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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttttaattttcacttatatgttgcaatttatttttgtctatattgcaataaatatatttccaatttctggtatatttaattttacttattcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCG

Basic information

species Zea mays
transcript GRMZM5G866758_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G866758_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os09g07830.1 (Oryza sativa), 3'ss of exon 6
cttttaattttcacttatatgttgcaatttatttttgtctatattgcaataaatatatttccaatttctggtatatttaa--ttttacttattcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCG
|   | ||   || | || ||||| ||| | | | | | ||  ||| |||| ||||||||   |||  |   |||| | |  ||||| | ||||||  ||||||||| | |||||| |||||||| ||||||||||||||||||||  |||||||||||||||||||||||||| |||||
ccggtgatca-cattgatttgttgtaatatttctat-tatactttgtaatacatatatttatcattagtaacatatctgatattttaataattcttctatagGATGCCTATGCTATTCAAAGCAATGAGCGTGGAATTGCTGCTCGGAACAGTGGTGCTTTTGCATGGGAGATTGTTCCG
















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|78087735|gb|DV516128.1|DV516128
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|148999650|gb|EE036638.2|EE036638
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|20300202|gb|BQ163145.1|BQ163145
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|149017000|gb|EE045657.2|EE045657
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|18661821|gb|BM501596.1|BM501596
EST:     CAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: CAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|76284260|gb|DV023828.1|DV023828
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|22490495|gb|BU050418.1|BU050418
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|32864391|gb|CF004073.1|CF004073
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAA
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAA
EST: gi|149081077|gb|EE170177.2|EE170177
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|18450558|gb|BM428836.1|BM428836
EST:     CAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: CAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|148983224|gb|EE029187.2|EE029187
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|18654813|gb|BM499618.1|BM499618
EST:     CAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: CAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|87152006|gb|DY396795.1|DY396795
EST:     CAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: CAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|148965993|gb|EE016923.2|EE016923
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|20300665|gb|BQ163608.1|BQ163608
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|149009773|gb|EE041672.2|EE041672
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|211292808|gb|FL187022.1|FL187022
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|19821841|gb|BQ047865.1|BQ047865
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|22490486|gb|BU050409.1|BU050409
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|89106507|gb|DY576724.1|DY576724
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|76017959|gb|DT945129.1|DT945129
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAA                         GATGCATTTGCTATCC
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCC
EST: gi|71327673|gb|DR800451.1|DR800451
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGGTGGA-TTGCTGCTCGTGACAG
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCG-TGGAATTGCTGCTCGTGACAG
EST: gi|19770473|gb|BQ035194.1|BQ035194
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|31353258|gb|CD437615.1|CD437615
EST:     TGTGTGCCGAGCTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAATGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|78091716|gb|DV520090.1|DV520090
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|20300437|gb|BQ163380.1|BQ163380
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|67042602|gb|CO468857.1|CO468857
EST:     TGTGTGCCGAGCTTTGTGCTGACAATCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|19058058|gb|BM736725.1|BM736725
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAAT
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|76921562|gb|DV168618.1|DV168618
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
EST: gi|50324587|gb|CO519713.1|CO519713
EST:     TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAG                         GATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT
genomic: TGTGTGCCGAGCTTTGTGCTGACAACCATGCCCTCACAAGAGAAGACCAGgtctcttaat ... tcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaataaatatatttccaatttctggtatatttaattttacttattcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCG
                             atttaat  putative branch site (score: 4)
                                   ttttacttattctt  CT-rich tract
     aaatatatttccaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttttaattttcacttatatgttgcaatttatttttgtctatattgcaataaatatatttccaatttctggtatatttaattttacttattcttgaatagGATGCATTTGCTATCCAAAGCAACGAGCGTGGAATTGCTGCTCGTGACAGTGGTGCTTTTGCATGGGAGATTATTCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT