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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAATCGTATTCCGGAAGCAGCATTGATGGCAAGATCTTATCTTCCCAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAGgtcttctgtcatgagtctccttagcttccgttctactcacttttatgatatttttttctgcagaacttaattaggttaacatggtcttagtgcgtatctc...

Basic information

species Zea mays
transcript GRMZM2G141587_T01
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G141587_T03 (Zea mays), 5'ss of exon 21
lower sequence: LOC_Os02g11840.1 (Oryza sativa), 5'ss of exon 12
CAATCGTATTCCGGAAGCAGCATTGATGGCAAGATCTTATCTTCCCAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAGgtcttctgtcatgagtctccttagcttccgttctactcacttttatgatatttttttctgcagaacttaattaggttaacatggtcttagtgcgtatctc
 |||||||| || ||||||||||||||| | |||||||||||||| ||||||||||||||||||||| |||| ||||||||||||||||| |||||    | |      || |||    |     | |  |   || ||     | |  | ||  |    ||    |  |  |   | || |  |  ||  |||
TAATCGTATACCAGAAGCAGCATTGATGTCGAGATCTTATCTTCCGAGCAAAGTCCCTGAGATTGTAACATTATGGAAAAAGGATCTCCAAAAGgtaccatctgccctatcccctataatatttctttgtttttttctacctattctcatgcttaatcttttgcacacctgtattagatcgtgctcagttgctc

upper sequence: GRMZM2G141587_T03 (Zea mays), 5'ss of exon 21
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 21
CAATCGTATTCCGGAAGCAGCATTGATGGCAAGATCTTATCTTCCCAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAGgt--cttctgtcatgagtctccttagcttccgttctactcacttttatgatatttttttctgcagaacttaattaggttaacatggtcttagtgcgtatctc
 |||||||| || ||||||||||||||| | |||||||||||||| ||||||||||||||||||||| |||| ||||||||||||||||| |||||  | ||||||     | |||    |        ||| || |||  || | ||  |           ||| | | |||  |||  |   ||   | ||  |
TAATCGTATACCAGAAGCAGCATTGATGTCGAGATCTTATCTTCCGAGCAAAGTCCCTGAGATTGTAACATTATGGAAAAAGGATCTCCAAAAGgtaccatctgtctcttttttccccctccaaaagg-tacccagtttc-tggtgttaatactgatgatttttagtgatgtttccatcctaacaggcagaatgcc
















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|211291668|gb|FL235608.1|FL235608
EST:     CAAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAG                         GTAAACTCAAAAGCAGCAGAGTCGCTGGCTGATCCCTA-TGAGTACCCAAA
genomic: CCAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAGgtcttctgtc ... tgctttttagGTAAACTCAAAAGCAGCAGAGTCGCTGGCTGATCC-TAATGAGTACCCAAA
EST: gi|32931477|gb|CF036289.1|CF036289
EST:     CCAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAG                         GTAAACTCAAAAGCAGCAGAGTCGCTGGCTGATCCTAATGAGTA
genomic: CCAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAGgtcttctgtc ... tgctttttagGTAAACTCAAAAGCAGCAGAGTCGCTGGCTGATCCTAATGAGTA
EST: gi|56382379|gb|CV985048.1|CV985048
EST:     CAAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAG                         GTAAACTCAAAAGCAGCAGAGTCGCTGGCTGATCCTAATGAGTACCCAAAC
genomic: CCAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAGgtcttctgtc ... tgctttttagGTAAACTCAAAAGCAGCAGAGTCGCTGGCTGATCCTAATGAGTACCCAAAC
EST: gi|78114292|gb|DV532681.1|DV532681
EST:     CCAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAG                         GTAAACTCAAAAGCAGCAGAGTCGCTGGCTGATCCTAATGAGTACCCAAAC
genomic: CCAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAGgtcttctgtc ... tgctttttagGTAAACTCAAAAGCAGCAGAGTCGCTGGCTGATCCTAATGAGTACCCAAAC
EST: gi|32795452|gb|CD947688.1|CD947688
EST:     GATCCCCAGAAG                         GTAAACTCAAAAGCAGCAGAGTCGCTGGCTGATCCTAATGAGTACCCAAAC
genomic: GATCTCCAGAAGgtcttctgtc ... tgctttttagGTAAACTCAAAAGCAGCAGAGTCGCTGGCTGATCCTAATGAGTACCCAAAC
EST: gi|32808372|gb|CD960606.1|CD960606
EST:     GATCTCCAGAAG                         GTAAACTCAAAAGCAGCAGAGTCGCTGGCTGATCCTAATGAGTACCCAAAC
genomic: GATCTCCAGAAGgtcttctgtc ... tgctttttagGTAAACTCAAAAGCAGCAGAGTCGCTGGCTGATCCTAATGAGTACCCAAAC
EST: gi|32791813|gb|CD944049.1|CD944049
EST:     GATCTCCAGAAG                         GTAAACTCAAAAGCAGCAGAGTCGCTGGCTGATCCTAATGAGTACCCAAAC
genomic: GATCTCCAGAAGgtcttctgtc ... tgctttttagGTAAACTCAAAAGCAGCAGAGTCGCTGGCTGATCCTAATGAGTACCCAAAC
EST: gi|71438645|gb|DR819695.1|DR819695
EST:     AAAGGATCTCCAGAAG                         GTAAACTCAAAAGCAGCAGAGTCGCTGGCTGATCCTAATGAGTACCCAAAC
genomic: AAAGGATCTCCAGAAGgtcttctgtc ... tgctttttagGTAAACTCAAAAGCAGCAGAGTCGCTGGCTGATCCTAATGAGTACCCAAAC
EST: gi|60337474|gb|DN204447.1|DN204447
EST:     CCAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAG                         GTAAACTCAAAAGCAGCATAGTCGCTGGCTGATCCTAATGAGTACCCAAAC
genomic: CCAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAGgtcttctgtc ... tgctttttagGTAAACTCAAAAGCAGCAGAGTCGCTGGCTGATCCTAATGAGTACCCAAAC
EST: gi|6095376|gb|AW120043.1|AW120043
EST:     CCAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAG                         GTAAACTCAAAAGCAGCA
genomic: CCAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAGgtcttctgtc ... tgctttttagGTAAACTCAAAAGCAGCA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAATCGTATTCCGGAAGCAGCATTGATGGCAAGATCTTATCTTCCCAGCAAAGTCCCTGAGATTGTAGCATTGTGGAAAAAGGATCTCCAGAAGgtcttctgtcatgagtctccttagcttccgttctactcacttttatgatatttttttctgcagaacttaattaggttaacatggtcttagtgcgtatctc

- - - - - - - - - - - - - - - - - - - - - - -  GCAAAG