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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAGgtacttgttatctcatgcagagattggtggtcaatgaaatttatttttttcacagcagccttcagagatgaatctagcgttgaatatatctaatttgcgg...

Basic information

species Zea mays
transcript GRMZM2G050484_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G050484_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os02g10230.1 (Oryza sativa), 5'ss of exon 8
GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAGgtacttgttat-ctcatgcagagattggtggtcaatgaaatttatttttttcacagcagccttcagagatgaatctagcgttgaatatatctaat--ttgcgg
||||||||||||||||| ||| |||||||||||||||| |||||| | || | | |||| |||||  ||   | ||| || || || |  ||||||| |||||||||| |||| |  |     |||||||| | ||   |  | 
GGGGTTGCTGTAGCTCTACCACTCTATTTTGCTACCAACAGgtacctattttacccatgtagaga--ggaactgaattaagtt-atatggttcacagtagccttcagaaatgagttcattaaagaatatatgttatggctttga
















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|88749903|gb|DY534044.1|DY534044
EST:     GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG                         CNNNNNNNNGGCATTTTATACGGCAGCATTCTCTGGTTTGGCTGAACCACT
genomic: GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAGgtacttgtta ... aatgtcacagCAAAAAAAAGGCATTTTATACGGCAGCATTCTCTGGTTTGGCTGAACCACT
EST: gi|101385255|gb|EB814673.1|EB814673
EST:     GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG                         CNNNNNNNNGGCATTTTATACGGCAGCATTCTCTGGTTTGGCTGAACCACT
genomic: GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAGgtacttgtta ... aatgtcacagCAAAAAAAAGGCATTTTATACGGCAGCATTCTCTGGTTTGGCTGAACCACT
EST: gi|71308419|gb|DR790442.1|DR790442
EST:     GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG                         CNNNNNNNNGGCATTTTATACGGCAGCATTCTCTGGTTTGGCTGAACCACT
genomic: GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAGgtacttgtta ... aatgtcacagCAAAAAAAAGGCATTTTATACGGCAGCATTCTCTGGTTTGGCTGAACCACT
EST: gi|76288875|gb|DV028443.1|DV028443
EST:     GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG                         C---AAAAAGGCATTTTATACGGCAGCATTCTCTGGTTTGGCTGAACCACT
genomic: GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAGgtacttgtta ... aatgtcacagCAAAAAAAAGGCATTTTATACGGCAGCATTCTCTGGTTTGGCTGAACCACT
EST: gi|50324963|gb|CO520089.1|CO520089
EST:     GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG                         C---AAAAAGGCATTTTATACGGCAGCATTCTCTGGTTTGGCTGAACCACT
genomic: GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAGgtacttgtta ... aatgtcacagCAAAAAAAAGGCATTTTATACGGCAGCATTCTCTGGTTTGGCTGAACCACT
EST: gi|71300310|gb|DR786224.1|DR786224
EST:     GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG                         CNNNNNNNNGGCATTTTATACGGCAGCATTCTCTGGTTTGGCTGAACCACT
genomic: GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAGgtacttgtta ... aatgtcacagCAAAAAAAAGGCATTTTATACGGCAGCATTCTCTGGTTTGGCTGAACCACT
EST: gi|89762575|gb|DY690101.1|DY690101
EST:     GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG                         CNNNNNNNNGGCATTTTATACGGCAGCATTCTCTGGTTTGGCTGAACCACT
genomic: GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAGgtacttgtta ... aatgtcacagCAAAAAAAAGGCATTTTATACGGCAGCATTCTCTGGTTTGGCTGAACCACT
EST: gi|71446246|gb|DR827296.1|DR827296
EST:     GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG                         CNNNNNNNNGGCATTTTATACGGCAGCATTCTCTGGTTTGGCTGAACCACT
genomic: GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAGgtacttgtta ... aatgtcacagCAAAAAAAAGGCATTTTATACGGCAGCATTCTCTGGTTTGGCTGAACCACT
EST: gi|91052253|gb|EB162671.1|EB162671
EST:     GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAG                         CNNNNNNNNGGCATTTTATACGGCAGCATTCTCTGGTTTGGCTGAACCACT
genomic: GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAGgtacttgtta ... aatgtcacagCAAAAAAAAGGCATTTTATACGGCAGCATTCTCTGGTTTGGCTGAACCACT

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: 47 (upstream exon), 46 (downstream exon)
Score: 37

GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAGgtacttgtta ... aatgtcacagCAAAAAAAAGGCATTTTATACGGCAGCATTCTCTGGTTTGGCTGAACCACTAGGAGTGGTTGCTGTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 82

GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAGgtacttgtta ... aatgtcacagCAAAAAAAAGGCATTTTATACGGCAGCATTCTCTGGTTTGGCTGAACCACTAGGAGTGGTTGCTGTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 166

GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAGgtacttgtta ... aatgtcacagCAAAAAAAAGGCATTTTATACGGCAGCATTCTCTGGTTTGGCTGAACCACTAGGAGTGGTTGCTGTAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 132

GGGGTTGCTGTAGCTCTTCCAATCTATTTTGCTACCAAAAGgtacttgtta ... aatgtcacagCAAAAAAAAGGCATTTTATACGGCAGCATTCTCTGGTTTGGCTGAACCACTAGGAGTGGTTGCTGTAG