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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgactttcaccatgacagcagtatgctttcacatgctgtgttggtttattctatggttacccttatttgcaggtttcccttgcgtctcatttggttacccttatttgcagGTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACTTCCAGCTTTGGTTACGATTACTTGCTTAGGCAG

Basic information

species Zea mays
transcript GRMZM2G043983_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G043983_T03 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g20750.1 (Oryza sativa), 3'ss of exon 8
gttgactttcaccatgacagcagtatgctttcacatgctgtgttggtttattctatggttacccttatttgcagGTTTCCCTTGCGTCTCATTTGGTTACCCTTATTTGCAGGTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACTTCCAGCTTTGGTTACGATTACTTGCTTAGGCAG
                      ||| |    |||            | | ||| |  |        | || ||   ||   ||   ||| |||         |  | |||||||||||||||||||||| ||||||||||| || |||||||| ||||| ||||||||||||||||| || ||  |||||||||||
----------------------gtagggccccaccaagaccaccattattttcaacaga-------agtttcacactttattttaatctgattgtaaggatatggtatgcagGTTTCCCTTGCGTCTGACTTCATGTATAATCACATGTCAAGGGACGTTACTTCCAGCTTTGGTTATGACTATATGCTTAGGCAG
















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|32911846|gb|CF016658.1|CF016658
EST:     CAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGTA-                         GTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACT
genomic: CAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGAAGgttgactttc ... ttatttgcagGTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACT
EST: gi|149065576|gb|EE286698.2|EE286698
EST:     CAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGAAG                         GTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACT
genomic: CAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGAAGgttgactttc ... ttatttgcagGTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACT
EST: gi|211255903|gb|FL358694.1|FL358694
EST:     CAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGAAG                         GTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACT
genomic: CAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGAAGgttgactttc ... ttatttgcagGTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACT
EST: gi|76280767|gb|DV020335.1|DV020335
EST:     CAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGAAG                         GTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACT
genomic: CAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGAAGgttgactttc ... ttatttgcagGTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACT
EST: gi|113702734|gb|EE680238.1|EE680238
EST:     CAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGAAG                         GTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACT
genomic: CAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGAAGgttgactttc ... ttatttgcagGTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACT
EST: gi|32867645|gb|CF007327.1|CF007327
EST:     CAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGAAG                         GTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACT
genomic: CAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGAAGgttgactttc ... ttatttgcagGTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACT
EST: gi|78025625|gb|DV494012.1|DV494012
EST:     CCAGAAGATTTCTGAGAAG                         GTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACT
genomic: CCAGAAGATTTCTGAGAAGgttgactttc ... ttatttgcagGTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACT
EST: gi|76016907|gb|DT944077.1|DT944077
EST:     CAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGAAG                         GTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACT
genomic: CAAGCACTGGAATAGTTGCCTTAAGTTATGTCCAGAAGATTTCTGAGAAGgttgactttc ... ttatttgcagGTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttacccttatttgcaggtttcccttgcgtctcatttggttacccttatttgcagGTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACTTCCAGCTTTGGTTACGATTACTTGCTTAGGCAG
                                          cccttattt  CT-rich tract
       ttattt  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
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgactttcaccatgacagcagtatgctttcacatgctgtgttggtttattctatggttacccttatttgcaggtttcccttgcgtctcatttggttacccttatttgcagGTTTCCCTTGCGTCTGATTTCATGTATAACCATATGTCAAGAGACGTAACTTCCAGCTTTGGTTACGATTACTTGCTTAGGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA