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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCAACTGCTGGCCCTCTTCGCCCCATTGTGCAATGCCAGACTCTCAAGTACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcattgctttgccattgtctttccatttgagttctattgagccatgttgctttcttgaatgttctagtttgtttttattggtgttctggaacaat...

Basic information

species Zea mays
transcript GRMZM2G409407_T02
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G409407_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os08g06560.1 (Oryza sativa), 5'ss of exon 1
CCCAACTGCTGGCCCTCTTCGCCCCATTGTGCAATGCCAGACTCTCAAGTACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatg-cattgctttgccattgtctttccatttgagttctattgagccatgttgctttcttgaatgttctagtttgtttttattggtgttctggaacaat--
                                                       ||||||||||||||||||||||| |||| |||||||| ||||||||||||| | ||| | | ||| | | |||   |   ||  ||  | |  |  ||   | | ||| |   |   | |  ||       | | | |  |    |  
-------------------------------------------------------ATGAAGTCGAGGGCTGGGAGAGGCTTTATCCTTGAGGTGCTGAAGgtgatgtccttgttgtaccactatatttgagt---agcccttatcaatctagtgtatcttttggaccctgggggtgtttagatccaggggtgtaaagtttttg
















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|211263649|gb|FL031053.1|FL031053
EST:     ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAG                         GCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
genomic: ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
EST: gi|211266085|gb|FL031064.1|FL031064
EST:     ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAK                         GCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
genomic: ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
EST: gi|13558589|gb|BG549945.1|BG549945
EST:     ACAACATGAAGTTGTTGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAG                         GCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
genomic: ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
EST: gi|211263644|gb|FL031048.1|FL031048
EST:     ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAG                         GCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
genomic: ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
EST: gi|211247721|gb|FL179851.1|FL179851
EST:     ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAG                         GCTGCCGGCATTCCAAAGAAGCTTG
genomic: ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTG
EST: gi|12046544|gb|BF728683.1|BF728683
EST:     GAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAG                         GCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
genomic: GAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
EST: gi|211266082|gb|FL031061.1|FL031061
EST:     ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAG                         GCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
genomic: ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
EST: gi|211266086|gb|FL031065.1|FL031065
EST:     ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAG                         GCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
genomic: ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
EST: gi|211263648|gb|FL031052.1|FL031052
EST:     ACAACATGAAGTCGAGGGCTGGAAGAGGATTTACCCTTGAGGAGCTGAAG                         GCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
genomic: ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
EST: gi|211247720|gb|FL179850.1|FL179850
EST:     ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAG                         GCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
genomic: ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
EST: gi|211456254|gb|FL273553.1|FL273553
EST:     ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAG                         GCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
genomic: ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
EST: gi|211129396|gb|FL066372.1|FL066372
EST:     ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAG                         GCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
genomic: ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
EST: gi|78085923|gb|DV514316.1|DV514316
EST:     ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAG                         GCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
genomic: ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
EST: gi|211266087|gb|FL031066.1|FL031066
EST:     ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAG                         GCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
genomic: ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
EST: gi|33091972|gb|CF051966.1|CF051966
EST:     ACAACATGAAGTCGAGGGCTGGGAGGGGATTTACCCTTGAGGAGCTGAAG                         GCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCGTTTCTGTGGAT
genomic: ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
EST: gi|211263643|gb|FL031047.1|FL031047
EST:     ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAG                         GCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
genomic: ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
EST: gi|211263650|gb|FL031054.1|FL031054
EST:     ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAG                         GCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
genomic: ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
EST: gi|44900414|gb|CK826959.1|CK826959
EST:     ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAG                         GCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
genomic: ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
EST: gi|27522089|gb|CA989195.1|CA989195
EST:     ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAG                         GCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
genomic: ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
EST: gi|6973668|gb|AW438242.1|AW438242
EST:     ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAG                         GCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
genomic: ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
EST: gi|29946616|gb|CB816239.1|CB816239
EST:     ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAG                         GCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
genomic: ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
EST: gi|211266077|gb|FL031056.1|FL031056
EST:     ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAG                         GCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
genomic: ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
EST: gi|211266083|gb|FL031062.1|FL031062
EST:     ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAG                         GCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
genomic: ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
EST: gi|7238188|gb|AW573410.1|AW573410
EST:     ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGTAGCTGAAG                         GCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
genomic: ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
EST: gi|211266080|gb|FL031059.1|FL031059
EST:     ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAG                         GCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
genomic: ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
EST: gi|116829000|gb|EC863170.1|EC863170
EST:     ACAACATGAAGTCGA-GGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAG                         GCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
genomic: ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
EST: gi|211263641|gb|FL031045.1|FL031045
EST:     ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAG                         GCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
genomic: ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
EST: gi|78086900|gb|DV515293.1|DV515293
EST:     ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAG                         GCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
genomic: ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
EST: gi|78180971|gb|DV551344.1|DV551344
EST:     ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAG                         GCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
genomic: ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
EST: gi|211263645|gb|FL031049.1|FL031049
EST:     ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAG                         GCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
genomic: ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
EST: gi|211266081|gb|FL031060.1|FL031060
EST:     ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAG                         GCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
genomic: ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
EST: gi|211266084|gb|FL031063.1|FL031063
EST:     ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAG                         GCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT
genomic: ACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGAT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 502

CCCAACTGCTGGCCCTCTTCGCCCCATTGTGCAATGCCAGACTCTCAAGTACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGATCACCGCCGCAAGAACAAATCTCTCGAGGGACTGCAGGCCAATGTCCAGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 461

CCCAACTGCTGGCCCTCTTCGCCCCATTGTGCAATGCCAGACTCTCAAGTACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGATCACCGCCGCAAGAACAAATCTCTCGAGGGACTGCAGGCCAATGTCCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 436

CCCAACTGCTGGCCCTCTTCGCCCCATTGTGCAATGCCAGACTCTCAAGTACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGATCACCGCCGCAAGAACAAATCTCTCGAGGGACTGCAGGCCAATGTCCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 201

CCCAACTGCTGGCCCTCTTCGCCCCATTGTGCAATGCCAGACTCTCAAGTACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcatt ... tcgattgcagGCTGCCGGCATTCCAAAGAAGCTTGCCCCAACCATTGGCATTTCTGTGGATCACCGCCGCAAGAACAAATCTCTCGAGGGACTGCAGGCCAATGTCCAGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCCAACTGCTGGCCCTCTTCGCCCCATTGTGCAATGCCAGACTCTCAAGTACAACATGAAGTCGAGGGCTGGGAGAGGATTTACCCTTGAGGAGCTGAAGgtgatgcattgctttgccattgtctttccatttgagttctattgagccatgttgctttcttgaatgttctagtttgtttttattggtgttctggaacaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG