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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gagagggattaaatctctttctattcaatttttagtagcaagggatttaatcccctcctaaccgaacaagcccttactaggttcatgtatgacacgtcagGTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGACCACTAGGGTGCTGTGTATTTACGGGGGATTATGAGGGGAATGCACTCG

Basic information

species Zea mays
transcript GRMZM2G051129_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G051129_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os09g36800.1 (Oryza sativa), 3'ss of exon 7
-----------------------------------------------------------------------gagagggattaaatctctttctattcaatttttagtagcaagg-----gatttaatcccctcctaaccgaacaagcccttactaggttcatgtatgac-acgtcagGTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGACCACTAGGGTGCTGTGTATTTACGGGGGATTATGAGGGGAATGCACTCG
                                                                          |   |||   | |  || ||| || |  |   |||||  |      | ||  |   |  |||    ||     | ||| |   ||| || ||||   | ||||||||| |||||||||||||||||  || |||| |||||||| ||||||||||| || ||  ||||||| || || || ||||| ||  ||||||| ||||
gtaagtaccctcgtaccttgatatgttacaaagtggatctgatcagcttttgtcaccaaacaaattgttggataacctattttttgttattgtatgcattggtatatagcagagctctcaagttgtttttcctctattgaaaagcagcattattgaattcctgaatgattgcatcagGTTGATAAGAAGGTTGCTGATGGATTGCTGAGGCTCATCCTCCTGAAAGGACCTCTGGGAAGCTGTGTTTTCACTGGCGATTACGACAGGAATGCCCTCG
















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|32849494|gb|CD989175.1|CD989175
EST:     TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCT                         GTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
genomic: TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCTgtaagtacct ... gacacgtcagGTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
EST: gi|148997310|gb|EE035805.2|EE035805
EST:     TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCT                         GTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
genomic: TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCTgtaagtacct ... gacacgtcagGTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
EST: gi|4688530|gb|AI637200.1|AI637200
EST:     TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCT                         GTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
genomic: TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCTgtaagtacct ... gacacgtcagGTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
EST: gi|14203054|gb|BG836731.1|BG836731
EST:     TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCT                         GTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
genomic: TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCTgtaagtacct ... gacacgtcagGTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
EST: gi|32850814|gb|CD990495.1|CD990495
EST:     TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCT                         GTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
genomic: TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCTgtaagtacct ... gacacgtcagGTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
EST: gi|71763312|gb|DR961249.1|DR961249
EST:     TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCT                         GTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
genomic: TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCTgtaagtacct ... gacacgtcagGTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
EST: gi|78112302|gb|DV530696.1|DV530696
EST:     TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCT                         GTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
genomic: TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCTgtaagtacct ... gacacgtcagGTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
EST: gi|148957874|gb|EC904028.2|EC904028
EST:     TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCT                         GTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
genomic: TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCTgtaagtacct ... gacacgtcagGTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
EST: gi|78085800|gb|DV514193.1|DV514193
EST:     TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCT                         GTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTTTGAAAGGA
genomic: TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCTgtaagtacct ... gacacgtcagGTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
EST: gi|71425836|gb|DR806927.1|DR806927
EST:     TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCT                         GTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTTTGAAAGGA
genomic: TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCTgtaagtacct ... gacacgtcagGTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
EST: gi|32850571|gb|CD990252.1|CD990252
EST:     TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCT                         GTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
genomic: TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCTgtaagtacct ... gacacgtcagGTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
EST: gi|32850627|gb|CD990308.1|CD990308
EST:     TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCT                         GTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
genomic: TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCTgtaagtacct ... gacacgtcagGTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
EST: gi|86467962|gb|DY234332.1|DY234332
EST:     TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCT                         GTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
genomic: TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCTgtaagtacct ... gacacgtcagGTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
EST: gi|32850630|gb|CD990311.1|CD990311
EST:     TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCT                         GTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
genomic: TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCTgtaagtacct ... gacacgtcagGTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
EST: gi|71770378|gb|DR968315.1|DR968315
EST:     TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCT                         GTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
genomic: TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCTgtaagtacct ... gacacgtcagGTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
EST: gi|32839131|gb|CD978812.1|CD978812
EST:     TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCT                         GTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
genomic: TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCTgtaagtacct ... gacacgtcagGTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
EST: gi|211518182|gb|FL036411.1|FL036411
EST:     TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCT                         GTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
genomic: TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCTgtaagtacct ... gacacgtcagGTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
EST: gi|149102612|gb|EE287968.2|EE287968
EST:     TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCT                         GTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
genomic: TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCTgtaagtacct ... gacacgtcagGTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
EST: gi|76293970|gb|DV033538.1|DV033538
EST:     TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCT                         GTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
genomic: TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCTgtaagtacct ... gacacgtcagGTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
EST: gi|71427078|gb|DR808128.1|DR808128
EST:     TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCT                         GTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
genomic: TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCTgtaagtacct ... gacacgtcagGTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
EST: gi|89764041|gb|DY690993.1|DY690993
EST:     TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCT                         GTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
genomic: TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCTgtaagtacct ... gacacgtcagGTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
EST: gi|74240471|gb|DT648385.1|DT648385
EST:     TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCT                         GTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
genomic: TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCTgtaagtacct ... gacacgtcagGTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
EST: gi|71772689|gb|DR970616.1|DR970616
EST:     TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCT                         GTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
genomic: TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCTgtaagtacct ... gacacgtcagGTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
EST: gi|13382031|gb|BG458706.1|BG458706
EST:     TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCT                         GTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
genomic: TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCTgtaagtacct ... gacacgtcagGTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
EST: gi|88751396|gb|DY535537.1|DY535537
EST:     TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCT                         GTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
genomic: TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCTgtaagtacct ... gacacgtcagGTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
EST: gi|211111680|gb|FL466618.1|FL466618
EST:     TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCT                         GTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
genomic: TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCTgtaagtacct ... gacacgtcagGTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
EST: gi|15426855|gb|BI542677.1|BI542677
EST:     TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCT                         GTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
genomic: TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCTgtaagtacct ... gacacgtcagGTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
EST: gi|110195268|gb|EC877165.1|EC877165
EST:     TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCT                         GTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
genomic: TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCTgtaagtacct ... gacacgtcagGTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
EST: gi|78086294|gb|DV514687.1|DV514687
EST:     TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCT                         GTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
genomic: TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCTgtaagtacct ... gacacgtcagGTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
EST: gi|5608150|gb|AI901817.1|AI901817
EST:     TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCT                         GTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA
genomic: TTGCACCTCCTGAGACCATGACCGTAGAGAAGTTTAAAAACATCATGGCTgtaagtacct ... gacacgtcagGTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gagagggattaaatctctttctattcaatttttagtagcaagggatttaatcccctcctaaccgaacaagcccttactaggttcatgtatgacacgtcagGTTGACAAGAAGGTTGCTGATGGTCTGTTGAGACTCATCCTTCTGAAAGGACCACTAGGGTGCTGTGTATTTACGGGGGATTATGAGGGGAATGCACTCG

- - - - - - - - - - - - - - - - -agtagca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caagccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gttcatg