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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTCAGCCAGTTGGTGTTCAACAACATGTGCTCTTTCCAGTAGGGGTGGGGAGCATTTGGGTGAGAGGAAGCGAGGAATGGACCCCACATTGACAATAGgtacggtactattgcaagctaagttcattgattgggaggaggcctacatcctactaaaagtttcctctgtcatgcacctctggtgtctggtctcatgtctctgaaaattacacttcacctactctgattgaattatcaggccatcatgctaatgcccccgtttaataacattttgctttgctggtctctggacag

Basic information

species Zea mays
transcript GRMZM5G882527_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G882527_T03 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os08g42470.1 (Oryza sativa), 5'ss of exon 7
------TGCTCAGCCAGTTGGTGTTCAACAACATGTGCTCTTTCCAGTAGGGGTGGGGAGCATTTGGGTGAGAGGAAGCGAGGAATGGACCCCACATTGACAATAGgtacggtactattgcaagctaagttcattgattgggaggaggcctacatcctacta--aaagtttcctctgtcatgcacctctggtgtctggtctcatgtctctgaaaattacacttcacctactctgattgaattatcaggccatcatgctaatgcccccgtttaataacattttgctttgctggtctctggacag
      ||||||  || ||||||||||||||||||||||||||||||||||||  | |      ||   ||||      ||  || ||||||||||||||||||||||||        ||||| | ||||||||| |||| ||    |       |  | ||    | || |  |||| |     ||||    |      ||   | | | ||| |    ||||    | | |||                                                                    
AGGAGATGCTCAATCAATTGGTGTTCAACAACATGTGCTCTTTCCAGTAGGGGAAGAG------TGACAGAGAAAGCAAGAAAAAAGGACCCCACATTGACAATAGgtac--------tgcaaccaaagttcattaattgtgactttgtgagaccctgaatattggatttactactgtaaattttctcttaactgcttcttctaatatataaaagt----cttctgaaattttgaacag----------------------------------------------------------------
















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|6057016|gb|AW091421.1|AW091421
EST:     AGC-TTTGGGTGAGAAGGGAAGCGAGGAATGGACCCCACATTGACAATAG                         GAAGGAAATAATGCTGCGAGATTTGGTAGGAGCATGCACGTACCAGATGAG
genomic: AGCATTTGGGTGAG-A-GGAAGCGAGGAATGGACCCCACATTGACAATAGgtacggtact ... ctctggacagGAAGGAAATAATGCTGCGAGATTTGGTAGGAGCATGCACGTACCAGATGAG
EST: gi|86475112|gb|DY241482.1|DY241482
EST:     GGAGCATTTGGGTGAGAGGAAGCGAGGAATGGACCCCACATTGACAATAG                         GAAGGAAATAATGCTGCGAGATTTGGTAGGAGCATGCACGTACCAGATGAG
genomic: GGAGCATTTGGGTGAGAGGAAGCGAGGAATGGACCCCACATTGACAATAGgtacggtact ... ctctggacagGAAGGAAATAATGCTGCGAGATTTGGTAGGAGCATGCACGTACCAGATGAG
EST: gi|94480072|gb|EB709030.1|EB709030
EST:     GGAGCATTTGGGTGAGAGGAAGCGAGGAATGGACCCCACATTGACAATAG                         GAAGGAAATAATGCTGCGAGATTTGGTAGGAGCATGCACGTACCAGATGAG
genomic: GGAGCATTTGGGTGAGAGGAAGCGAGGAATGGACCCCACATTGACAATAGgtacggtact ... ctctggacagGAAGGAAATAATGCTGCGAGATTTGGTAGGAGCATGCACGTACCAGATGAG
EST: gi|101392951|gb|EB818406.1|EB818406
EST:     GGAGCATTTGGGTGAGAGGAAGCGAGGAATGGACCCCACATTGACAATAG                         GAAGGAAATAATGCTGCGAGATTTGGTAGGAGCATGCACGTACCAGATGAG
genomic: GGAGCATTTGGGTGAGAGGAAGCGAGGAATGGACCCCACATTGACAATAGgtacggtact ... ctctggacagGAAGGAAATAATGCTGCGAGATTTGGTAGGAGCATGCACGTACCAGATGAG
EST: gi|78024412|gb|DV492799.1|DV492799
EST:     GGAGCATTTGGGTGAGAGGAAGCGAGGAATGGACCCCACATTGACAATAG                         GAAGGAAATAATGCTGCGAGATTTGGTAGGAGCATGCACGTACCAGATGAG
genomic: GGAGCATTTGGGTGAGAGGAAGCGAGGAATGGACCCCACATTGACAATAGgtacggtact ... ctctggacagGAAGGAAATAATGCTGCGAGATTTGGTAGGAGCATGCACGTACCAGATGAG
EST: gi|60342009|gb|DN208982.1|DN208982
EST:     GGAGCATTTGGGTGAGAGGAAGCGAGGAATGGACCCCACATTGACAATAG                         GAAGGAAATAATGCTGCGAGATTTGGTAGGAGCATGCACGTACCAGATGAG
genomic: GGAGCATTTGGGTGAGAGGAAGCGAGGAATGGACCCCACATTGACAATAGgtacggtact ... ctctggacagGAAGGAAATAATGCTGCGAGATTTGGTAGGAGCATGCACGTACCAGATGAG
EST: gi|71760000|gb|DR957937.1|DR957937
EST:     GGAGCATTTGGGTGAGAGGAAGCGAGGAATGGACCCCACATTGACAATAG                         GAAGGAAATAATGCTGCGAGATTTGGTAGGAGCATGCACGTACCAGATGAG
genomic: GGAGCATTTGGGTGAGAGGAAGCGAGGAATGGACCCCACATTGACAATAGgtacggtact ... ctctggacagGAAGGAAATAATGCTGCGAGATTTGGTAGGAGCATGCACGTACCAGATGAG
EST: gi|14243392|gb|BG841045.2|BG841045
EST:     GGAGCATTTGGGTGAGAGGAAGCGAGGAATGGACCCCACATTGACAATAG                         GAAGGAAATAATGCTGCGAGATTTGGTAGGAGCATGCACGTACCAGATGAG
genomic: GGAGCATTTGGGTGAGAGGAAGCGAGGAATGGACCCCACATTGACAATAGgtacggtact ... ctctggacagGAAGGAAATAATGCTGCGAGATTTGGTAGGAGCATGCACGTACCAGATGAG
EST: gi|91869215|gb|EB400298.1|EB400298
EST:     GGAGCATTTGGGTGAGAGGAAGCGAGGAATGGACCCCACATTGACAATAG                         GAAGGAAATAATACTGCGAGATTTGGTAGGAGCATGCACGTCCCAGAGGAG
genomic: GGAGCATTTGGGTGAGAGGAAGCGAGGAATGGACCCCACATTGACAATAGgtacggtact ... ctctggacagGAAGGAAATAATGCTGCGAGATTTGGTAGGAGCATGCACGTACCAGATGAG
EST: gi|74243762|gb|DT651676.1|DT651676
EST:     GGAGCATTTGGGTGAGAGGAAGCGAGGAATGGACCCCACATTGACAATAG                         GAAGGAAATAATGCTGCGAGATTTGGTAGGAGCATGCACGTACCAGATGAG
genomic: GGAGCATTTGGGTGAGAGGAAGCGAGGAATGGACCCCACATTGACAATAGgtacggtact ... ctctggacagGAAGGAAATAATGCTGCGAGATTTGGTAGGAGCATGCACGTACCAGATGAG
EST: gi|71769016|gb|DR966953.1|DR966953
EST:     GGAGCATTTGGGTGAGAGGAAGCGAGGAATGGACCCCACATTGACAATAG                         GAAGGAAATAATGCTGCGAGATTTGGTAGGAGCATGCACGTACCAGATGAG
genomic: GGAGCATTTGGGTGAGAGGAAGCGAGGAATGGACCCCACATTGACAATAGgtacggtact ... ctctggacagGAAGGAAATAATGCTGCGAGATTTGGTAGGAGCATGCACGTACCAGATGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTCAGCCAGTTGGTGTTCAACAACATGTGCTCTTTCCAGTAGGGGTGGGGAGCATTTGGGTGAGAGGAAGCGAGGAATGGACCCCACATTGACAATAGgtacggtactattgcaagctaagttcattgattgggaggaggcctacatcctactaaaagtttcctctgtcatgcacctctggtgtctggtctcatgtctctgaaaattacacttcacctactctgattgaattatcaggccatcatgctaatgcccccgtttaataacattttgctttgctggtctctggacag

- - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA