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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcactttgcatcgcttttgtctcgaataagatcttgctaatctaggatggtttcttgtttctgctgaacttactaccaagttatacgccacatcaagcacgagagatcgtgtgatactggacatgtccatgacgaactttctgcaacatttcag

Basic information

species Zea mays
transcript GRMZM5G828229_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G828229_T02 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os08g05570.3 (Oryza sativa), 5'ss of exon 16
ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattg-cactttgcatcgcttttgtctcgaataagatcttgctaatctaggatggtttcttgtttctgctgaacttactaccaagttatacgccacatcaagcacgagagatcgtgtgatactggacatgtccatgacgaactttctgcaacatttcag
|||| || ||||||||||||||||| |||||||| | ||||||||||||   |   | ||||  ||| ||||   || || ||  | |   ||   |        |||   | |     |||| |   || || |     | ||  ||                                                         
ATAGTCGACTGAAGGGTGTTTTCCTTGAGAGTGGTAGCTCAGAGgtaataaactactggcataacttctgtcat-aacaaaatactacc--tccgtgcccaacgtttga--ccgtccgtcttatttaaaaattttgaaa-atatttagtc-------------------------------------------------------
















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|113665703|gb|DW828711.1|DW828711
EST:     ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG                         GAATTCTCGCTTCTTCCGCAGC
genomic: ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGC
EST: gi|211009192|gb|FL302293.1|FL302293
EST:     ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG                         GAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
genomic: ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
EST: gi|86466009|gb|DY232382.1|DY232382
EST:     ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG                         GAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
genomic: ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
EST: gi|86471329|gb|DY237699.1|DY237699
EST:     ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG                         GAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
genomic: ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
EST: gi|60340056|gb|DN207029.1|DN207029
EST:     ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG                         GAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
genomic: ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
EST: gi|87152588|gb|DY397377.1|DY397377
EST:     ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG                         GAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
genomic: ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
EST: gi|60342475|gb|DN209448.1|DN209448
EST:     ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG                         GAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
genomic: ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
EST: gi|18655110|gb|BM499915.1|BM499915
EST:     ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG                         GAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
genomic: ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
EST: gi|211009193|gb|FL302294.1|FL302294
EST:     ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG                         GAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
genomic: ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
EST: gi|211410389|gb|FL480482.1|FL480482
EST:     ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG                         GAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
genomic: ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
EST: gi|110943981|gb|EE164138.1|EE164138
EST:     ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG                         GAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
genomic: ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
EST: gi|60355749|gb|DN222722.1|DN222722
EST:     ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG                         GAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
genomic: ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
EST: gi|32848350|gb|CD988031.1|CD988031
EST:     ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG                         GAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTCGTTGACAAG
genomic: ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
EST: gi|86467590|gb|DY233960.1|DY233960
EST:     ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG                         GAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
genomic: ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
EST: gi|40303824|gb|CK348211.1|CK348211
EST:     ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG                         GAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
genomic: ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
EST: gi|148929039|gb|EC874295.2|EC874295
EST:     ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG                         GAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
genomic: ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
EST: gi|211520540|gb|FL475907.1|FL475907
EST:     ATAGCCGGCTGAAGGGTGTTTTGGTCGAGAGTGGAACCTCAGAG                         GAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
genomic: ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
EST: gi|71760295|gb|DR958232.1|DR958232
EST:     ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG                         GAATTTTCGCTTCTTCCGCAGCTCGCCAAATTTCAGCCTGTTGTTGACAAG
genomic: ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
EST: gi|22490231|gb|BU050154.1|BU050154
EST:     ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG                         GAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
genomic: ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
EST: gi|148990926|gb|EE032349.2|EE032349
EST:     ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG                         GAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
genomic: ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
EST: gi|78103955|gb|DV522373.1|DV522373
EST:     ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG                         GAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
genomic: ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
EST: gi|87153578|gb|DY398367.1|DY398367
EST:     ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG                         GAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
genomic: ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
EST: gi|5510847|gb|AI857231.1|AI857231
EST:     ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG                         GAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
genomic: ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
EST: gi|4572936|gb|AI586585.1|AI586585
EST:     ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG                         GAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
genomic: ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
EST: gi|6021971|gb|AW066899.1|AW066899
EST:     CTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG                         GAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
genomic: CTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
EST: gi|60341998|gb|DN208971.1|DN208971
EST:     ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG                         GAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
genomic: ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
EST: gi|33101850|gb|CF061810.1|CF061810
EST:     ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG                         GAATTCTCGCTTCTTCCGCAGCTCGCCAAAGCTCAGCCTGTTGTTGACAAG
genomic: ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
EST: gi|148933345|gb|EC877007.2|EC877007
EST:     ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG                         GAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
genomic: ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
EST: gi|33102180|gb|CF062140.1|CF062140
EST:     ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG                         GAATTCTCGCTTCTTCCGCAGCTCGCCAAAGCTCAGCCTGTTGTTGACAAG
genomic: ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
EST: gi|33090861|gb|CF050855.1|CF050855
EST:     ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG                         GAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTCGTTGACAAG
genomic: ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
EST: gi|32831851|gb|CD971529.1|CD971529
EST:     ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG                         GAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTCGTTGACAAG
genomic: ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
EST: gi|14190977|gb|BG833207.1|BG833207
EST:     ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAG                         GAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG
genomic: ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAG

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: 197

ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAGTCAAAGCTCCAGGCCGCGACTTCTGTTGAAGATGCATTAGAGATTGCAA


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 177

ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAGTCAAAGCTCCAGGCCGCGACTTCTGTTGAAGATGCATTAGAGATTGCAA


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 121

ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAGTCAAAGCTCCAGGCCGCGACTTCTGTTGAAGATGCATTAGAGATTGCAA


Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 127

ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcac ... aacatttcagGAATTCTCGCTTCTTCCGCAGCTCGCCAAATCTCAGCCTGTTGTTGACAAGTCAAAGCTCCAGGCCGCGACTTCTGTTGAAGATGCATTAGAGATTGCAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAGCCGGCTGAAGGGTGTTTTCCTCGAGAGTGGAACCTCAGAGgtaattgcactttgcatcgcttttgtctcgaataagatcttgctaatctaggatggtttcttgtttctgctgaacttactaccaagttatacgccacatcaagcacgagagatcgtgtgatactggacatgtccatgacgaactttctgcaacatttcag

- - - - CTGAAG
- - - - - - - - - - - - - -  AGTGGA