: AGGAGGCAGAGAGAGGGGTAACTGAGCTCTCACAGGCTAGCAGATGGCCAgtaagtccac ... accattgcagGTATGGGCTTCCCTGTTGTTGTACAGGCAGATCCTGGATGAGATCGAAGCC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGGAGAAACTTCATGAAGAGGCAGATCAAGAGGGCCAGGATGTTTTTTGAGGAGGCAGAGAGAGGGGTAACTGAGCTCTCACAGGCTAGCAGATGGCCAgtaagtccactcaacttcacatttcccacccagtatagcacagcatcctcacttccttttctttgttaccattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG