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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATCGGTGATTATACTACTCAATACCGTGTACCGTGATCGGAACTACGCCAGGTTTTTTGTGCTGGAGACGATTGCCAGGGTGCCGTATTTCGgtgagggctccgttttgtcatatgcttgcagttgcggtgtatgaaaaggtccctaaagagttttgcagcgttggtttcggtcgtgccgttgctgttctttcttttttactctgcttggttatgaacag

Basic information

species Zea mays
transcript GRMZM2G102349_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102349_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os04g57320.1 (Oryza sativa), 5'ss of exon 3
GAATCGGTGATTATACTACTCAATACCGTGTACCGTGATCGGAACTACGCCAGGTTTTTTGTGCTGGAGACGATTGCCAGGGTGCCGTATTTCGgtgagggctccgttttgt-catatgcttgcagttgcggtgtatgaaaaggtccctaaagagttttgcagcgttggtttcg-gtcgtgccgttgctgttctttcttttttactctgcttggttat-gaacag
|| || || || |   ||||  ||    |||||||||| || |||||||| || ||||| ||  ||||||||||||| |||||||||||||| |||||||    ||| ||        |||   |  ||| | || |   ||  || | | |      |   |          |    || | ||| | |||  |  ||   |   |||| ||  ||| ||||||
GAGTCAGTCATCACGATACTTGATGGATTGTACCGTGACCGCAACTACGCTAGATTTTTCGTATTGGAGACGATTGCTAGGGTGCCGTATTTTGgtgaggatctcgtcttacatgctcgctataacctgcag-gtctctgaatttcgcaatatgcaagtatggttcctacacagtactgtactgtttcagttactgtttcactga-ctgcctgactattgaacag

upper sequence: GRMZM2G102349_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g63010.2 (Oryza sativa), 5'ss of exon 2
GAATCGGTGATTATACTACTCAATACCGTGTACCGTGATCGGAACTACGCCAGGTTTTTTGTGCTGGAGACGATTGCCAGGGTGCCGTATTTCGgtgagggctccgttttgtcatatgcttgcagttgcggtgtatgaaaaggtccctaaagagttttgcagcgttggtttcggtcgtgccgttgctgttctttcttttttact--ctgcttggttat-gaacag
                                |||||| || |||||||| || ||||| ||  ||||||||||||| |||||||||||||| |||||||    |||  |   | ||||| ||  | ||  || | |     |    | |  |  | | ||    ||||| |   |       || |    || || ||| |||  |||| ||  ||| ||||||
--------------------------------CCGTGACCGCAACTACGCTAGATTTTTCGTCTTGGAGACGATTGCTAGGGTGCCGTATTTTGGTGAGGATCTCGTCGT---ACATGCTCGCTATAGCC-TGCAGgtctctgaatttcacaa--tatacaagtatggttccta-cacagtaatgtttcggttactgtttcactgactgcctgactattgaacag
















