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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGCATAAATTCTGTGTTCTATTTCTCATCAACTGTATTCAGAAGTGTGGGGGTGCCCTCTAACCTTGCCAACATATGCATGGGGATTTCTAATCTATCAGgtgcactcaaagctgtctcatacagtggtattatgttcattttgtcacatgacttatttttgtgtgctgtcttacag

Basic information

species Zea mays
transcript GRMZM2G412899_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G412899_T05 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os02g17500.2 (Oryza sativa), 5'ss of exon 9
GGCATAAATTCTGTGTTCTATTTCTCATCAACTGTATTCAGAAGTGTGGGGGTGCCCTCTAACCTTGCCAACATATGCATGGGGATTTCTAATCTATCAGgtgcactca---aagc----tgtctcatacagtggtattatgttcattttgtcacatgacttatttttgtgtgctgtcttacag------------
||||||||||||||||||||||||||||||||||| |||||||||||||| |||||| |||||||||| |||||||||||||||||  | ||| |||||||||  ||||    |||    | |||  |    || | || |  |  || ||| | ||   |  ||  ||  |  ||| | |               
GGCATAAATTCTGTGTTCTATTTCTCATCAACTGTGTTCAGAAGTGTGGGTGTGCCCCCTAACCTTGCGAACATATGCATGGGGATAGCAAATTTATCAGgtgggctcattggagcatcttctctttttttctgttgttctact-gttctgttatattgatggttgatggattttgtttgatgtgtttgcttccag

upper sequence: GRMZM2G412899_T05 (Zea mays), 5'ss of exon 10
lower sequence: AT1G79820.2 (Arabidopsis thaliana), 5'ss of exon 10
GGCATAAATTCTGTGTTCTATTTCTCATCAACTGTATTCAGAAGTGTGGGGGTGCCCTCTAACCTTGCCAACATATGCATGGGGATTTCTAATCTATCAGgtgcactcaaagctgtctcatacagtggtattatgttcattttgtcacatgac-ttatttttgtgtgctgtcttacag-------------------------
|| |||||| ||||||||||||||||||||||||| ||||  |  |  || || || ||   |  ||| ||||||||  | ||  |||  || || | ||||  | | |||  || ||  | |      ||| |  | ||    | | | | | | || ||  ||    |    | |                          
GGGATAAATGCTGTGTTCTATTTCTCATCAACTGTCTTCAAGAAAGCTGGTGTACCTTCAGCCTCTGCAAACATATGTGTAGGAGTTTGCAACCTCTTAGgt--attgaaatgtgactttttcttgtacattctact-atggcttgaaaggccatcatattcatgataagctagataagcaagtaggtgaatgcagtcttcct

upper sequence: GRMZM2G412899_T05 (Zea mays), 5'ss of exon 10
lower sequence: Vv09s0002g04380.t01 (Vitis vinifera), 5'ss of exon 9
GGCATAAATTCTGTGTTCTATTTCTCATCAACTGTATTCAGAAGTGTGGGGGTGCCCTCTAACCTTGCCAACATATGCATGGGGATTTCTAATCTATCAGgtg-----cactcaaagctgtctcatacagt--ggtattatgttcattttgtcacatgacttatttttgtgtgctgtcttacag----------
||||||||| |||||||||||||||| |||||||| |||| | | |  || || ||  |  ||||||| || || ||  | || ||| | ||| ||||||||      |||| |   | ||  || | |     || ||   |||      |   || |   |||| | |    |  | |  |           
GGCATAAATGCTGTGTTCTATTTCTCTTCAACTGTCTTCAAAGGAGCTGGAGTACCTCCAGACCTTGCAAATATGTGTGTTGGAATTGCAAATTTATCAGgtaaagatcactgacttcagttgcaaatatctcagttttgcattccaaaattatgattagccatttctttactgtaccctttaaacttctttag

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|110961485|gb|EE181537.1|EE181537
EST:     CCTTGCCAACATATGCATGGGGATTTCTAATCTATCAG                         GATCAATTGTAGCAATGCTTCTAATGGACAAGCTAGGTAGAAAAGTGCTTC
genomic: CCTTGCCAACATATGCATGGGGATTTCTAATCTATCAGgtgcactcaa ... tgtcttacagGATCAATTGTAGCAATGCTTCTAATGGACAAGCTAGGTAGAAAAGTGCTTC
EST: gi|78110186|gb|DV528601.1|DV528601
EST:     GGGGA-TTCTAATCTATCAG                         GATCAATGGTAGCAATGCTTCTAATGGACAAGCTAGGTAGAAAAGTGCTTC
genomic: GGGGATTTCTAATCTATCAGgtgcactcaa ... tgtcttacagGATCAATTGTAGCAATGCTTCTAATGGACAAGCTAGGTAGAAAAGTGCTTC
EST: gi|148974491|gb|EE025274.2|EE025274
EST:     ATGCATGGGGATTTCTAATCTATCAG                         GATCAATTGTAGCAATGCTTCTAATGGACAAGCTAGGTAGAAAAGTGCTTC
genomic: ATGCATGGGGATTTCTAATCTATCAGgtgcactcaa ... tgtcttacagGATCAATTGTAGCAATGCTTCTAATGGACAAGCTAGGTAGAAAAGTGCTTC

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: 153

GGCATAAATTCTGTGTTCTATTTCTCATCAACTGTATTCAGAAGTGTGGGGGTGCCCTCTAACCTTGCCAACATATGCATGGGGATTTCTAATCTATCAGgtgcactcaa ... tgtcttacagGATCAATTGTAGCAATGCTTCTAATGGACAAGCTAGGTAGAAAAGTGCTTCTTTCAGGGAGTTTTCTTGGGATG


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

GGCATAAATTCTGTGTTCTATTTCTCATCAACTGTATTCAGAAGTGTGGGGGTGCCCTCTAACCTTGCCAACATATGCATGGGGATTTCTAATCTATCAGgtgcactcaa ... tgtcttacagGATCAATTGTAGCAATGCTTCTAATGGACAAGCTAGGTAGAAAAGTGCTTCTTTCAGGGAGTTTTCTTGGGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 120

GGCATAAATTCTGTGTTCTATTTCTCATCAACTGTATTCAGAAGTGTGGGGGTGCCCTCTAACCTTGCCAACATATGCATGGGGATTTCTAATCTATCAGgtgcactcaa ... tgtcttacagGATCAATTGTAGCAATGCTTCTAATGGACAAGCTAGGTAGAAAAGTGCTTCTTTCAGGGAGTTTTCTTGGGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 228

GGCATAAATTCTGTGTTCTATTTCTCATCAACTGTATTCAGAAGTGTGGGGGTGCCCTCTAACCTTGCCAACATATGCATGGGGATTTCTAATCTATCAGgtgcactcaa ... tgtcttacagGATCAATTGTAGCAATGCTTCTAATGGACAAGCTAGGTAGAAAAGTGCTTCTTTCAGGGAGTTTTCTTGGGATG