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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAAATCCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccggctcacaacgaatcaagctgatgcatcagnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn...

Basic information

species Zea mays
transcript GRMZM2G000510_T04
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000510_T04 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os11g48040.1 (Oryza sativa), 5'ss of exon 3
GTCAAATCCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccggct-cacaacgaatcaagctgatgcatcagnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn
|| |||||||||||||| ||||||||||| || |||||||| ||| |  |||||||||| || ||||||| ||| ||   | |  ||      || |                                                             
GTGAAATCCTTCTACGTTGGCAAAGACCATGTCGGGGATGTGCCTCTCACCAAGAAGATCGCTGCCGGCTTCACCACTGgt-actctaccaactctgctttgcttcccattcccaactagtactcactccgttatatgctgcttcttctcatctcag-
















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|78179369|gb|DV549742.1|DV549742
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|31349105|gb|CD433462.1|CD433462
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|211209142|gb|FL374139.1|FL374139
EST:     CCTTCTACGTCGGCAAAGACCACGTTNGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGG-TTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|211047692|gb|FL371292.1|FL371292
EST:     CCTTCTACGTCGGCAAAGACCATGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|76291091|gb|DV030659.1|DV030659
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|22545542|gb|BU097901.1|BU097901
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|211227505|gb|FL377297.1|FL377297
EST:     CTTCTACGTCGGCAAAGAACCATGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CTTCTACGTCGGCAAAGA-CCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|12045964|gb|BF727999.1|BF727999
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|149110174|gb|EE293989.2|EE293989
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|76911479|gb|DV164289.1|DV164289
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|211415548|gb|FL372632.1|FL372632
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|211234205|gb|FK951233.1|FK951233
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|211253778|gb|FL369138.1|FL369138
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|50324459|gb|CO519585.1|CO519585
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|78109062|gb|DV527479.1|DV527479
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|67028232|gb|CO456981.1|CO456981
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|211229469|gb|FL370963.1|FL370963
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACT
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACT
EST: gi|76292715|gb|DV032283.1|DV032283
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|71437614|gb|DR818664.1|DR818664
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|211285989|gb|FL388300.1|FL388300
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|78108615|gb|DV527033.1|DV527033
EST:     CCTTCTACGTCGGCAAAGACCAAGTTGGGGATGTCCCTTTGTCCAA-AAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|211421416|gb|FL412840.1|FL412840
EST:     CCTTCTACGTCGGCAAAGACCATGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTGGTGCCATC
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTGGTGCCATC
EST: gi|6827024|gb|AW330667.1|AW330667
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|148947408|gb|EC892822.2|EC892822
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|71437391|gb|DR818441.1|DR818441
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|148932353|gb|EC875981.2|EC875981
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|148986615|gb|EE030385.2|EE030385
EST:     CTTCTACGTCGGCAAAGACCCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CTTCTACGTCGGCAAAGACC-ACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|88751922|gb|DY536063.1|DY536063
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|31348998|gb|CD433355.1|CD433355
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|50333857|gb|CO528983.1|CO528983
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|149072257|gb|EE160513.2|EE160513
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|76294190|gb|DV033758.1|DV033758
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|211527528|gb|FL409931.1|FL409931
EST:     CCTTCTACGTCGGCAAAGACCATGTTGGGGATGTCC-TTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTGGTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTGGTG
EST: gi|76281516|gb|DV021084.1|DV021084
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|93015136|gb|EB640656.1|EB640656
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|148954532|gb|EC899968.2|EC899968
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|89249688|gb|DY621474.1|DY621474
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|93281478|gb|EB673742.1|EB673742
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|71303282|gb|DR787744.1|DR787744
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|71332543|gb|DR803241.1|DR803241
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|211234204|gb|FK951232.1|FK951232
EST:     CCTTCTACGTCGGCAAAGACCATGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|149014447|gb|EE044057.2|EE044057
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|31363588|gb|CD447945.1|CD447945
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|148931428|gb|EC874386.2|EC874386
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG
EST: gi|71447490|gb|DR828540.1|DR828540
EST:     CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAG                         ATAGCCGCCGGCTTCACAACTG
genomic: CCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG

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: 145

GTCAAATCCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 443

GTCAAATCCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 659

GTCAAATCCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 282

GTCAAATCCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccg ... tgtccagaagATAGCCGCCGGCTTCACAACTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAAATCCTTCTACGTCGGCAAAGACCACGTTGGGGATGTCCCTTTGTCCAAGAAGatagccgccggctcacaacgaatcaagctgatgcatcagnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnn

- - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG