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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGACTTGCCCTGCCGACCTCGACAGCAAATGCGACGGTGGCGCGCCTGATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccacgaaaaccctcagattgtgatgtcgttgtgcaccgagccattgttccttgaacaattgatgcttgtgctgcag

Basic information

species Zea mays
transcript GRMZM2G005493_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G005493_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os07g47290.1 (Oryza sativa), 5'ss of exon 3
GCAGACTTGCCCTGCCGACCTCGACAGCAAATGCGACGGTGGCGCGCCTGATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgagg----ccacgaaaaccctcagattgtgatgtcgttgtgcaccgagccattgttccttgaacaattgatgcttgtgctgcag-----------------
||| || || || ||||||||||| ||||| || |  | ||  ||  | |  || ||||| ||||| |||||||| ||| |||| || ||||||||||||||||||    ||| |||| |   ||| || ||||    || |      |  | | |    ||  |  ||||    |||  ||  |                  
GCAAACCTGTCCGGCCGACCTCGATAGCAAGTGTGGTGATGCTGCTTCAGGGGATTGGGAAGGGGAGTTCTTCCCTGGCATCCCCAAGATCAAGTATGAGgtgagggaggccatgaaagcttacagctt-tgattagattattggataaagcttggaaatttatattattgta--ttggactataactgctgtgactctttga
















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|211458130|gb|FL012366.1|FL012366
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211458127|gb|FL012363.1|FL012363
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|149080694|gb|EE169755.2|EE169755
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211023369|gb|FK982681.1|FK982681
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAG
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAG
EST: gi|211302405|gb|FL012357.1|FL012357
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211302401|gb|FL012353.1|FL012353
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211458128|gb|FL012364.1|FL012364
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211458140|gb|FL012376.1|FL012376
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211302399|gb|FL012351.1|FL012351
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211458138|gb|FL012374.1|FL012374
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211302400|gb|FL012352.1|FL012352
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211020950|gb|FK982676.1|FK982676
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211458126|gb|FL012362.1|FL012362
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|148979224|gb|EE026582.2|EE026582
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211458134|gb|FL012370.1|FL012370
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGYGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211302409|gb|FL012361.1|FL012361
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211460651|gb|FL012377.1|FL012377
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGA-
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211458129|gb|FL012365.1|FL012365
EST:     ATGACTGGKAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACC-TCTTGC
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGC
EST: gi|211302404|gb|FL012356.1|FL012356
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211458132|gb|FL012368.1|FL012368
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAARTCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTAT
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTAT
EST: gi|211302403|gb|FL012355.1|FL012355
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|32913601|gb|CF018413.1|CF018413
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211458133|gb|FL012369.1|FL012369
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211302408|gb|FL012360.1|FL012360
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211458135|gb|FL012371.1|FL012371
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|148950087|gb|EC895623.2|EC895623
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|32910736|gb|CF015548.1|CF015548
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211023371|gb|FK982683.1|FK982683
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211458139|gb|FL012375.1|FL012375
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|76286923|gb|DV026491.1|DV026491
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211460652|gb|FL012378.1|FL012378
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|21389921|gb|BQ527970.1|BQ527970
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211020954|gb|FK982680.1|FK982680
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211458131|gb|FL012367.1|FL012367
EST:     ATGACTGGGAAGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAAACCTCTTGC
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGC
EST: gi|211458137|gb|FL012373.1|FL012373
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
EST: gi|211302406|gb|FL012358.1|FL012358
EST:     ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAG                         GGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA
genomic: ATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAA

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: 49 (upstream exon), 49 (downstream exon)
Score: 253

GCAGACTTGCCCTGCCGACCTCGACAGCAAATGCGACGGTGGCGCGCCTGATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAAGTCATTCTCGGAAAGAAGATGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 287

GCAGACTTGCCCTGCCGACCTCGACAGCAAATGCGACGGTGGCGCGCCTGATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAAGTCATTCTCGGAAAGAAGATGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 283

GCAGACTTGCCCTGCCGACCTCGACAGCAAATGCGACGGTGGCGCGCCTGATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAAGTCATTCTCGGAAAGAAGATGAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 285

GCAGACTTGCCCTGCCGACCTCGACAGCAAATGCGACGGTGGCGCGCCTGATGACTGGGAGGGGGAATTCTTCCCCGGCGTCCCGAAAATCAAGTATGAGgtgaggccac ... tgtgctgcagGGTCCAACAAGCAAGAACCCTCTTGCTTATAAGTGGTATAACAAGGAGGAAGTCATTCTCGGAAAGAAGATGAAG