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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatgccttcctatattcattcaatttaaatttaaaaatgtgccaaatgtgttctgttaagaatacatttctcgcctatctttgtatttccattcctttaatatattttagtttttttcccaattctcatcctatttctataagttttaaggctgtgttttttttcttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGCTCAACTGTTCCAG

Basic information

species Zea mays
transcript GRMZM2G063851_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063851_T04 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 7
gtatatgccttcctatattcattcaatttaaatttaaaaatgtgccaaatgtgttctgttaagaatacatttctcgcctatctttgtatttccattcctttaatatattttagtttttt-tcccaattctcatcc-tatttctataagttttaaggctg-tgttttttttcttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGCTCAACTGTTCCAG
                                                                         | | ||   ||||| |  |  ||  | |  || | ||   |||  | | |  ||| |  ||   ||||   |     |   | ||| |   | |||  ||||||||||| ||||||||||||||||||||||| |||||||||||||||  |   || || | ||||||||
-----------------------------------------------------------------------gtttggcttcttttgtttaactgtttttcttgtaaacttggttttcctgttcttatttttgtcggcatttagctgctagtgtggactgataggtatttgtttgtttcagGTGCCAACCAAAGAGCAAGTTGATGCTCTATCAAAGGAATTGGCTAGTCGTTCGAGTGTTCCAG

upper sequence: GRMZM2G063851_T04 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os11g33240.3 (Oryza sativa), 3'ss of exon 6
gtatatgccttcctatattcattcaatttaaatttaaaaatgtgccaaatgtgttctgttaagaatacatttctcgcctatct-ttgtatttccattcctttaatatattttagtttttttcccaattctcatcctatttctataagttttaaggctg-tgttttttttcttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGCTCAACTGTTCCAG
                                                                      |  | |  || || || || ||  | ||  |  || | |  || | || ||     || ||| | | |  |||| ||| |   | ||| ||  | |||  ||||||||||| ||||||||||||||||| ||||| ||||||||||||||| || | || || | ||||||||
----------------------------------------------------------------------tctttgtttacctgttatacttgtaatc--tcgattt-tcctattcttattt----ttgtcagcatttagctattagtgt--ggactgatgcgtatttgtttgtttcagGTGCCAACCAAAGAGCAAGTCGATGCTCTATCAAAGGAATTGGTTACCCGTTCGAGTGTTCCAG
















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|51592469|gb|CV071615.1|CV071615
EST:     GCGGCGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAG                         GTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
genomic: GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAGgtatatgcct ... cttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
EST: gi|211131287|gb|FL186946.1|FL186946
EST:     GCGGCGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAG                         GTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
genomic: GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAGgtatatgcct ... cttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
EST: gi|149084983|gb|EE174493.2|EE174493
EST:     GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAG                         GTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
genomic: GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAGgtatatgcct ... cttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
EST: gi|21480820|gb|BQ577503.1|BQ577503
EST:     GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAG                         GTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
genomic: GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAGgtatatgcct ... cttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
EST: gi|67013663|gb|CO442412.1|CO442412
EST:     GCGGCGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAG                         GTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
genomic: GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAGgtatatgcct ... cttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
EST: gi|211131286|gb|FL186945.1|FL186945
EST:     GCGGCGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAG                         GTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
genomic: GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAGgtatatgcct ... cttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
EST: gi|149100799|gb|EE186893.2|EE186893
EST:     GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAG                         GTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
genomic: GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAGgtatatgcct ... cttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
EST: gi|32868179|gb|CF007861.1|CF007861
EST:     GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAG                         GTCCCAACCAAAGAGCAAGGTGATGCACTATCAAAGGAATTGCTTGCGCGC
genomic: GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAGgtatatgcct ... cttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
EST: gi|149014218|gb|EE043773.2|EE043773
EST:     GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAG                         GTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
genomic: GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAGgtatatgcct ... cttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
EST: gi|211510240|gb|FL228187.1|FL228187
EST:     GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAG                         GTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
genomic: GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAGgtatatgcct ... cttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
EST: gi|149105261|gb|EE290752.2|EE290752
EST:     GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAG                         GTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
genomic: GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAGgtatatgcct ... cttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
EST: gi|148991806|gb|EE033387.2|EE033387
EST:     GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAG                         GTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
genomic: GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAGgtatatgcct ... cttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
EST: gi|148931316|gb|EC874179.2|EC874179
EST:     GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAG                         GTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
genomic: GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAGgtatatgcct ... cttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
EST: gi|78087725|gb|DV516118.1|DV516118
EST:     GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAG                         GTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
genomic: GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAGgtatatgcct ... cttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
EST: gi|148990704|gb|EE032108.2|EE032108
EST:     GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAG                         GTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
genomic: GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAGgtatatgcct ... cttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
EST: gi|71771089|gb|DR969026.1|DR969026
EST:     GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAG                         GTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
genomic: GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAGgtatatgcct ... cttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
EST: gi|148939431|gb|EC883987.2|EC883987
EST:     GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAG                         GTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
genomic: GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAGgtatatgcct ... cttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
EST: gi|67040702|gb|CO466957.1|CO466957
EST:     GCGGCGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAG                         GTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
genomic: GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAGgtatatgcct ... cttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
EST: gi|89758059|gb|DY687401.1|DY687401
EST:     GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAG                         GTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
genomic: GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAGgtatatgcct ... cttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
EST: gi|149082974|gb|EE172211.2|EE172211
EST:     GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAG                         GTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
genomic: GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAGgtatatgcct ... cttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
EST: gi|211510238|gb|FL228185.1|FL228185
EST:     GCGGCGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAG                         GTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
genomic: GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAGgtatatgcct ... cttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGC
EST: gi|74035022|gb|DT535512.1|DT535512
EST:     GCGGCGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAG                         GTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAAATTGCTTTGCGC
genomic: GCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAGgtatatgcct ... cttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAA-TTGCTT-GCGC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 334

GGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCAACAGCAGTTAAGGGCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAGgtatatgcct ... cttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGCTCAACTGTTCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1308

GGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCAACAGCAGTTAAGGGCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAGgtatatgcct ... cttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGCTCAACTGTTCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1379

GGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCAACAGCAGTTAAGGGCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAGgtatatgcct ... cttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGCTCAACTGTTCCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 887

GGGCCTCTCAATTCCAGAATGCCAAAAAGTGCTGCCAACAGCAGTTAAGGGCGGTGAACCTTTGCCTGAGGGTCTCCTTTGGCTTCTTTTGACGGGGAAGgtatatgcct ... cttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGCTCAACTGTTCCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caattctcatcctatttctataagttttaaggctgtgttttttttcttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGCTCAACTGTTCCAG
                                ctgtgttttttttctt  CT-rich tract
            tatttctataagtttt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatgccttcctatattcattcaatttaaatttaaaaatgtgccaaatgtgttctgttaagaatacatttctcgcctatctttgtatttccattcctttaatatattttagtttttttcccaattctcatcctatttctataagttttaaggctgtgttttttttcttgtttcagGTCCCAACCAAAGAGCAAGTTGATGCACTATCAAAGGAATTGCTTGCGCGCTCAACTGTTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA