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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actatttttgcttgctagcttctgcactgattagaatcttggttgtcacttgtcagtggttccagagttctttgtttgtaagatttctgatgtcatgcagATGCAAACAAGAACCTACGTCTTGGTTCTGGGATTCTTATTGCAGTACCGATCCCCAAGCAGCATGCAACTTCAGGGAAAATTATAGAGTCTGCAATACA

Basic information

species Zea mays
transcript GRMZM2G126517_T01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G126517_T01 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os08g39420.1 (Oryza sativa), 3'ss of exon 8
--actatttttgcttgctagcttctgca--ctgattagaatcttggtt-gtcacttgtcagtggtt-ccagagttctttgtttgtaagatttctgatgtcatgcagATGCAAACAAGAACCTACGTCTTGGTTCTGGGATTCTTATTGCAGTACCGATCCCCAAGCAGCATGCAACTTCAGGGAAAATTATAGAGTCTGCAATACA
     |||||  | |   |  | ||  |     | | |||      ||  |       ||| | ||  |||  ||  |  ||| ||     ||| || |  | ||||||||||||||||  ||| ||| || ||||||||| | ||||| || ||||| |||||| | |||||| ||||||| ||   ||||||||||||||||||
gtttgattttatcctatgaattactataactcaactggaaaaagaatttattgtaacacagagtttatcagcattgctgatttata-----tct-attttttacagATGCAAACAAGAATTTACATCTAGGATCTGGGATTTTGATTGCTGTGCCGATTCCCAAGGAACATGCAGCTTCAGGAAATGCTATAGAGTCTGCAATACA
















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|67038503|gb|CO464823.1|CO464823
EST:     GTGCCATGTCGTGTTGATTCTCCAGAAGAGTGTGCCAAAATAATAT                         ATGCAAACAAGAACCTACGTCTTGGTTCTGGGATTTCT-ATTGCAGTACCG
genomic: GTGCCATGTCGTGTTGATTCTCCAGAAGAGTGTGCCAAAATAATATgtgagtagta ... tgtcatgcagATGCAAACAAGAACCTACGTCTTGGTTCTGGGATT-CTTATTGCAGTACCG
EST: gi|149082843|gb|EE172069.2|EE172069
EST:     GTGCCATGTCGTGTTGATTCTCCAGAAGAGTGTGCCAAAATAATAT                         ATGCAAACAAGAACCTACGTCTTGGTTCTGGGATTCTTATTGCAGTACCGA
genomic: GTGCCATGTCGTGTTGATTCTCCAGAAGAGTGTGCCAAAATAATATgtgagtagta ... tgtcatgcagATGCAAACAAGAACCTACGTCTTGGTTCTGGGATTCTTATTGCAGTACCGA
EST: gi|149015839|gb|EE045506.2|EE045506
EST:     GTGCCATGTCGTGTTGATTCTCCAGAAGAGTGTGCCAAAATAATAT                         ATGCAAACAAGAACCTACGTCTTGGTTCTGGGATTCTTATTGCAGTACCGA
genomic: GTGCCATGTCGTGTTGATTCTCCAGAAGAGTGTGCCAAAATAATATgtgagtagta ... tgtcatgcagATGCAAACAAGAACCTACGTCTTGGTTCTGGGATTCTTATTGCAGTACCGA
EST: gi|31355893|gb|CD440250.1|CD440250
EST:     GTGCCATGTCGTGTTGATTCTCCAGAAGAGTGTGCCAAAATAATAT                         ATGCAAANCA-GAACCTACGTCTTGGTTCTGGGATTCTTATTGCAGTACCG
genomic: GTGCCATGTCGTGTTGATTCTCCAGAAGAGTGTGCCAAAATAATATgtgagtagta ... tgtcatgcagATGCAAA-CAAGAACCTACGTCTTGGTTCTGGGATTCTTATTGCAGTACCG
EST: gi|71764026|gb|DR961963.1|DR961963
EST:     GTGCCATGTCGTGTTGATTCTCCAGAAGAGTGTGCCAAAATAATAT                         ATGCAAACAAGAACCTACGTCTTGGTTCTGGGATTCTTATTGCAGTACCGA
genomic: GTGCCATGTCGTGTTGATTCTCCAGAAGAGTGTGCCAAAATAATATgtgagtagta ... tgtcatgcagATGCAAACAAGAACCTACGTCTTGGTTCTGGGATTCTTATTGCAGTACCGA
EST: gi|88748923|gb|DY533064.1|DY533064
EST:     GTGCCATGTCGTGTTGATTCTCCAGAAGAGTGTGCCAAAATAATAT                         ATGCAAACAAGAACCTACGTCTTGGTTCTGGGATTCTTATTGCAGTACCGA
genomic: GTGCCATGTCGTGTTGATTCTCCAGAAGAGTGTGCCAAAATAATATgtgagtagta ... tgtcatgcagATGCAAACAAGAACCTACGTCTTGGTTCTGGGATTCTTATTGCAGTACCGA
EST: gi|74236391|gb|DT644305.1|DT644305
EST:     GTGCCATGTCGTGTTGATTCTCCAGAAGAGTGTGCCAAAATAATAT                         ATGCAAACAAGAACCTACGTCTTGGTTCTGGGATTCTTATTGCAGTACCGA
genomic: GTGCCATGTCGTGTTGATTCTCCAGAAGAGTGTGCCAAAATAATATgtgagtagta ... tgtcatgcagATGCAAACAAGAACCTACGTCTTGGTTCTGGGATTCTTATTGCAGTACCGA
EST: gi|149082842|gb|EE172068.2|EE172068
EST:     GTGCCATGTCGTGTTGATTCTCCAGAAGAGTGTGCCAAAATAATAT                         ATGCAAACAAGAACCTACGTCTTGGTTCTGGGATTCTTATTGCAGTACCGA
genomic: GTGCCATGTCGTGTTGATTCTCCAGAAGAGTGTGCCAAAATAATATgtgagtagta ... tgtcatgcagATGCAAACAAGAACCTACGTCTTGGTTCTGGGATTCTTATTGCAGTACCGA
EST: gi|31355559|gb|CD439916.1|CD439916
EST:     GTGCCATGTCGTGTTGATTCTCCAGAAGAGTGTGCCAAAATAATAT                         ATGCAAACAAGAACCTACGTCTTGGTTCTGGGATTCTTATTGCAGTACCGA
genomic: GTGCCATGTCGTGTTGATTCTCCAGAAGAGTGTGCCAAAATAATATgtgagtagta ... tgtcatgcagATGCAAACAAGAACCTACGTCTTGGTTCTGGGATTCTTATTGCAGTACCGA
EST: gi|71764027|gb|DR961964.1|DR961964
EST:     GTGCCATGTCGTGTTGATTCTCCAGAAGAGTGTGCCAAAATAATAT                         ATGCAAACAAGAACCTACGTCTTGGTTCTGGGATTCTTATTGCAGTACCGA
genomic: GTGCCATGTCGTGTTGATTCTCCAGAAGAGTGTGCCAAAATAATATgtgagtagta ... tgtcatgcagATGCAAACAAGAACCTACGTCTTGGTTCTGGGATTCTTATTGCAGTACCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcacttgtcagtggttccagagttctttgtttgtaagatttctgatgtcatgcagATGCAAACAAGAACCTACGTCTTGGTTCTGGGATTCTTATTGCAGTACCGATCCCCAAGCAGCATGCAACTTCAGGGAAAATTATAGAGTCTGCAATACA
                                       ttctgat  putative branch site (score: 3)
                                 taagattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actatttttgcttgctagcttctgcactgattagaatcttggttgtcacttgtcagtggttccagagttctttgtttgtaagatttctgatgtcatgcagATGCAAACAAGAACCTACGTCTTGGTTCTGGGATTCTTATTGCAGTACCGATCCCCAAGCAGCATGCAACTTCAGGGAAAATTATAGAGTCTGCAATACA

- - - - tgcttgc
- - - - - - - - -gcttctg
- - - - - - - - - - - - -actgatt
- - - - - - - - - - - - - - - - - - - ttggttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttctga