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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatatgtttcttctctgctacctacttttagtgcagaactggagattatctggcatagcaatagcattgatacttcattctgtttgcag

Basic information

species Zea mays
transcript GRMZM2G540403_T03
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G540403_T02 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g15860.1 (Oryza sativa), 5'ss of exon 5
CTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcat--------------atgtttcttctctgctacctacttttagtgcagaactggagattatctggcatagcaatagcattgatacttcattct-gtttgcag
 ||||| |||||||| ||||||||||| ||||||||  ||||||||||||||||||| || |                | ||  ||| |  ||  |||||||||||| |  |   || |||   ||||| | |  |    |  ||| |||||||| || |||||
ATGTGTTAATGTACTTCTCACAAACCCAATTTGGGTAATTGTTACACGAATGCAAgtaagtaatgcacattattgcagtattatttcccaactgactacttttagtgtaata--agaaattcagtggcacatcc-tgaagt--ataattcattcttgtctgcag
















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|24934302|gb|CA452520.1|CA452520
EST:     ACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
genomic: ACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
EST: gi|149071944|gb|EE160331.2|EE160331
EST:     TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
genomic: TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
EST: gi|78120502|gb|DV538886.1|DV538886
EST:     TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
genomic: TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
EST: gi|88756340|gb|DY540481.1|DY540481
EST:     TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
genomic: TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
EST: gi|148952677|gb|EC898511.2|EC898511
EST:     TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
genomic: TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
EST: gi|91877627|gb|EB407584.1|EB407584
EST:     TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
genomic: TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
EST: gi|32929640|gb|CF034452.1|CF034452
EST:     ACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGGATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
genomic: ACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
EST: gi|71766550|gb|DR964487.1|DR964487
EST:     TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
genomic: TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
EST: gi|148964459|gb|EC905815.2|EC905815
EST:     TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
genomic: TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
EST: gi|76936044|gb|DV174582.1|DV174582
EST:     TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
genomic: TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
EST: gi|148957275|gb|EC903307.2|EC903307
EST:     TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
genomic: TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
EST: gi|149027549|gb|EE046558.2|EE046558
EST:     TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
genomic: TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
EST: gi|71422924|gb|DR805897.1|DR805897
EST:     TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
genomic: TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
EST: gi|149013466|gb|EE042980.2|EE042980
EST:     TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
genomic: TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
EST: gi|71448089|gb|DR829139.1|DR829139
EST:     TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
genomic: TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT
EST: gi|91051844|gb|EB162262.1|EB162262
EST:     TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAA                         ACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAAATGTGCT
genomic: TCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCT

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: 201

CTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCTCTTGATAAGCCCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 265

CTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCTCTTGATAAGCCCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 271

CTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCTCTTGATAAGCCCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 231

CTGTGTCAATGTACTGCTCACAAACCCGATTTGGGTTGTTGTTACACGAATGCAAgtgagcatat ... ctgtttgcagACTCACAGAAAGGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCTCTTGATAAGCCCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAA