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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAGCTATACAAAGCTTGATTCTGTCAATGCTGAGGATTTCTTCTGCCGCTTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacacagcaagacttgcaatttcattattttggatttgcattcatgttgcatttacaatttgtagcaagttcatctagtctgattctttaacttg...

Basic information

species Zea mays
transcript GRMZM2G097726_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G097726_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os07g08880.2 (Oryza sativa), 5'ss of exon 2
GTAGCTATACAAAGCTTGATTCTGTCAATGCTGAGGATTTCTTCTGCCGCTTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacacagcaagactt--gcaatttcattattttggatttgcattcatgttgcatttacaatttgtagcaagttcatctagtctgattctttaacttg--
||||||| ||||||||||||||||||||||||||||| |||||||| ||||| ||||| |||||||| || || ||||| || || || || || || |||||||||   |     || |  || || | ||     || |   | | |  | | | |||| || ||  |  |     ||||| |    ||   || |  ||  
GTAGCTACACAAAGCTTGATTCTGTCAATGCTGAGGACTTCTTCTGTCGCTTTGAGTACAAATCAGCCACAGGAAGCTTCGTGCCCGACCGCATTGCTGTgtaagaatttaatgcaacctccgctatgtgatagccctgaaaa-gaacttgtttcgtatttgcagttaattccgttgacatct-gcacaata--ttgatctgtt
















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|148940632|gb|EC885443.2|EC885443
EST:     TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGT                         GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
genomic: TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... catgtgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
EST: gi|211072810|gb|FL228287.1|FL228287
EST:     TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGT                         GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
genomic: TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... catgtgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
EST: gi|148942300|gb|EC887317.2|EC887317
EST:     TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGT                         GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
genomic: TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... catgtgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
EST: gi|148941206|gb|EC886093.2|EC886093
EST:     TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGT                         GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
genomic: TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... catgtgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
EST: gi|93282376|gb|EB674640.1|EB674640
EST:     TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGT                         GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
genomic: TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... catgtgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
EST: gi|211075543|gb|FL228301.1|FL228301
EST:     TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGT                         GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCC
genomic: TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... catgtgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCC
EST: gi|8551650|gb|BE128821.1|BE128821
EST:     ATCGTATAGCAGT                         GTTTTGCAAGTGCGAGATGCCATGCAATCCAGATG-CCTTATGATCCAATG
genomic: ATCGTATAGCAGTgtaagaacac ... catgtgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
EST: gi|211075545|gb|FL228303.1|FL228303
EST:     TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGT                         GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
genomic: TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... catgtgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
EST: gi|91872374|gb|EB402331.1|EB402331
EST:     TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGT                         GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
genomic: TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... catgtgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
EST: gi|32825292|gb|CD965014.1|CD965014
EST:     TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGT                         GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
genomic: TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... catgtgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
EST: gi|78082597|gb|DV511009.1|DV511009
EST:     TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGT                         GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
genomic: TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... catgtgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
EST: gi|211072814|gb|FL228291.1|FL228291
EST:     TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGT                         GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
genomic: TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... catgtgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
EST: gi|78074295|gb|DV502729.1|DV502729
EST:     TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGT                         GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
genomic: TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... catgtgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
EST: gi|76927199|gb|DV171172.1|DV171172
EST:     TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGT                         GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
genomic: TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... catgtgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
EST: gi|67022285|gb|CO451034.1|CO451034
EST:     TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGT                         GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
genomic: TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... catgtgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
EST: gi|50336946|gb|CO532072.1|CO532072
EST:     TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGT                         GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
genomic: TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... catgtgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
EST: gi|9743182|gb|BE519330.1|BE519330
EST:     TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGT                         GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
genomic: TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... catgtgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
EST: gi|91872230|gb|EB402187.1|EB402187
EST:     TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGT                         GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
genomic: TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... catgtgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
EST: gi|22818819|gb|BU498909.1|BU498909
EST:     TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGG                         GTTTTGCAAG-GCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
genomic: TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... catgtgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
EST: gi|9733235|gb|BE511987.1|BE511987
EST:     TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGT                         GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
genomic: TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... catgtgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
EST: gi|5566990|gb|AI881901.1|AI881901
EST:     TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGT                         GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
genomic: TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... catgtgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
EST: gi|148951992|gb|EC897774.2|EC897774
EST:     TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGT                         GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
genomic: TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... catgtgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
EST: gi|148957892|gb|EC904047.2|EC904047
EST:     TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGT                         GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCCTTATGATCCAAT
genomic: TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... catgtgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACC-TTATGATCCAAT
EST: gi|32823010|gb|CD962719.1|CD962719
EST:     TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGT                         GTTTTGCAAGGGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
genomic: TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... catgtgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
EST: gi|60354816|gb|DN221789.1|DN221789
EST:     TACTGGCAGCTTTGTACCAGATCGTATAGCAGT                         GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
genomic: TACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... catgtgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
EST: gi|60357704|gb|DN224677.1|DN224677
EST:     TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGT                         GTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG
genomic: TTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... catgtgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATG

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: 49 (upstream exon), 48 (downstream exon)
Score: 541

GTAGCTATACAAAGCTTGATTCTGTCAATGCTGAGGATTTCTTCTGCCGCTTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... catgtgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 187

GTAGCTATACAAAGCTTGATTCTGTCAATGCTGAGGATTTCTTCTGCCGCTTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... catgtgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 248

GTAGCTATACAAAGCTTGATTCTGTCAATGCTGAGGATTTCTTCTGCCGCTTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... catgtgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 190

GTAGCTATACAAAGCTTGATTCTGTCAATGCTGAGGATTTCTTCTGCCGCTTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacac ... catgtgccagGTTTTGCAAGTGCGAGATGCCATACAATCCAGATGACCTTATGATCCAATGCGAGGAATGTTCTGACTG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAGCTATACAAAGCTTGATTCTGTCAATGCTGAGGATTTCTTCTGCCGCTTCGAGTATAAATCAGCTACTGGCAGCTTTGTACCAGATCGTATAGCAGTgtaagaacacagcaagacttgcaatttcattattttggatttgcattcatgttgcatttacaatttgtagcaagttcatctagtctgattctttaacttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT