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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGATCCTACTCGACTTGTTGCTGTCAACATCAGCACGGATATGATCCATACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAGgtaataatttcgtaccaggttttaacttattttgcaggcttggtccaataagatagtctttatgcaaaagtggcttggattagaggtagtagatctcaaa...

Basic information

species Zea mays
transcript GRMZM2G038588_T02
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G038588_T02 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os02g12570.1 (Oryza sativa), 5'ss of exon 8
CAGATCCTACTCGACTTGTTGCTGTCAACATCAGCACGGATATGATCCATACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAGgtaataatttcgtaccaggttttaacttattttgcaggcttggtccaataagatagtctttatgcaaaagtggcttggattagaggtagt-agatctcaaa
|||| |||||||||||||||||||| ||||||||||| |||||| |||| || ||||||||  |||| ||||||||||||||||| |||||| | || |||| |||    |   |||  ||    |||||  |  |    |  |  |||    ||  |||   || | |||   |     | ||    || | | || |  
CAGACCCTACTCGACTTGTTGCTGTTAACATCAGCACAGATATGGTCCACACCGTGCTTGCTGTTTCATATGCTAAGGAACCTGATGAAATAGTTTCCAGgtgataccaactgcccaaattagtgcttatgctttacatctactaaaatgtt-tatgcttagagccatagtcaatacagcttgatacggtgataccttatt
















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|71323423|gb|DR798362.1|DR798362
EST:     ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATTTAG                         CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
genomic: ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAGgtaataattt ... tacactgcagCAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
EST: gi|148999969|gb|EE037044.2|EE037044
EST:     ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATTTAG                         CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
genomic: ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAGgtaataattt ... tacactgcagCAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
EST: gi|149010086|gb|EE041893.2|EE041893
EST:     ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAG                         CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
genomic: ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAGgtaataattt ... tacactgcagCAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
EST: gi|211229043|gb|FL456610.1|FL456610
EST:     ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAG                         CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAGGAAG
genomic: ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAGgtaataattt ... tacactgcagCAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCC--A--AAG
EST: gi|50338769|gb|CO533895.1|CO533895
EST:     ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAG                         CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
genomic: ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAGgtaataattt ... tacactgcagCAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
EST: gi|31405753|gb|CD484485.1|CD484485
EST:     ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAG                         CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
genomic: ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAGgtaataattt ... tacactgcagCAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
EST: gi|50338323|gb|CO533449.1|CO533449
EST:     ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAG                         CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
genomic: ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAGgtaataattt ... tacactgcagCAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
EST: gi|71763129|gb|DR961066.1|DR961066
EST:     ACAGTGCTTGCAATTTCTTATGTTAAGGAACCTGAAGAAATAATATCTAG                         CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
genomic: ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAGgtaataattt ... tacactgcagCAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
EST: gi|71324526|gb|DR798964.1|DR798964
EST:     ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAG                         CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
genomic: ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAGgtaataattt ... tacactgcagCAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
EST: gi|86471476|gb|DY237846.1|DY237846
EST:     ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAG                         CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
genomic: ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAGgtaataattt ... tacactgcagCAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
EST: gi|93014406|gb|EB639926.1|EB639926
EST:     ACAGTGCTTGCAATTTCTTATGTTAAGGAACCTGAAGAAATAATATCTAG                         CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
genomic: ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAGgtaataattt ... tacactgcagCAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
EST: gi|110518920|gb|EE023507.1|EE023507
EST:     ACAGTGCTTGCAATTTCCTATGTTAAGGAACCTGAAGAAATAATATCTAG                         CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
genomic: ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAGgtaataattt ... tacactgcagCAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
EST: gi|149073620|gb|EE161922.2|EE161922
EST:     ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATTTAG                         CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
genomic: ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAGgtaataattt ... tacactgcagCAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
EST: gi|148965176|gb|EE015985.2|EE015985
EST:     ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAG                         CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
genomic: ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAGgtaataattt ... tacactgcagCAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
EST: gi|78075700|gb|DV504134.1|DV504134
EST:     ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAG                         CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
genomic: ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAGgtaataattt ... tacactgcagCAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
EST: gi|149034778|gb|EE155078.2|EE155078
EST:     ACAGTGCTTGCAATTTCCTATGTTAAGGAACCTGAAGAAATAATATCTAG                         CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
genomic: ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAGgtaataattt ... tacactgcagCAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
EST: gi|60401015|gb|DN233822.1|DN233822
EST:     ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAG                         CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
genomic: ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAGgtaataattt ... tacactgcagCAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
EST: gi|78081105|gb|DV509517.1|DV509517
EST:     ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAG                         CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
genomic: ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAGgtaataattt ... tacactgcagCAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
EST: gi|71756919|gb|DR954856.1|DR954856
EST:     ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAG                         CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
genomic: ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAGgtaataattt ... tacactgcagCAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
EST: gi|211013387|gb|FL466952.1|FL466952
EST:     ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAG                         CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
genomic: ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAGgtaataattt ... tacactgcagCAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
EST: gi|78122373|gb|DV540757.1|DV540757
EST:     ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATTTAG                         CAATGTTGCCGGATTCATTCATGTTTCTGATGTTGACATCCAAAG
genomic: ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAGgtaataattt ... tacactgcagCAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
EST: gi|86471665|gb|DY238035.1|DY238035
EST:     ACAGTGCTTGCAATTTCCTATGTTAAGGAACCTGAAGAAATAATATCTAG                         CAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG
genomic: ACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAGgtaataattt ... tacactgcagCAATGTTGCCGGATTCATTCATGTTACTGATGTTGACATCCAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGATCCTACTCGACTTGTTGCTGTCAACATCAGCACGGATATGATCCATACAGTGCTTGCAATTTCCTATGCTAAGGAACCTGAAGAAATAATATCTAGgtaataatttcgtaccaggttttaacttattttgcaggcttggtccaataagatagtctttatgcaaaagtggcttggattagaggtagtagatctcaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA