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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacggtactattgcaagctaagttcattgattgggaggaggcctacatcctactaaaagtttcctctgtcatgcacctctggtgtctggtctcatgtctctgaaaattacacttcacctactctgattgaattatcaggccatcatgctaatgcccccgtttaataacattttgctttgctggtctctggacagGAAGGAAATAATGCTGCGAGATTTGGTAGGAGCATGCACGTACCAGATGAGTTTGAGATGTTGGATCTAGTCCATCCCCTTGTCTGGATTTGGAGAGAGC

Basic information

species Zea mays
transcript GRMZM5G882527_T04
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G882527_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os08g42470.1 (Oryza sativa), 3'ss of exon 7
gtacggtactattgcaagctaagttcattgattgggaggaggcctacatcctactaaaagtttcctctgtcatgcacctctggtgtctggtctcatgtctctgaaaattacacttcacctactctgattgaattatcaggccatcatgctaatgcccccgtttaataacattttgctttgctggtctctggacagGAAGGAA--ATAATGCTGCGAGATTTGGTAGGAGCATGCA-CGTACCAGATGAGTTTGAGATGTTGGATCTAGTCCATCCCCTTGTCTGGATTTGGAGAGAGC
                                                             | |  |     | ||    | ||| ||  |     | | ||||| |||  | ||   ||||| | | |    | | |     |  | |||||       | ||| |   || ||           | || |||||| | ||  |||||||||| ||||| ||||||||||||||  | ||||||| |||||||||||||||||||||||||||||||||||||||    |       
---------------------------------------------------------gtactgcaaccaaagttcattaattgtgact--ttgtgagaccctgaatattggattta--ctactgtaaattttctcttaactgcttcttctaata------tataaaagtcttctg-------aaattttgaacagGAGGAAATAATAATGCTGCAAGATT-GGTAGGAGCATGCAATGCACCAGATAAGTTTGAGATGTTGGATCTAGTCCATCCCCTTGTCTGGAGGCAGTCTAC--
















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|78083553|gb|DV511946.1|DV511946
EST:     GGAGCATTTGGGTGAGAGGAAGCGAGGAATGGACCCCACATTGACAATAG                         GAAGGAAATAATGCTGCGAGATTTGGTAGGAGCATGCACGTACCAGATGAG
genomic: GGAGCATTTGGGTGAGAGGAAGCGAGGAATGGACCCCACATTGACAATAGgtacggtact ... ctctggacagGAAGGAAATAATGCTGCGAGATTTGGTAGGAGCATGCACGTACCAGATGAG
EST: gi|94480072|gb|EB709030.1|EB709030
EST:     GGAGCATTTGGGTGAGAGGAAGCGAGGAATGGACCCCACATTGACAATAG                         GAAGGAAATAATGCTGCGAGATTTGGTAGGAGCATGCACGTACCAGATGAG
genomic: GGAGCATTTGGGTGAGAGGAAGCGAGGAATGGACCCCACATTGACAATAGgtacggtact ... ctctggacagGAAGGAAATAATGCTGCGAGATTTGGTAGGAGCATGCACGTACCAGATGAG
EST: gi|86475112|gb|DY241482.1|DY241482
EST:     GGAGCATTTGGGTGAGAGGAAGCGAGGAATGGACCCCACATTGACAATAG                         GAAGGAAATAATGCTGCGAGATTTGGTAGGAGCATGCACGTACCAGATGAG
genomic: GGAGCATTTGGGTGAGAGGAAGCGAGGAATGGACCCCACATTGACAATAGgtacggtact ... ctctggacagGAAGGAAATAATGCTGCGAGATTTGGTAGGAGCATGCACGTACCAGATGAG
EST: gi|71760000|gb|DR957937.1|DR957937
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|78024412|gb|DV492799.1|DV492799
EST:     GGAGCATTTGGGTGAGAGGAAGCGAGGAATGGACCCCACATTGACAATAG                         GAAGGAAATAATGCTGCGAGATTTGGTAGGAGCATGCACGTACCAGATGAG
genomic: GGAGCATTTGGGTGAGAGGAAGCGAGGAATGGACCCCACATTGACAATAGgtacggtact ... ctctggacagGAAGGAAATAATGCTGCGAGATTTGGTAGGAGCATGCACGTACCAGATGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatcatgctaatgcccccgtttaataacattttgctttgctggtctctggacagGAAGGAAATAATGCTGCGAGATTTGGTAGGAGCATGCACGTACCAGATGAGTTTGAGATGTTGGATCTAGTCCATCCCCTTGTCTGGATTTGGAGAGAGC
                      taataac  putative branch site (score: 1)
                                            tctct  putative PPT
                    tttaataacatttt  TA-rich tract
















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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacggtactattgcaagctaagttcattgattgggaggaggcctacatcctactaaaagtttcctctgtcatgcacctctggtgtctggtctcatgtctctgaaaattacacttcacctactctgattgaattatcaggccatcatgctaatgcccccgtttaataacattttgctttgctggtctctggacagGAAGGAAATAATGCTGCGAGATTTGGTAGGAGCATGCACGTACCAGATGAGTTTGAGATGTTGGATCTAGTCCATCCCCTTGTCTGGATTTGGAGAGAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA