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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATGGTGAGAGTGCTAATGAGAAAGAAAAATCATATGGTTCCATTATGATGGAAAGGTTGACCAGTTCACCGAATGGTCGAATTGATCATGTGCTTCAGgtgataaaatttgctccactttgaccttatatttttggcttgttcctgcatgcttttatcgttcaatgagtttttttctttaatcttaaatctcaaatctatttttgcag

Basic information

species Zea mays
transcript GRMZM2G318860_T02
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G318860_T02 (Zea mays), 5'ss of exon 19
lower sequence: LOC_Os08g01920.1 (Oryza sativa), 5'ss of exon 19
GGATGGTGAGAGTGCTAATGAGAAAGAAAAATCATATGGTTCCATTATGATGGAAAGGTTGACCAGTTCACCGAATGGTCGAATTGATCATGTGCTTCAGgtgataaaatttgctccactttgaccttatatttttggcttgttcctgcatgcttttatcgttcaatgagtttttttctttaatcttaaatctcaaatctatttttgcag
||| | ||| ||   |||||||||||| || |||||||||| ||| |||||||||||| ||||  |||||||  ||||||| ||||| ||||| |||||||| || ||| ||   | | |    |    |   |||  ||   | |||  ||  | ||| |  || |||  || | |  |     ||  || | |||  ||         
GGACGTTGACAGCAATAATGAGAAAGAGAAGTCATATGGTTACATGATGATGGAAAGGCTGACAGGTTCACCAGATGGTCGGATTGACCATGTACTTCAGgttattaaacttttcctattaaagcaagttcaatttcactccctgctg-gtgtatgtatagg-cattgaaattgtgtactctgctttggatgtgaaaagtac--------
















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|67015052|gb|CO443801.1|CO443801
EST:     TGGAAAGGTTGACCAGTTCACCGAATGGTCGAATTGATCATGTGCTTCAG                         GAGAAAACATTTCAGCATCCATATCTATCTGCTTTGGGAGCTCATAC
genomic: TGGAAAGGTTGACCAGTTCACCGAATGGTCGAATTGATCATGTGCTTCAGgtgataaaat ... atttttgcagGAGAAAACATTTCAGCATCCATATCTATCTGCTTTGGGAGCTCATAC
EST: gi|78075263|gb|DV503697.1|DV503697
EST:     TGGAAAGGTTGACCAGTTCACCGAATGGTCGAATTGATCATGTGCTTCAG                         GAGAAAACATTTCAGCATCCATATCTATCTGCTTTGGGAGCTCATAC
genomic: TGGAAAGGTTGACCAGTTCACCGAATGGTCGAATTGATCATGTGCTTCAGgtgataaaat ... atttttgcagGAGAAAACATTTCAGCATCCATATCTATCTGCTTTGGGAGCTCATAC
EST: gi|28873574|gb|CB329545.1|CB329545
EST:     TGGAAAGGTTGACCAGTTCACCGAATGGTCGAATTGATCATGTGCTTCAG                         GAGAAAACATTTCAGCATCCATATCTATCTGCTTTGGGAGCTCATAC
genomic: TGGAAAGGTTGACCAGTTCACCGAATGGTCGAATTGATCATGTGCTTCAGgtgataaaat ... atttttgcagGAGAAAACATTTCAGCATCCATATCTATCTGCTTTGGGAGCTCATAC
EST: gi|211270821|gb|FL023496.1|FL023496
EST:     TGGAAAGGTTGACCAGTTCACCGAATGGTCGAATTGATCATGTGCTTCAG                         GAGAAAACATTTCAGCATCCATATCTATCTGCTTTGGGAGCTCATAC
genomic: TGGAAAGGTTGACCAGTTCACCGAATGGTCGAATTGATCATGTGCTTCAGgtgataaaat ... atttttgcagGAGAAAACATTTCAGCATCCATATCTATCTGCTTTGGGAGCTCATAC

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), 44 (downstream exon)
Score: 87

GGATGGTGAGAGTGCTAATGAGAAAGAAAAATCATATGGTTCCATTATGATGGAAAGGTTGACCAGTTCACCGAATGGTCGAATTGATCATGTGCTTCAGgtgataaaat ... atttttgcagGAGAAAACATTTCAGCATCCATATCTATCTGCTTTGGGAGCTCATAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 118

GGATGGTGAGAGTGCTAATGAGAAAGAAAAATCATATGGTTCCATTATGATGGAAAGGTTGACCAGTTCACCGAATGGTCGAATTGATCATGTGCTTCAGgtgataaaat ... atttttgcagGAGAAAACATTTCAGCATCCATATCTATCTGCTTTGGGAGCTCATAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 209

GGATGGTGAGAGTGCTAATGAGAAAGAAAAATCATATGGTTCCATTATGATGGAAAGGTTGACCAGTTCACCGAATGGTCGAATTGATCATGTGCTTCAGgtgataaaat ... atttttgcagGAGAAAACATTTCAGCATCCATATCTATCTGCTTTGGGAGCTCATAC


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 68

GGATGGTGAGAGTGCTAATGAGAAAGAAAAATCATATGGTTCCATTATGATGGAAAGGTTGACCAGTTCACCGAATGGTCGAATTGATCATGTGCTTCAGgtgataaaat ... atttttgcagGAGAAAACATTTCAGCATCCATATCTATCTGCTTTGGGAGCTCATAC