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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACTGTTGTGGATGGGgtaatacatggagttatttatttgttcttttttctttagcttcagttatgagtcatttaaactcagtgtgtctgcttttcag

Basic information

species Zea mays
transcript GRMZM5G840928_T03
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G840928_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os11g17610.1 (Oryza sativa), 5'ss of exon 5
GAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACTGTTGTGGATGGGgtaatacatggagttattt-atttgttcttttttctttagctt--cagttatgagtcatttaaactcagtgtgtctgcttttcag
|| ||||| |||||||||||||| || ||||| ||||| ||||||||||| || || || ||||||  |  ||   || ||| |           | ||| |  ||   | ||||||           |   | |   || | | |||
GACTGTGTAAGTAATATCATGAGACATGCACGGCAGGCAAATATTCCAACAGTCGTTGACGGGgtaccatttgacttttttttaaaaaaaaaacatacttgaaattataaattatgaacaggacttgatattttttagtgatctgcag
















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|78120737|gb|DV539121.1|DV539121
EST:     ATATCATGAGGCACGCACGACAGGCTAATATTCCAACTGTTGTGGATGGG                         GATGGCCTATTTCTTGTAAACAATAACCTTAATCTTGTTGAAGGAAACCCT
genomic: ATATCATGAGGCACGCACGACAGGCTAATATTCCAACTGTTGTGGATGGGgtaatacatg ... tgcttttcagGATGGCCTATTTCTTGTAAACAATAACCTTAATCTTGTTGAAGGAAACCCT
EST: gi|71763117|gb|DR961054.1|DR961054
EST:     ATATCATGAGGCACGCACGACAGGCTAATATTCCAACTGTTGTGGATGGG                         GATGGCCTATTTCTTGTAAACAATAACCTTAATCTTGTTGAAGGAAACCCT
genomic: ATATCATGAGGCACGCACGACAGGCTAATATTCCAACTGTTGTGGATGGGgtaatacatg ... tgcttttcagGATGGCCTATTTCTTGTAAACAATAACCTTAATCTTGTTGAAGGAAACCCT
EST: gi|76282803|gb|DV022371.1|DV022371
EST:     ATATCATGAGGCACGCACGACAGGCTAATATTCCAACTGTTGTGGATGGG                         GATGGCCTATTTCTTGTAAACAATAACCTTAATCTTGTTGAAGGAAACCCT
genomic: ATATCATGAGGCACGCACGACAGGCTAATATTCCAACTGTTGTGGATGGGgtaatacatg ... tgcttttcagGATGGCCTATTTCTTGTAAACAATAACCTTAATCTTGTTGAAGGAAACCCT
EST: gi|60400995|gb|DN233802.1|DN233802
EST:     ATATCATGAGGCACGCACGACAGGCTAATATTCCAACTGTTGTGGATGGG                         GATGGCCTATTTCTTGTAAACAATAACCTTAATCTTGTTGAAGGAAACCCT
genomic: ATATCATGAGGCACGCACGACAGGCTAATATTCCAACTGTTGTGGATGGGgtaatacatg ... tgcttttcagGATGGCCTATTTCTTGTAAACAATAACCTTAATCTTGTTGAAGGAAACCCT
EST: gi|71766336|gb|DR964273.1|DR964273
EST:     ATATCATGAGGCACGCACGACAGGCTAATATTCCAACTGTTGTGGATGGG                         GATGGCCTATTTCTTGTAAACAATAACCTTAATCTTGTTGAAGGAAACCCT
genomic: ATATCATGAGGCACGCACGACAGGCTAATATTCCAACTGTTGTGGATGGGgtaatacatg ... tgcttttcagGATGGCCTATTTCTTGTAAACAATAACCTTAATCTTGTTGAAGGAAACCCT
EST: gi|76011914|gb|DT939084.1|DT939084
EST:     ATATCATGAGGCACGCACGACAGGCTAATATTCCAACTGTTGTGGATGGG                         GATGGCCTATTTCTTGTAAACAATAACCTTAATCTTGTTGAAGGAAACCCT
genomic: ATATCATGAGGCACGCACGACAGGCTAATATTCCAACTGTTGTGGATGGGgtaatacatg ... tgcttttcagGATGGCCTATTTCTTGTAAACAATAACCTTAATCTTGTTGAAGGAAACCCT
EST: gi|76020591|gb|DT947761.1|DT947761
EST:     ATATCATGAGGCACGCACGGCAGGCTAATATTCCAACTGTTGTGGAGGGG                         GATGGCCTATTTCTTGTAAACAATAACCTTAATCTTGTTGAAGGAAACCCT
genomic: ATATCATGAGGCACGCACGACAGGCTAATATTCCAACTGTTGTGGATGGGgtaatacatg ... tgcttttcagGATGGCCTATTTCTTGTAAACAATAACCTTAATCTTGTTGAAGGAAACCCT
EST: gi|60345505|gb|DN212478.1|DN212478
EST:     ATATCATGAGGCACGCACGACAGGCTAATATTCCAACTGTTGTGGATGGG                         GATGGCCTATTTCTTGTAAACAATAACCTTAATCTTGTTGAAGGAAACCCT
genomic: ATATCATGAGGCACGCACGACAGGCTAATATTCCAACTGTTGTGGATGGGgtaatacatg ... tgcttttcagGATGGCCTATTTCTTGTAAACAATAACCTTAATCTTGTTGAAGGAAACCCT
EST: gi|78122651|gb|DV541035.1|DV541035
EST:     ATATCATGAGGCACGCACGACGGGCTAATATTCCAACTGTTGGGGATGGG                         GATGGCCTATTTCTTGTAAACAATAACCTTAATCTTGTTGAAGGAAACCCT
genomic: ATATCATGAGGCACGCACGACAGGCTAATATTCCAACTGTTGTGGATGGGgtaatacatg ... tgcttttcagGATGGCCTATTTCTTGTAAACAATAACCTTAATCTTGTTGAAGGAAACCCT
EST: gi|60400210|gb|DN233017.1|DN233017
EST:     ATATCATGAGGCACGCACGACAGGCTAATATTCCAACTGTTGTGGATGGG                         GATGGCCTATTTCTTGTAAACAATAACCTTAATCTTGTTGAAGGAAACCCT
genomic: ATATCATGAGGCACGCACGACAGGCTAATATTCCAACTGTTGTGGATGGGgtaatacatg ... tgcttttcagGATGGCCTATTTCTTGTAAACAATAACCTTAATCTTGTTGAAGGAAACCCT
EST: gi|78122650|gb|DV541034.1|DV541034
EST:     ATATCATGAGGCACGCACGACAGGCTAATATTCCAACTGTTGTGGATGGG                         GATGGCCTATTTCTTGTAAACAATAACCTTAATCTTGTTGAAGGAAACCCT
genomic: ATATCATGAGGCACGCACGACAGGCTAATATTCCAACTGTTGTGGATGGGgtaatacatg ... tgcttttcagGATGGCCTATTTCTTGTAAACAATAACCTTAATCTTGTTGAAGGAAACCCT

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), 48 (downstream exon)
Score: 187

GAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACTGTTGTGGATGGGgtaatacatg ... tgcttttcagGATGGCCTATTTCTTGTAAACAATAACCTTAATCTTGTTGAAGGAAACCCTCTTGCCATTTTAACACCAAATGTCTATGAGTACAAGCGTCTTGTTCAGA


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 88

GAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACTGTTGTGGATGGGgtaatacatg ... tgcttttcagGATGGCCTATTTCTTGTAAACAATAACCTTAATCTTGTTGAAGGAAACCCTCTTGCCATTTTAACACCAAATGTCTATGAGTACAAGCGTCTTGTTCAGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 112

GAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACTGTTGTGGATGGGgtaatacatg ... tgcttttcagGATGGCCTATTTCTTGTAAACAATAACCTTAATCTTGTTGAAGGAAACCCTCTTGCCATTTTAACACCAAATGTCTATGAGTACAAGCGTCTTGTTCAGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 64

GAATGTGTGAGTAATATCATGAGGCACGCACGACAGGCTAATATTCCAACTGTTGTGGATGGGgtaatacatg ... tgcttttcagGATGGCCTATTTCTTGTAAACAATAACCTTAATCTTGTTGAAGGAAACCCTCTTGCCATTTTAACACCAAATGTCTATGAGTACAAGCGTCTTGTTCAGA