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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtcacacttacaatcttagccagcttgccccactaggtatataaaggtattgctctatcctaacttctgaagcatgcatactattttctgctgatcttagATCCCAACAACAAGAGCTCGATCACCAAAGCTTGGTCGCTCCAAGAACACACCCTCAGGAGGGACAGAAGGAAATTCAAACCCCCCAGCTCGTTCAGCTC

Basic information

species Zea mays
transcript GRMZM2G137479_T02
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G137479_T02 (Zea mays), 3'ss of exon 8
lower sequence: LOC_Os06g40450.3 (Oryza sativa), 3'ss of exon 7
gtcacacttacaatcttagccagcttgccccactaggtatataaaggtattgctctatcctaacttctgaagcatgcatactattttctgctg---atcttagATCCCAACAACAAGAGCTCGATCACCAAAGCTTGGTCGCTCCAAGAACACACCCTCAGGAGGGACAGAAGGAAATTCAAACCCCCCAGCTCGTTCAGCTC
  || | |    | |  |  || |||       ||      || || | | ||  | ||    |||||||   |||     ||||| | |      ||   ||||||| || || |||||| |||||||||||||||| ||||| |||||||||  ||||| | | || |||| || | |    ||  ||   ||  ||||||
-ccaaaatcttga-caaaaacatcttcaatttttataatagtagagatgt-gcattttctgttcttctgataaatgatacttatttaccgtcattcattgcagATCCCTACCACCAGAGCTAGATCACCAAAGCTTGGCCGCTCAAAGAACACAAGCTCAGTAAGCACTGAAGAAAGTACCGTTCCTTCAAGCCGCCCAGCTC
















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|211091020|gb|FL435480.1|FL435480
EST:     TGCCCAGCTTTTATAAGGAACCACCTCCTCCCAAGGTTGAGTTGAAGAAG                         ATCCCAACAACAAGAGCTCGATCACCAAAGCTTGGTCGCTCCAAGAACACA
genomic: TGCCCAGCTTTTATAAGGAACCACCTCCTCCCAAGGTTGAGTTGAAGAAGgtaattcttc ... ctgatcttagATCCCAACAACAAGAGCTCGATCACCAAAGCTTGGTCGCTCCAAGAACACA
EST: gi|31406439|gb|CD485171.1|CD485171
EST:     CTTTTATAAGGAACCACCTCCTCCCAAGGTTGAGTTGAAGAAG                         ATCCCAACAACAAGAGCTCGATCACCAAAGCTTGGTCGCTCCAAGAACACA
genomic: CTTTTATAAGGAACCACCTCCTCCCAAGGTTGAGTTGAAGAAGgtaattcttc ... ctgatcttagATCCCAACAACAAGAGCTCGATCACCAAAGCTTGGTCGCTCCAAGAACACA
EST: gi|21331527|gb|BQ486908.1|BQ486908
EST:     TGCCCAGCTTTTATAAGGAACCACCTCCCCCCAAGGTTGAGTTGAAGAAG                         ATCCCAACAACAAGAGCTCGATCACCAAAGCTTGGTCGCTCCAAGAACACA
genomic: TGCCCAGCTTTTATAAGGAACCACCTCCTCCCAAGGTTGAGTTGAAGAAGgtaattcttc ... ctgatcttagATCCCAACAACAAGAGCTCGATCACCAAAGCTTGGTCGCTCCAAGAACACA
EST: gi|211099832|gb|FL388145.1|FL388145
EST:     TGCCCAGCTTTTATAAGGAACCACCTCCTCCCAAGGTTGAGTTGAAGAAG                         ATCCCAACAACAAGAGCTCGATCACCAAAGCTTGGTCGCTCCAAGAACACA
genomic: TGCCCAGCTTTTATAAGGAACCACCTCCTCCCAAGGTTGAGTTGAAGAAGgtaattcttc ... ctgatcttagATCCCAACAACAAGAGCTCGATCACCAAAGCTTGGTCGCTCCAAGAACACA
EST: gi|60357789|gb|DN224762.1|DN224762
EST:     TGCCCAGCTTTTATAAGGAACCACCTCCTCCCAAGGTTGAGTTGAAGAAG                         ATCCCAACAACAAGAGCTCGATCACCAAAGCTTGGTCGCTCCAAGAACACA
genomic: TGCCCAGCTTTTATAAGGAACCACCTCCTCCCAAGGTTGAGTTGAAGAAGgtaattcttc ... ctgatcttagATCCCAACAACAAGAGCTCGATCACCAAAGCTTGGTCGCTCCAAGAACACA
EST: gi|148965555|gb|EE016383.2|EE016383
EST:     TGCCCAGCTTTTATAAGGAACCACCTCCTCCCAAGGTTGAGTTGAAGAAG                         ATCCCAACAACAAGAGCTCGATCACCAAAGCTTGGTCGCTCCAAGAACACA
genomic: TGCCCAGCTTTTATAAGGAACCACCTCCTCCCAAGGTTGAGTTGAAGAAGgtaattcttc ... ctgatcttagATCCCAACAACAAGAGCTCGATCACCAAAGCTTGGTCGCTCCAAGAACACA
EST: gi|31440903|gb|CD510334.1|CD510334
EST:     TGCCCAGCTTTTATAAGGAACCACCTCCTCCCAAGGTTGAGTTGAAGAAG                         ATCCCAACAACAAGAGCTCGATCACCAAAGCTTGGTCGCTCCAAGAACACA
genomic: TGCCCAGCTTTTATAAGGAACCACCTCCTCCCAAGGTTGAGTTGAAGAAGgtaattcttc ... ctgatcttagATCCCAACAACAAGAGCTCGATCACCAAAGCTTGGTCGCTCCAAGAACACA
EST: gi|26456844|gb|CA828427.1|CA828427
EST:     TGCCCAGCTTTTATAAGGAACCACCTCCCCCCAAGGTTGAGTTGAAGAAG                         ATCCCAACAACAAGAGCTCGATCACCAAAGCTTGGTCGCTCCAAGAACACA
genomic: TGCCCAGCTTTTATAAGGAACCACCTCCTCCCAAGGTTGAGTTGAAGAAGgtaattcttc ... ctgatcttagATCCCAACAACAAGAGCTCGATCACCAAAGCTTGGTCGCTCCAAGAACACA
EST: gi|50326186|gb|CO521312.1|CO521312
EST:     TGCCCAGCTTTTATAAGGAACCACCTCCTCCCAAGGTTGAGTTGAAGAAG                         ATCCCAACAACAAGAGCTCGATCACCAAAGCTTGGTCGCTCCAAGAACACA
genomic: TGCCCAGCTTTTATAAGGAACCACCTCCTCCCAAGGTTGAGTTGAAGAAGgtaattcttc ... ctgatcttagATCCCAACAACAAGAGCTCGATCACCAAAGCTTGGTCGCTCCAAGAACACA
EST: gi|31406079|gb|CD484811.1|CD484811
EST:     TGCCCAGCTTTTATAAGGAACCACCTCCTCCCAAGGTTGAGTTGAAGAAG                         ATCCCAACAACAAGAGCTCGATCACCAAAGCTTGGTCGCTCCAAGAACACA
genomic: TGCCCAGCTTTTATAAGGAACCACCTCCTCCCAAGGTTGAGTTGAAGAAGgtaattcttc ... ctgatcttagATCCCAACAACAAGAGCTCGATCACCAAAGCTTGGTCGCTCCAAGAACACA
EST: gi|22818997|gb|BU499087.1|BU499087
EST:     TGCCCAGCTTTTATAAGGAACCACCTCCCCCCAAGGTTGAGTTGAAGAAG                         ATCCCAACAACAAGAGCTCGATCACCAAAGCTTGGTCGCTCCAAGAACACA
genomic: TGCCCAGCTTTTATAAGGAACCACCTCCTCCCAAGGTTGAGTTGAAGAAGgtaattcttc ... ctgatcttagATCCCAACAACAAGAGCTCGATCACCAAAGCTTGGTCGCTCCAAGAACACA
EST: gi|20506971|gb|BQ279426.1|BQ279426
EST:     TGCCCAGCTTTTATAAGGAACCACCTCCCCCCAAGGTTGAGTTGAAGAAG                         ATCCCAACAACAAGAGCTCGATCACCAAAGCTTGGTCGCTCCAAGAACACA
genomic: TGCCCAGCTTTTATAAGGAACCACCTCCTCCCAAGGTTGAGTTGAAGAAGgtaattcttc ... ctgatcttagATCCCAACAACAAGAGCTCGATCACCAAAGCTTGGTCGCTCCAAGAACACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtattgctctatcctaacttctgaagcatgcatactattttctgctgatcttagATCCCAACAACAAGAGCTCGATCACCAAAGCTTGGTCGCTCCAAGAACACACCCTCAGGAGGGACAGAAGGAAATTCAAACCCCCCAGCTCGTTCAGCTC
                                      ttttctgct  CT-rich tract
                                atactatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcacacttacaatcttagccagcttgccccactaggtatataaaggtattgctctatcctaacttctgaagcatgcatactattttctgctgatcttagATCCCAACAACAAGAGCTCGATCACCAAAGCTTGGTCGCTCCAAGAACACACCCTCAGGAGGGACAGAAGGAAATTCAAACCCCCCAGCTCGTTCAGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC