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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACGAGTGCGGCCTCAACGGCCTCCTCACCCCCGAGCAGTTCCTCGAGGAGCGCGAGAGCATGCTCCAAGCGCTCTTCCCATCCTGTACCAAGCTGCCAGgtgtgtcattgatgaacttggacgctgttggcgtcgatctgtacgccaatcactagtgtagtaccgtcttgtggtgctctctgtgaaggtgatctggacg...

Basic information

species Zea mays
transcript GRMZM2G102231_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102231_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os08g14580.1 (Oryza sativa), 5'ss of exon 2
GACGAGTGCGGCCTCAACGGCCTCCTCACCCCCGAGCAGTTCCTCGAGGAGCGCGAGAGCATGCTCCAAGCGCTCTTCCCATCCTGTACCAAGCTGCCAGgtgtgtcattgatgaacttggacgctgttggcgtcgatctgtacgccaatcactagtgtagtaccgtcttgtggtgctctctgtgaag-gtgatctggacg--
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GACGAGTGCGGCCTCGACGGCCTCCTCACCCCGGAGCAGTTCCTCGAGGAGCGCGAGAGCATGCTCCAGGAGCTCTTCCCCTCCTGCGCCGTCTTGCCTGgtcagggtttgctcctctgtatctatcttccccttcttcttctttttcttcaggag---atgtctgtcctttactgtttattgcattgtgaaagcttggcagc
















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|50338090|gb|CO533216.1|CO533216
EST:     GCGCGAGAGCATGCTCCAAGCGCTCTTCCCATCCTGTACCAAGCTGCCAG                         GAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTG
genomic: GCGCGAGAGCATGCTCCAAGCGCTCTTCCCATCCTGTACCAAGCTGCCAGgtgtgtcatt ... tttcttgcagGAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTG
EST: gi|211004136|gb|FL435012.1|FL435012
EST:     CATCCTGTACCAAGCTGCCAG                         GAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTG
genomic: CATCCTGTACCAAGCTGCCAGgtgtgtcatt ... tttcttgcagGAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTG
EST: gi|148994252|gb|EE034006.2|EE034006
EST:     GCGCGAGAGCATGCTCCAAGCGCTCTTCCCATCCTGTACCAAGCTGCCAG                         GAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTG
genomic: GCGCGAGAGCATGCTCCAAGCGCTCTTCCCATCCTGTACCAAGCTGCCAGgtgtgtcatt ... tttcttgcagGAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTG
EST: gi|211016904|gb|FL048021.1|FL048021
EST:     CCATCCTGTACCAAGCTGCCAG                         GAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTG
genomic: CCATCCTGTACCAAGCTGCCAGgtgtgtcatt ... tttcttgcagGAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTG
EST: gi|149013687|gb|EE043137.2|EE043137
EST:     GCGCGAGAGCATGCTCCAAGCGCTCTTCCCATCCTGTACCAAGCTGCCAG                         GAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTG
genomic: GCGCGAGAGCATGCTCCAAGCGCTCTTCCCATCCTGTACCAAGCTGCCAGgtgtgtcatt ... tttcttgcagGAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTG
EST: gi|211019679|gb|FL048024.1|FL048024
EST:     GCGCGAGAGCATGCTCCAAGCGCTCTTCCCATCCTGTACCAAGCTGCCAG                         GAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTG
genomic: GCGCGAGAGCATGCTCCAAGCGCTCTTCCCATCCTGTACCAAGCTGCCAGgtgtgtcatt ... tttcttgcagGAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTG
EST: gi|148954135|gb|EC899536.2|EC899536
EST:     GCGCGAGAGCATGCTCCAAGCGCTCTTCCCATCCTGTACCAAGCTGCCAG                         GAGTACTACGTTTGGTGCATCATTCTTCATGCCAACGGAGTAACAATGACT
genomic: GCGCGAGAGCATGCTCCAAGCGCTCTTCCCATCCTGTACCAAGCTGCCAGgtgtgtcatt ... tttcttgcagGAGTACTACGTTTGGTGCATCAT-CTTCATGCCAACGGAGTACCAATGGCT
EST: gi|14245028|gb|BG842966.2|BG842966
EST:     CCAAGCTGCCAG                         GAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTG
genomic: CCAAGCTGCCAGgtgtgtcatt ... tttcttgcagGAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTG
EST: gi|211016903|gb|FL048020.1|FL048020
EST:     GCGCGAGAGCATGCTCCAAGCGCTCTTCCCATCCTGTACCAAGCTGCCAG                         GAGTACTACGTTTGGTGCATCATCTTCAT
genomic: GCGCGAGAGCATGCTCCAAGCGCTCTTCCCATCCTGTACCAAGCTGCCAGgtgtgtcatt ... tttcttgcagGAGTACTACGTTTGGTGCATCATCTTCAT
EST: gi|50325634|gb|CO520760.1|CO520760
EST:     TCCCATCCTGTACCAAGCTGCCAG                         GAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTG
genomic: TCCCATCCTGTACCAAGCTGCCAGgtgtgtcatt ... tttcttgcagGAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTG
EST: gi|71773066|gb|DR970984.1|DR970984
EST:     GCGCGAGAGCATGCTCCAAGCGCTCTTCCCATCCTGTACCAAGCTGCCAG                         GAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTG
genomic: GCGCGAGAGCATGCTCCAAGCGCTCTTCCCATCCTGTACCAAGCTGCCAGgtgtgtcatt ... tttcttgcagGAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTG
EST: gi|211016905|gb|FL048022.1|FL048022
EST:     GCGCGAGAGCATGCTCCAAGCGCTCTTCCCATCCTGTACCAAGCTGCCAG                         GAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTG
genomic: GCGCGAGAGCATGCTCCAAGCGCTCTTCCCATCCTGTACCAAGCTGCCAGgtgtgtcatt ... tttcttgcagGAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTG
EST: gi|50338089|gb|CO533215.1|CO533215
EST:     AGAGCATGCTCCAAGCGCTCTTCCCATCCTGTACCAAGCTGCCAG                         GAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTG
genomic: AGAGCATGCTCCAAGCGCTCTTCCCATCCTGTACCAAGCTGCCAGgtgtgtcatt ... tttcttgcagGAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTG
EST: gi|44901216|gb|CK827761.1|CK827761
EST:     ATGCTCCAAGCGCTCTTCCCATCGTGTACCAAGCTGCCAG                         GAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTG
genomic: ATGCTCCAAGCGCTCTTCCCATCCTGTACCAAGCTGCCAGgtgtgtcatt ... tttcttgcagGAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTG
EST: gi|89250658|gb|DY622444.1|DY622444
EST:     GCGCGAGAGCATGCTCCAAGCGCTCTTCCCATCCTGTACCAAGCTGCCAG                         GAATACTACGT
genomic: GCGCGAGAGCATGCTCCAAGCGCTCTTCCCATCCTGTACCAAGCTGCCAGgtgtgtcatt ... tttcttgcagGAGTACTACGT
EST: gi|211019681|gb|FL048026.1|FL048026
EST:     GCGCGAGAGCATGCTCCAAGCGCTCTTTCCATCCTGTACCAAGCTGCCAG                         GAGTACTACGTTTGGTGCATCATCTTCATGCCCACGGAGTACCAATGGCTG
genomic: GCGCGAGAGCATGCTCCAAGCGCTCTTCCCATCCTGTACCAAGCTGCCAGgtgtgtcatt ... tttcttgcagGAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTG
EST: gi|211016902|gb|FL048019.1|FL048019
EST:     GCGCGAGAGCATGCTCCAAGCGCTCTTCCCATCCTGTACCAAGCTGCCAG                         GAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTG
genomic: GCGCGAGAGCATGCTCCAAGCGCTCTTCCCATCCTGTACCAAGCTGCCAGgtgtgtcatt ... tttcttgcagGAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTG
EST: gi|60346823|gb|DN213796.1|DN213796
EST:     GCGCGAGAGCATGCTCCAAGCGCTCTTCCCATCCTGTACCAAGCTGCCAG                         GAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTG
genomic: GCGCGAGAGCATGCTCCAAGCGCTCTTCCCATCCTGTACCAAGCTGCCAGgtgtgtcatt ... tttcttgcagGAGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGCTG
EST: gi|149013686|gb|EE043136.2|EE043136
EST:     CGCGAGAGCATGGTCCAAGCGCTCTTCCCATTCCTGTACCAAGCTGCCAGG                         GAGGTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGC
genomic: CGCGAGAGCATGCTCCAAGCGCTCTTCCCA-TCCTGTACCAAGCTGCCA-Ggtgtgtcatt ... tttcttgcagGA-GTACTACGTTTGGTGCATCATCTTCATGCCAACGGAGTACCAATGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACGAGTGCGGCCTCAACGGCCTCCTCACCCCCGAGCAGTTCCTCGAGGAGCGCGAGAGCATGCTCCAAGCGCTCTTCCCATCCTGTACCAAGCTGCCAGgtgtgtcattgatgaacttggacgctgttggcgtcgatctgtacgccaatcactagtgtagtaccgtcttgtggtgctctctgtgaaggtgatctggacg

- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC