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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgcatttatatttcttaataaacagagttctatgtagactagtgttctcgttattgatatattaaccttatttgtatcattgtgctctactttgggcagACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGACATATCACGCACATTTCCATCTCATATATTCTTTCAACAAAGGCATGGTC

Basic information

species Zea mays
transcript GRMZM2G047223_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G047223_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os08g31840.2 (Oryza sativa), 3'ss of exon 3
----------------------------------------------------------------ttgcatttatatt-tcttaataaacagagttctatg--tagactagtgttct---cgttattgatatattaaccttat--ttgtatcattgtgctctactttgggcagACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGACATATCACGCACATTTCCATCTCATATATTCTTTCAACAAAGGCATGGTC
                                                                ||   ||| | || ||||| ||   |    |  ||    ||  || |||  |    || ||  |||| ||  |   ||  ||  ||   | | || |  ||||| ||||||||||| ||||| |||||||| || || ||||||||||| ||||||||||||||||| || |||||||| ||||| ||||| ||||| || |||||||
gtacctataacaattgtgaaagaactgcttgccctgatttttgttgaatgttccctattattttttaactttctgttgtcttagtagttatttctaaattatcaggatattgtcttaagagtcatacatatcttgtcaacattattacatttctatactattttttggacagACACTGGTCATATACGAGACATCTGCATCAGAATTGGAAATAATTCGTGACATATCACGTACTTTTCCATCACATATTTTCTTCCAACAGAGACATGGTC

upper sequence: GRMZM2G047223_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA19G05360.1 (Glycine max), 3'ss of exon 3
ttgcatttatatttcttaataaacagagttctatgtagactagtgttctcgttattg-atatattaaccttatttgtatcattgtgctctactttgggcagACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGACATATCACGCACATTTCCATCTCATATATTCTTTCAACAAAGGCATGGTC
 ||   ||   |   ||| |      | || | |  ||  |      |    | ||  || | ||    ||     |  |       | ||| |   ||||  ||| || |||||||||||||| ||||||||| |||| || ||||| || || || || || || || || ||| ||||||||||||| || ||||| |
-tgaggtttcctcctttactttttgaaattatcttgaggtttactaccctactgttccatgttttggagtttgcattgactagacattatacctattgcagCAACTAGTCATATATGAGACATCTGCCTCTGAACTGGATATAATTCGAGATATTTCTCGAACCTTCCCTTCACATGTATTCTTTCAACAGAGACATGGAC
















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|78113905|gb|DV532294.1|DV532294
EST:     TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAG                         ACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC
genomic: TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaa ... ctttgggcagACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC
EST: gi|211004390|gb|FL335892.1|FL335892
EST:     TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAG                         ACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC
genomic: TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaa ... ctttgggcagACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC
EST: gi|211402149|gb|FL346428.1|FL346428
EST:     TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAG                         ACACTGGTGAT
genomic: TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaa ... ctttgggcagACACTGGTGAT
EST: gi|61118400|gb|DN559361.1|DN559361
EST:     TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAG                         ACACTGGTGATATATGAGACATCGGCCCCTGAATTGGAAATTATTCGTGAC
genomic: TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaa ... ctttgggcagACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC
EST: gi|211274707|gb|FL354611.1|FL354611
EST:     TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAG                         ACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC
genomic: TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaa ... ctttgggcagACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC
EST: gi|91877110|gb|EB407067.1|EB407067
EST:     TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAG                         ACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTC
genomic: TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaa ... ctttgggcagACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTC
EST: gi|89758012|gb|DY687355.1|DY687355
EST:     TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAG                         ACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC
genomic: TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaa ... ctttgggcagACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC
EST: gi|89756849|gb|DY686713.1|DY686713
EST:     TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAG                         ACACTGGTGATATATG
genomic: TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaa ... ctttgggcagACACTGGTGATATATG
EST: gi|91874336|gb|EB404293.1|EB404293
EST:     TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAG                         ACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC
genomic: TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaa ... ctttgggcagACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC
EST: gi|211241359|gb|FL313117.1|FL313117
EST:     TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAG                         ACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC
genomic: TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaa ... ctttgggcagACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC
EST: gi|211342758|gb|FL350527.1|FL350527
EST:     TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAG                         ACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC
genomic: TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaa ... ctttgggcagACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC
EST: gi|78117555|gb|DV535942.1|DV535942
EST:     TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAG                         ACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC
genomic: TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaa ... ctttgggcagACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC
EST: gi|71771758|gb|DR969695.1|DR969695
EST:     TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAG                         ACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC
genomic: TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaa ... ctttgggcagACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC
EST: gi|78118515|gb|DV536899.1|DV536899
EST:     TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAG                         ACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC
genomic: TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaa ... ctttgggcagACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC
EST: gi|211258118|gb|FL346785.1|FL346785
EST:     TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAG                         ACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC
genomic: TGATTTCAGGCAGTCGGGACCTCTTACTAATGAACCCAGGGGTTTACGAGgtacccacaa ... ctttgggcagACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctcgttattgatatattaaccttatttgtatcattgtgctctactttgggcagACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGACATATCACGCACATTTCCATCTCATATATTCTTTCAACAAAGGCATGGTC
               tattaac  putative branch site (score: 1)
                                        ctctacttt  putative PPT
      ttattgatatattaac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgcatttatatttcttaataaacagagttctatgtagactagtgttctcgttattgatatattaaccttatttgtatcattgtgctctactttgggcagACACTGGTGATATATGAGACATCGGCCTCTGAATTGGAAATTATTCGTGACATATCACGCACATTTCCATCTCATATATTCTTTCAACAAAGGCATGGTC

ttgcatt
- - - - - - - - - - aaacaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtgctc