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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTCCGGGCTTCTTCTAAGGGTTTGACACTAGAGCTTTGTCGGTGGATTGGCAAAGACCCTGTAAAGTCTATTTTATTTGAGAAGATGAGAGATACTATGgtgcgttattttttcaaaattttaacatgtgtaattctgttctatcactcaataaaataaccaatattctttgtgtttacag

Basic information

species Zea mays
transcript GRMZM2G068755_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G068755_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g60040.2 (Oryza sativa), 5'ss of exon 5
TGTCCGGGCTTCTTCTAAGGGTTTGACACTAGAGCTTTGTCGGTGGATTGGCAAAGACCCTGTAAAGTCTATTTTATTTGAGAAGATGAGAGATACTATGgtgcgttattt--tttcaaaattttaa-----catgtgtaattc-------tgttctatcactcaataaaataaccaatattctttgtgtttacag
||| |||||||| || |||||||||||||| |||||||||||||||||||||||||| ||||||||| | |||||||||||||||||||||||||| ||||| |  |||||  |  ||     |||      ||||   |  |        ||| |  |  || ||||  |||| ||   || ||  |||||  ||
TGTTCGGGCTTCATCCAAGGGTTTGACACTTGAGCTTTGTCGGTGGATTGGCAAAGAGCCTGTAAAGGCAATTTTATTTGAGAAGATGAGAGATACAATGgtacaatatttcataccaggccattagagcagcatgcacacattgatcatatgtaccttgcctgaatagtataatcacacttattcctgtttgtag

upper sequence: GRMZM2G068755_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g60050.1 (Oryza sativa), 5'ss of exon 5
TGTCCGGGCTTCTTCTAAGGGTTTGACACTAGAGCTTTGTCGGTGGATTGGCAAAGACCCTGTAAAGTCTATTTTATTTGAGAAGATGAGAGATACTATGgtgcgttatttt-ttcaaaattttaacatgtgtaattctgttctatcactcaataaaataaccaatattctttgtgtttacag
||| ||||||||||| |||||||||||| | ||||||||| |||||||||||||||| ||||||||| | ||||||||||||||||| || ||||  |||||  | |||||  | | | |   | ||   ||    | | | | ||  |   |||  | || ||   ||| || |||||  ||
TGTTCGGGCTTCTTCCAAGGGTTTGACAGTTGAGCTTTGTTGGTGGATTGGCAAAGAGCCTGTAAAGGCAATTTTATTTGAGAAGATTAGGGATATGATGgtaggatatttcataccagaccattac---tgatcatatataccat-gcgtgatagtacaagcacacttcgttctgtttgtag

upper sequence: GRMZM2G068755_T03 (Zea mays), 5'ss of exon 5
lower sequence: AT2G35630.1 (Arabidopsis thaliana), 5'ss of exon 5
TGTCCGGGCTTCTTCTAAGGGTTTGACACTAGAGCTTTGTCGGTGGATTGGCAAAGACCCTGTAAAGTCTATTTTATTTGAGAAGATGAGAGATACTATGgtgcgttattttttcaaaattttaacatgtgtaattctgttctatcactcaataaa-ataacc-------aatattctttgtgtttacag-------------
|||||| || ||| | || ||  |||| || ||||| || || |||||||| |||||||||||||||||||| || ||||| || ||||| ||||| |||||  | | | | ||    |     |||| || || |  | | |    |  | |  | || | |       |||  ||||  | |||   |             
TGTCCGTGCATCTGCCAAAGGAGTGACTCTTGAGCTATGCCGTTGGATTGGAAAAGACCCTGTAAAGTCTATATTGTTTGAAAAAATGAGGGATACGATGgtaagatttatgtt---gagccgcacatttgcaacttagctatgctgccaagttgatatgaactggattaaatcctcttgatttttcttggaattggaaaact

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|211517040|gb|FL438272.1|FL438272
EST:     GCAAAGACCCTGTAAAGTCTATTTTATTTGAGAAGATGAGAGATACTATG                         AAAAAGGAGTTGGAAGCAGAGTTGGCAAATGTGTCCGGACTTGCTAAGCCA
genomic: GCAAAGACCCTGTAAAGTCTATTTTATTTGAGAAGATGAGAGATACTATGgtgcgttatt ... gtgtttacagAAAAAGGAGTTGGAAGCAGAGTTGGCAAATGTGTCCGGACTTGCTAAGCCA
EST: gi|71441120|gb|DR822170.1|DR822170
EST:     GCAAAGACCCTGTAAAGTCTATTTTATTTGAGAAGATGAGAGATACTATG                         AAAAAGGAGTTG
genomic: GCAAAGACCCTGTAAAGTCTATTTTATTTGAGAAGATGAGAGATACTATGgtgcgttatt ... gtgtttacagAAAAAGGAGTTG
EST: gi|18963448|gb|BM660440.1|BM660440
EST:     GCAAAGCCCCTGTAAAGTCTATTTTATTTGAGAAGATGAGAGATACTATG                         AAAAAGGAGTTGGAAGCAGAGTTGGCAAATGTGTCCGGACTTGCTAAGCCA
genomic: GCAAAGACCCTGTAAAGTCTATTTTATTTGAGAAGATGAGAGATACTATGgtgcgttatt ... gtgtttacagAAAAAGGAGTTGGAAGCAGAGTTGGCAAATGTGTCCGGACTTGCTAAGCCA
EST: gi|32934909|gb|CF039721.1|CF039721
EST:     GCAAAGACCCTGTAAAGTCTATTTTATTTGAGAAGATGAGAGATACTATG                         AAAAAGGAGTTGGAAGCAGAGTTGGCAAATGTGTCCGGACTTGCTAAGCCA
genomic: GCAAAGACCCTGTAAAGTCTATTTTATTTGAGAAGATGAGAGATACTATGgtgcgttatt ... gtgtttacagAAAAAGGAGTTGGAAGCAGAGTTGGCAAATGTGTCCGGACTTGCTAAGCCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTCCGGGCTTCTTCTAAGGGTTTGACACTAGAGCTTTGTCGGTGGATTGGCAAAGACCCTGTAAAGTCTATTTTATTTGAGAAGATGAGAGATACTATGgtgcgttattttttcaaaattttaacatgtgtaattctgttctatcactcaataaaataaccaatattctttgtgtttacag

- - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG