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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAGgtacacaagacatctgtttattttttatgtgtaaagatattagagttctttttgattttttttcctgctcaatgggttttcctctcgtttaatcagcatttccaatgcag

Basic information

species Zea mays
transcript GRMZM2G063151_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063151_T01 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g16700.4 (Oryza sativa), 5'ss of exon 5
TGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAGgtacacaa-----gacat-------ctgtttattttttatgtg-taaagatattagagttctttttgattttttttcctgctcaatgggttttcctctcgtttaatcagcatttccaatgcag
| |||||||| || |||||||| || ||||||||||||||  |||| |||||||| | ||| |||||||| ||||| |||||||  ||     |||||       ||||||  |  |||  || | |  | |      |  |    || |||      |  || |||   |||||     ||||||  | ||||  |||||||
TAAAACTTAGGATCAAGTCTTTCAAGGTGCCTGAACTTCTAATTGAGATCCCAGAAACTGCGACTGTTGGTTCACTGAAGgtacggaaaaagagacattttgctcctgttttctcattaattgatcagcacaaagagatgttgcaagaatttcaccttttgtcgatgatgtttccgtgt-tttaatatgtatttataatgcag
















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|211462608|gb|FK992343.1|FK992343
EST:     CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAG                         AAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
genomic: CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAGgtacacaaga ... tccaatgcagAAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
EST: gi|211457563|gb|FK992319.1|FK992319
EST:     CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAG                         AAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
genomic: CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAGgtacacaaga ... tccaatgcagAAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
EST: gi|211462609|gb|FK992344.1|FK992344
EST:     CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAG                         AAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACCGTGT
genomic: CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAGgtacacaaga ... tccaatgcagAAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTAC-GTGT
EST: gi|211462605|gb|FK992340.1|FK992340
EST:     CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAG                         AAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
genomic: CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAGgtacacaaga ... tccaatgcagAAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
EST: gi|13558490|gb|BG549846.1|BG549846
EST:     CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAG                         AAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
genomic: CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAGgtacacaaga ... tccaatgcagAAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
EST: gi|211465137|gb|FK992354.1|FK992354
EST:     CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAG                         AAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
genomic: CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAGgtacacaaga ... tccaatgcagAAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
EST: gi|211460083|gb|FK992329.1|FK992329
EST:     CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAG                         AAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
genomic: CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAGgtacacaaga ... tccaatgcagAAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
EST: gi|211460082|gb|FK992328.1|FK992328
EST:     CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAG                         AAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
genomic: CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAGgtacacaaga ... tccaatgcagAAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
EST: gi|211462610|gb|FK992345.1|FK992345
EST:     CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAG                         AAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
genomic: CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAGgtacacaaga ... tccaatgcagAAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
EST: gi|211457565|gb|FK992321.1|FK992321
EST:     CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAG                         AAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
genomic: CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAGgtacacaaga ... tccaatgcagAAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
EST: gi|211460080|gb|FK992326.1|FK992326
EST:     CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAG                         AAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
genomic: CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAGgtacacaaga ... tccaatgcagAAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
EST: gi|211457566|gb|FK992322.1|FK992322
EST:     CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAG                         AAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
genomic: CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAGgtacacaaga ... tccaatgcagAAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
EST: gi|211460085|gb|FK992331.1|FK992331
EST:     CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAG                         AAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
genomic: CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAGgtacacaaga ... tccaatgcagAAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
EST: gi|211462604|gb|FK992339.1|FK992339
EST:     CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAG                         AAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
genomic: CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAGgtacacaaga ... tccaatgcagAAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
EST: gi|211465138|gb|FK992355.1|FK992355
EST:     CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAG                         AAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
genomic: CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAGgtacacaaga ... tccaatgcagAAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
EST: gi|211462606|gb|FK992341.1|FK992341
EST:     CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAG                         AAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
genomic: CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAGgtacacaaga ... tccaatgcagAAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
EST: gi|211460077|gb|FK992323.1|FK992323
EST:     CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAG                         AAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
genomic: CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAGgtacacaaga ... tccaatgcagAAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
EST: gi|211457564|gb|FK992320.1|FK992320
EST:     CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAG                         AAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
genomic: CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAGgtacacaaga ... tccaatgcagAAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
EST: gi|13249860|gb|BG360765.1|BG360765
EST:     CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAG                         AAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGT
genomic: CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAGgtacacaaga ... tccaatgcagAAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGT
EST: gi|211457560|gb|FK992316.1|FK992316
EST:     CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAG                         AAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
genomic: CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAGgtacacaaga ... tccaatgcagAAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
EST: gi|211462603|gb|FK992338.1|FK992338
EST:     CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAG                         AAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACCGTGT
genomic: CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAGgtacacaaga ... tccaatgcagAAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTAC-GTGT
EST: gi|211462614|gb|FK992349.1|FK992349
EST:     CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAG                         AAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT
genomic: CTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAGgtacacaaga ... tccaatgcagAAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTT

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), 45 (downstream exon)
Score: 79

TGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAGgtacacaaga ... tccaatgcagAAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTTGGTGTTCTTCACCATGGAAAGAAAGTCAGAGATGATAGTAAAACGTTAA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 111

TGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAGgtacacaaga ... tccaatgcagAAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTTGGTGTTCTTCACCATGGAAAGAAAGTCAGAGATGATAGTAAAACGTTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 149

TGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAGgtacacaaga ... tccaatgcagAAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTTGGTGTTCTTCACCATGGAAAGAAAGTCAGAGATGATAGTAAAACGTTAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 122

TGAAACTTAGAATTAAGTCTTTTAACGTGCCTGAACTTCTTGTTGAAATCCCAGACAGTGCAACTGTTGGCTCACTAAAGgtacacaaga ... tccaatgcagAAAACTGTTCTCGAGGCAGTGACTGCGATTCTTGGAGGTGGCCTACGTGTTGGTGTTCTTCACCATGGAAAGAAAGTCAGAGATGATAGTAAAACGTTAA