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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGATGGTCTTATTAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaatctgtgttttcgtatgtacattcctgtggtaaccaagttgggtcccatcttcttcagttcttctaaatggttgtaacttgtgccgcag

Basic information

species Zea mays
transcript GRMZM2G165357_T02
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G165357_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os03g16980.4 (Oryza sativa), 5'ss of exon 10
------------------------------------GTTGATGGTCTTATTAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaa-tctgtgtt---------------------------ttcgtatgtacattcctgtggtaaccaagttgggtcccatcttcttcagttcttctaaatggttgtaac---ttgtgccgcag
                                    ||| |||||||||||||||||||||| ||  |||| |||||||| ||||| ||||| |||||||||| ||| |  ||||  ||                           |  |||    || |||||||||||  || |||  |  ||  | |||        |||||||||  |||    |||||  | ||
TTGCATCACATCATCACTGGTACCATTTTAATGCAGGTTAATGGTCTTATTAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttacctctgcattcgtttgatttttctctacatgtggtaatctgtactagcaatcctgtggtaatgaaattgattttcacgtccttg----tcactaaatggtcataatatattgtgttgtag

upper sequence: GRMZM2G165357_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os03g16980.2 (Oryza sativa), 5'ss of exon 10
GTTGATGGTCTTATTAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattca-----------atctgtgttttc-----------------gtatgtacattcctgtggtaaccaagttgggtcccatcttcttcagttcttctaaatggttgtaac---ttgtgccgcag
||| |||||||||||||||||||||| ||  |||| |||||||| ||||| ||||| |||||||||| ||| |            | ||  |||||                 |||    || |||||||||||  || |||  |  ||  | |||        |||||||||  |||    |||||  | ||
GTTAATGGTCTTATTAAGCTGATGAACGGGGACAACACTGGACCAATTAATTTGGGAAACCCAGgtagatttacctctgcattcgtttgatttttctctacatgtggtaatctgtactagcaatcctgtggtaatgaaattgattttcacgtccttg----tcactaaatggtcataatatattgtgttgtag
















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|18169307|gb|BM339147.1|BM339147
EST:     TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaa ... tgtgccgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|13562266|gb|BG550486.1|BG550486
EST:     TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaa ... tgtgccgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|13558126|gb|BG549482.1|BG549482
EST:     TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaa ... tgtgccgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|32850602|gb|CD990283.1|CD990283
EST:     TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCT
genomic: TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaa ... tgtgccgcagGTGAATTCACCATGCTGGAACTTGCT
EST: gi|5525817|gb|AI861710.1|AI861710
EST:     TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaa ... tgtgccgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|5871227|gb|AW017698.1|AW017698
EST:     TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaa ... tgtgccgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|18168819|gb|BM338659.1|BM338659
EST:     TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaa ... tgtgccgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|18172685|gb|BM348073.1|BM348073
EST:     TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaa ... tgtgccgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|149070502|gb|EE158906.2|EE158906
EST:     TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaa ... tgtgccgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|71444249|gb|DR825299.1|DR825299
EST:     TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaa ... tgtgccgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|211023433|gb|FL440281.1|FL440281
EST:     TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaa ... tgtgccgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|60394382|gb|DN227252.1|DN227252
EST:     TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaa ... tgtgccgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|6012581|gb|AW062018.1|AW062018
EST:     TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaa ... tgtgccgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|211023434|gb|FL440282.1|FL440282
EST:     AAGCTGATGAATGGAAACAAGACTGGACCCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: AAGCTGATGAATGGAAACAAGACTGGA-CCGATTAACTTGGGGAACCCAGgtaaattcaa ... tgtgccgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|32848833|gb|CD988514.1|CD988514
EST:     TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaa ... tgtgccgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|18164214|gb|BM334053.1|BM334053
EST:     TAAGCTGATGAATGAAAACAAGACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaa ... tgtgccgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|60342197|gb|DN209170.1|DN209170
EST:     TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaa ... tgtgccgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|32864569|gb|CF004251.1|CF004251
EST:     TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaa ... tgtgccgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|71449952|gb|DR831002.1|DR831002
EST:     TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaa ... tgtgccgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|211225103|gb|FL464256.1|FL464256
EST:     TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaa ... tgtgccgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|14243914|gb|BG841625.2|BG841625
EST:     TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaa ... tgtgccgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|32850797|gb|CD990478.1|CD990478
EST:     TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaa ... tgtgccgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|149082964|gb|EE172200.2|EE172200
EST:     TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaa ... tgtgccgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|18166053|gb|BM335892.1|BM335892
EST:     TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaa ... tgtgccgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|18171739|gb|BM341579.1|BM341579
EST:     TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaa ... tgtgccgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|149065531|gb|EE286651.2|EE286651
EST:     TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaa ... tgtgccgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|60339871|gb|DN206844.1|DN206844
EST:     TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaa ... tgtgccgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|18173577|gb|BM348965.1|BM348965
EST:     TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaa ... tgtgccgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|18176777|gb|BM351710.1|BM351710
EST:     TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaa ... tgtgccgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|45213764|gb|CK850000.1|CK850000
EST:     TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaa ... tgtgccgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
EST: gi|5847454|gb|AW000533.1|AW000533
EST:     TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAG                         GTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG
genomic: TAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaa ... tgtgccgcagGTGAATTCACCATGCTGGAACTTGCTGAGAATGTGAAGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGATGGTCTTATTAAGCTGATGAATGGAAACAAGACTGGACCGATTAACTTGGGGAACCCAGgtaaattcaatctgtgttttcgtatgtacattcctgtggtaaccaagttgggtcccatcttcttcagttcttctaaatggttgtaacttgtgccgcag

- - - - - - -  AAGCTG
- - - - - - - - AGCTGA
- - - - - - - -  GCTGAT