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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagggactaaaatttagcacgtgccgcattggatgttaaatacctattacgagtaatataatctgattacaaaactaagaaactctattctgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGCTCCAGGCCGAGGGCAAGCTTGCGCCTGGTGTGCCACGCCGCTACACTGG

Basic information

species Zea mays
transcript GRMZM2G000510_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G000510_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os11g48040.1 (Oryza sativa), 3'ss of exon 3
tagggactaaaatttagcacgtgccgcattggatgttaaatacctattacgagtaatataatctgattacaaaactaagaaactctattctgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGCTCCAGGCCGAGGGCAAGCTTGCGCCTGGTGTGCCACGCCGCTACACTGG
                | ||    |  | |     ||   | ||  |  | | || ||        | ||     ||       ||  |    ||   ||||||||| || ||||| ||||||||||| ||||||||||||||||| ||||| ||||| ||||||||||| ||||| || |  || ||||| ||  ||||
----------------gtactctaccaactctgctttgcttcccattcccaactagtac-------tcactccgttatatgctgcttcttctcatctcagGTGCCATTGCGATCAGTATCGCCAACCCCACTGACCTTGTCAAGGTTAGGCTTCAGGCGGAGGGCAAGCTGGCGCCCGGCGCCCCGCGCCGATATGCTGG
















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|149072257|gb|EE160513.2|EE160513
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|71332543|gb|DR803241.1|DR803241
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|211253778|gb|FL369138.1|FL369138
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|78108615|gb|DV527033.1|DV527033
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTC
EST: gi|31348998|gb|CD433355.1|CD433355
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|71303282|gb|DR787744.1|DR787744
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|211285989|gb|FL388300.1|FL388300
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|50333857|gb|CO528983.1|CO528983
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|31363588|gb|CD447945.1|CD447945
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|89249688|gb|DY621474.1|DY621474
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|148986615|gb|EE030385.2|EE030385
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCCTCGCTATCAACATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|211234205|gb|FK951233.1|FK951233
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTTACTGACCTTGTCAAGGTCAGG
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCT-ACTGACCTTGTCAAGGTCAGG
EST: gi|31349105|gb|CD433462.1|CD433462
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|211227505|gb|FL377297.1|FL377297
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|149014447|gb|EE044057.2|EE044057
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|50324459|gb|CO519585.1|CO519585
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|71437614|gb|DR818664.1|DR818664
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|76291091|gb|DV030659.1|DV030659
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|148932353|gb|EC875981.2|EC875981
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|211209142|gb|FL374139.1|FL374139
EST:     AAGATAGCCGCCGG-TTCACAACTG                         GTGCYATCGCTATCAGCATCGCCAACCCTACT
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACT
EST: gi|71437391|gb|DR818441.1|DR818441
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|211047692|gb|FL371292.1|FL371292
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCG
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCG
EST: gi|76281516|gb|DV021084.1|DV021084
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|211234204|gb|FK951232.1|FK951232
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCA
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCA
EST: gi|71447490|gb|DR828540.1|DR828540
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|93281478|gb|EB673742.1|EB673742
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|76294190|gb|DV033758.1|DV033758
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|93015136|gb|EB640656.1|EB640656
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|148954532|gb|EC899968.2|EC899968
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|12045964|gb|BF727999.1|BF727999
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|78179369|gb|DV549742.1|DV549742
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|78109062|gb|DV527479.1|DV527479
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|211415548|gb|FL372632.1|FL372632
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCGTCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|22545542|gb|BU097901.1|BU097901
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|6827024|gb|AW330667.1|AW330667
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|148947408|gb|EC892822.2|EC892822
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|76292715|gb|DV032283.1|DV032283
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|88751922|gb|DY536063.1|DY536063
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|148931428|gb|EC874386.2|EC874386
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|76911479|gb|DV164289.1|DV164289
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|67028232|gb|CO456981.1|CO456981
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
EST: gi|149110174|gb|EE293989.2|EE293989
EST:     AAGATAGCCGCCGGCTTCACAACTG                         GTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC
genomic: AAGATAGCCGCCGGCTTCACAACTGgtatggtagg ... tgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attacgagtaatataatctgattacaaaactaagaaactctattctgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGCTCCAGGCCGAGGGCAAGCTTGCGCCTGGTGTGCCACGCCGCTACACTGG
               atctgat  putative branch site (score: 4)
                                     ctctattct  putative PPT
        taatataatctgatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagggactaaaatttagcacgtgccgcattggatgttaaatacctattacgagtaatataatctgattacaaaactaagaaactctattctgaattgaagGTGCCATCGCTATCAGCATCGCCAACCCTACTGACCTTGTCAAGGTCAGGCTCCAGGCCGAGGGCAAGCTTGCGCCTGGTGTGCCACGCCGCTACACTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT