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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaccccaacttgcttgacactaaaaagactatgttgttgttgttgttgttcatgttgatttcaacataccaagttattaatgctttcttgtaatttcagGGGAGGTTCTTGCAATGCACTTCGCAAATTTAGGAGCAAAGCTGATACTATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGAAAAAAAACATCCTCA

Basic information

species Zea mays
transcript GRMZM2G003692_T07
intron # 3
splice site 3'
intron type U2

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|211527525|gb|FL409928.1|FL409928
EST:     GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG                         GGGAGGTTCTTGCAATGCACTTCGCAAATTTAGGAGCAAAGCTGATACTAT
genomic: GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTGgtcagcgtgc ... gtaatttcagGGGAGGTTCTTGCAATGCACTTCGCAAATTTAGGAGCAAAGCTGATACTAT
EST: gi|211174932|gb|FL421412.1|FL421412
EST:     GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG                         GGGAGGTTCTTGCAATGCACTTCGCAAATTTAGGAGCAAAGCTGATACTAT
genomic: GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTGgtcagcgtgc ... gtaatttcagGGGAGGTTCTTGCAATGCACTTCGCAAATTTAGGAGCAAAGCTGATACTAT
EST: gi|149101270|gb|EE187382.2|EE187382
EST:     GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG                         GGGAGGTTCTTGCAATGCACTTCGCAAATTTAGGAGCAAAGCTGATACTAT
genomic: GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTGgtcagcgtgc ... gtaatttcagGGGAGGTTCTTGCAATGCACTTCGCAAATTTAGGAGCAAAGCTGATACTAT
EST: gi|211280391|gb|FL376816.1|FL376816
EST:     GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG                         GGGAGGTTCTTGCAATGCACTTCGCAAATTTAGGAGCAAAGCTGATACTAT
genomic: GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTGgtcagcgtgc ... gtaatttcagGGGAGGTTCTTGCAATGCACTTCGCAAATTTAGGAGCAAAGCTGATACTAT
EST: gi|211267130|gb|FL426696.1|FL426696
EST:     GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG                         GGGAGGTTCTTGCAATGCACTTCGCAAATTTAGGAGCAAAGCTGATACTAT
genomic: GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTGgtcagcgtgc ... gtaatttcagGGGAGGTTCTTGCAATGCACTTCGCAAATTTAGGAGCAAAGCTGATACTAT
EST: gi|211126709|gb|FL428259.1|FL428259
EST:     GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG                         GGGAGGTTCTTGCAATGCACTTCGCAAATTTAGGAGCAAAGCTGATACTAT
genomic: GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTGgtcagcgtgc ... gtaatttcagGGGAGGTTCTTGCAATGCACTTCGCAAATTTAGGAGCAAAGCTGATACTAT
EST: gi|211245303|gb|FL400469.1|FL400469
EST:     GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG                         GGGAGGTTCTTGCAATGCACTTCGCAAATTTAGGAGCAAAGCTGATACTAT
genomic: GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTGgtcagcgtgc ... gtaatttcagGGGAGGTTCTTGCAATGCACTTCGCAAATTTAGGAGCAAAGCTGATACTAT
EST: gi|211070635|gb|FL369038.1|FL369038
EST:     GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG                         GGGAGGTTCTTGCAATGCACTTCGCAAATTTAGGAGCAAAGCTGATACTAT
genomic: GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTGgtcagcgtgc ... gtaatttcagGGGAGGTTCTTGCAATGCACTTCGCAAATTTAGGAGCAAAGCTGATACTAT
EST: gi|32919174|gb|CF023986.1|CF023986
EST:     GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG                         GGGAGGTTCTTGCAATGCACTTCGCAAATTTAGGAGCAAAGCTGATACTAT
genomic: GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTGgtcagcgtgc ... gtaatttcagGGGAGGTTCTTGCAATGCACTTCGCAAATTTAGGAGCAAAGCTGATACTAT
EST: gi|211455863|gb|FL399438.1|FL399438
EST:     GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG                         GGGAGGTTCTTGCAATGCACTTCGCAAATTTAGGAGCAAAGCTGGATACTA
genomic: GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTGgtcagcgtgc ... gtaatttcagGGGAGGTTCTTGCAATGCACTTCGCAAATTTAGGAGCAAAGCTG-ATACTA
EST: gi|71438969|gb|DR820019.1|DR820019
EST:     GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTG                         GGGAGGTTCTTGCAATGCACTTCGCAAATTTAGGAGCAAAGCTGATACTAT
genomic: GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTGgtcagcgtgc ... gtaatttcagGGGAGGTTCTTGCAATGCACTTCGCAAATTTAGGAGCAAAGCTGATACTAT

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: 34 (upstream exon), 48 (downstream exon)
Score: 254

GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTGgtcagcgtgc ... gtaatttcagGGGAGGTTCTTGCAATGCACTTCGCAAATTTAGGAGCAAAGCTGATACTATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGAAAAAAAACATCCTCA


Block sizes: 34 (upstream exon), 49 (downstream exon)
Score: 757

GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTGgtcagcgtgc ... gtaatttcagGGGAGGTTCTTGCAATGCACTTCGCAAATTTAGGAGCAAAGCTGATACTATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGAAAAAAAACATCCTCA


Block sizes: 38 (upstream exon), 49 (downstream exon)
Score: 564

GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTGgtcagcgtgc ... gtaatttcagGGGAGGTTCTTGCAATGCACTTCGCAAATTTAGGAGCAAAGCTGATACTATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGAAAAAAAACATCCTCA


Block sizes: 34 (upstream exon), 49 (downstream exon)
Score: 640

GTCGTGTGGATTACTGGAGCTAGCCGCGGGATTGgtcagcgtgc ... gtaatttcagGGGAGGTTCTTGCAATGCACTTCGCAAATTTAGGAGCAAAGCTGATACTATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGAAAAAAAACATCCTCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgttcatgttgatttcaacataccaagttattaatgctttcttgtaatttcagGGGAGGTTCTTGCAATGCACTTCGCAAATTTAGGAGCAAAGCTGATACTATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGAAAAAAAACATCCTCA
                              tattaat  putative branch site (score: 640)
                                      ctttcttgt  CT-rich tract
                          aagttattaat  TA-rich tract