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|149101185|gb|EE187296.2|EE187296
EST:     CTACGCCAGGTTTTTTGTGCTGGAGACGATTGCCAGGGTGCCGTATTTCG                         CGTTCATATCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGACGAG
genomic: CTACGCCAGGTTTTTTGTGCTGGAGACGATTGCCAGGGTGCCGTATTTCGgtgagggctc ... ttatgaacagCGTTCATATCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGACGAG
EST: gi|148980796|gb|EE027352.2|EE027352
EST:     CTACGCCAGGTTTTTTGTGCTGGAGACGATTGCCAGGGTGCCGTATTTCG                         CGTTCATATCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGACGAG
genomic: CTACGCCAGGTTTTTTGTGCTGGAGACGATTGCCAGGGTGCCGTATTTCGgtgagggctc ... ttatgaacagCGTTCATATCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGACGAG
EST: gi|91048932|gb|EB159350.1|EB159350
EST:     CTACGCCAGGTTTTTTGTGCTGGAGACGATTGCCAGGGTGCCGTATTTCG                         CGTTCATATCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGACGAG
genomic: CTACGCCAGGTTTTTTGTGCTGGAGACGATTGCCAGGGTGCCGTATTTCGgtgagggctc ... ttatgaacagCGTTCATATCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGACGAG
EST: gi|91871244|gb|EB401317.1|EB401317
EST:     CTACGCCAGGTTTTTTGTGCTGGAGACGATTGCCAGGGTGCCGTATTTCG                         CGTTCATATCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGACGAG
genomic: CTACGCCAGGTTTTTTGTGCTGGAGACGATTGCCAGGGTGCCGTATTTCGgtgagggctc ... ttatgaacagCGTTCATATCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGACGAG
EST: gi|148999937|gb|EE036995.2|EE036995
EST:     CTACGCCAGGTTTTTTGTGCTGGAGACGATTGCCAGGGTGCCGTATTTCG                         CGTTCATATCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGACGAG
genomic: CTACGCCAGGTTTTTTGTGCTGGAGACGATTGCCAGGGTGCCGTATTTCGgtgagggctc ... ttatgaacagCGTTCATATCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGACGAG
EST: gi|78116562|gb|DV534949.1|DV534949
EST:     CTACGCCAGGTTTTTTGTGCTGGAGACGATTGCCAGGGTGCCGTATTTCG                         CGTTCATATCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGACGAG
genomic: CTACGCCAGGTTTTTTGTGCTGGAGACGATTGCCAGGGTGCCGTATTTCGgtgagggctc ... ttatgaacagCGTTCATATCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGACGAG
EST: gi|76018164|gb|DT945334.1|DT945334
EST:     CTACGCCAGGTTTTTTGTGCTGGAGACGATTGCCAGGGTGCCGTATTTCG                         CGTTCATATCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGACGAG
genomic: CTACGCCAGGTTTTTTGTGCTGGAGACGATTGCCAGGGTGCCGTATTTCGgtgagggctc ... ttatgaacagCGTTCATATCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGACGAG
EST: gi|149080867|gb|EE169947.2|EE169947
EST:     CTACGCCAGGTTTTTTGTGCTGGAGACGATTGCCAGGGTGCCGTATTTCG                         CGTTCATATCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGACGAG
genomic: CTACGCCAGGTTTTTTGTGCTGGAGACGATTGCCAGGGTGCCGTATTTCGgtgagggctc ... ttatgaacagCGTTCATATCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGACGAG
EST: gi|60357246|gb|DN224219.1|DN224219
EST:     CTACGCCAGGTTTTTTGTGCTGGAGACGATTGCCAGGGTGCCGTATTTCG                         CGTTCATATCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGACGAG
genomic: CTACGCCAGGTTTTTTGTGCTGGAGACGATTGCCAGGGTGCCGTATTTCGgtgagggctc ... ttatgaacagCGTTCATATCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGACGAG
EST: gi|89759812|gb|DY688510.1|DY688510
EST:     CTACGCCAGGTTTTTTGTGCTGGAGACGATTGCCAGGGTGCCGTATTTCG                         CGTTCATATCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGACGAG
genomic: CTACGCCAGGTTTTTTGTGCTGGAGACGATTGCCAGGGTGCCGTATTTCGgtgagggctc ... ttatgaacagCGTTCATATCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGACGAG
EST: gi|148952083|gb|EC897874.2|EC897874
EST:     CTACGCCAGGTTTTTTGTGCTGGAGACGATTGCCAGGGTGCCGTATTTCG                         CGTTCATATCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGACGAG
genomic: CTACGCCAGGTTTTTTGTGCTGGAGACGATTGCCAGGGTGCCGTATTTCGgtgagggctc ... ttatgaacagCGTTCATATCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGACGAG
EST: gi|78116561|gb|DV534948.1|DV534948
EST:     CTACGCCAGGTTTTTTGTGCTGGAGACGATTGCCAGGGTGCCGTATTTCG                         CGTTCATATCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGACGAG
genomic: CTACGCCAGGTTTTTTGTGCTGGAGACGATTGCCAGGGTGCCGTATTTCGgtgagggctc ... ttatgaacagCGTTCATATCGGTGCTTCACATGTATGAAACCTTTGGCTGGTGGAGACGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAATCGGTGATTATACTACTCAATACCGTGTACCGTGATCGGAACTACGCCAGGTTTTTTGTGCTGGAGACGATTGCCAGGGTGCCGTATTTCGgtgagggctccgttttgtcatatgcttgcagttgcggtgtatgaaaaggtccctaaagagttttgcagcgttggtttcggtcgtgccgttgctgttctttcttttttactctgcttggttatgaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA