Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTGGGACATCAGAACAAAAGCACATGTTTCTGCTTTAACAGGGCATGACAACACTGTCTGTTCAGTGTTTGCTCGTCCTACGgtaagaatgcattttaacctgtcaagtactcaagttcacgattcacaacaatattgagttctgccaaacagtacactttatttcatgatatggtttcatt...

Basic information

species Zea mays
transcript GRMZM2G017089_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017089_T01 (Zea mays), 5'ss of exon 10
lower sequence: LOC_Os03g21990.1 (Oryza sativa), 5'ss of exon 12
GTGTGGGACATCAGAACAAAAGCACATGTTTCTGCTTTAACAGGGCATGACAACACTGTCTGTTCAGTGTTTGCTCGTCCTACGgtaagaatgcattttaacctgtcaagtactcaagttcacgattcacaacaatattgagttctgcca---aacagtacactttatttcatgatatggt--ttcatt------
|| ||||||||| |||| ||||| ||||||||||||||||| || ||||| ||||| || || |||||||||||||||||||||||||||| || ||| || || |          || | |    | ||  ||||||  |||| ||| |   ||   ||  ||||| ||   |   |  |  |||||       
GTCTGGGACATCCGAACGAAAGCTCATGTTTCTGCTTTAACTGGTCATGATAACACCGTATGCTCAGTGTTTGCTCGTCCTACGgtaagaaagcttttgaatcttttgc-------agctta----ttactgcaatatctagttttgcgacttaatgttattctttagttggaggctttcttgttcatagccatg
















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|116814103|gb|EC856623.1|EC856623
EST:     CTTTAACAAGGCATGACAACACTGTCTGTTCAGTGTTTGCTCGTCCTACG                         GATCCTCAAGTTGTTACTGGTTCACATGATACAACTATTAAATTCTGGGAT
genomic: CTTTAACAGGGCATGACAACACTGTCTGTTCAGTGTTTGCTCGTCCTACGgtaagaatgc ... cttgtctcagGATCCTCAAGTTGTTACTGGTTCACATGATACAACTATTAAATTCTGGGAT
EST: gi|71432304|gb|DR813354.1|DR813354
EST:     CTTTAACAGGGCATGACAACACTGTCTGTTCAGTGTTTGCTCGTCCTACG                         GATCCTCAAGTTGTTACTGGTTCACATGATACAACTATTAAATTCTGGGAT
genomic: CTTTAACAGGGCATGACAACACTGTCTGTTCAGTGTTTGCTCGTCCTACGgtaagaatgc ... cttgtctcagGATCCTCAAGTTGTTACTGGTTCACATGATACAACTATTAAATTCTGGGAT
EST: gi|60357310|gb|DN224283.1|DN224283
EST:     CTTTAACAGGGCATGACAACACTGTCTGTTCAGTGTTTGCTCGTCCTACG                         GATCCTCAAGTTGTTACTGGTTCACATGATACAACTATTAAATTCTGGGAT
genomic: CTTTAACAGGGCATGACAACACTGTCTGTTCAGTGTTTGCTCGTCCTACGgtaagaatgc ... cttgtctcagGATCCTCAAGTTGTTACTGGTTCACATGATACAACTATTAAATTCTGGGAT
EST: gi|32933221|gb|CF038033.1|CF038033
EST:     CTTTAACAGGGCATGACAACACTGTCTGTTCAGTGTTTGCTCGTCCTACG                         GATCCTCAAGTTGTTACTGGTTCACATGATACAACTATTAAATTCTGGGAT
genomic: CTTTAACAGGGCATGACAACACTGTCTGTTCAGTGTTTGCTCGTCCTACGgtaagaatgc ... cttgtctcagGATCCTCAAGTTGTTACTGGTTCACATGATACAACTATTAAATTCTGGGAT
EST: gi|211016045|gb|FL237689.1|FL237689
EST:     CTTTAACAGGGCATGACAACACTGTCTGTTCAGTGTTTGCTCGTCCTACG                         GATCCTCAAGTTGTTACTGGTTCACATGATACAACTATTAAATTCTGGGAT
genomic: CTTTAACAGGGCATGACAACACTGTCTGTTCAGTGTTTGCTCGTCCTACGgtaagaatgc ... cttgtctcagGATCCTCAAGTTGTTACTGGTTCACATGATACAACTATTAAATTCTGGGAT
EST: gi|148943610|gb|EC888673.2|EC888673
EST:     CTTTAACAGGGCATGACAACACTGTCTGTTCAGTGTTTGCTCGTCCTACG                         GATCCTCAAGTTGTTACTGGTTCACATGATACAACTATTAAATTCTGGGAT
genomic: CTTTAACAGGGCATGACAACACTGTCTGTTCAGTGTTTGCTCGTCCTACGgtaagaatgc ... cttgtctcagGATCCTCAAGTTGTTACTGGTTCACATGATACAACTATTAAATTCTGGGAT
EST: gi|71432303|gb|DR813353.1|DR813353
EST:     AGGGCAGGACAACACTGTCTGTTCAGTGTTTGCTCGTCCTACG                         GATCCTCAAGTTGTTACTGGTTCACATGATACAACTATTAAATTCTGGGAT
genomic: AGGGCATGACAACACTGTCTGTTCAGTGTTTGCTCGTCCTACGgtaagaatgc ... cttgtctcagGATCCTCAAGTTGTTACTGGTTCACATGATACAACTATTAAATTCTGGGAT

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: 48 (upstream exon), 48 (downstream exon)
Score: 181

GTGTGGGACATCAGAACAAAAGCACATGTTTCTGCTTTAACAGGGCATGACAACACTGTCTGTTCAGTGTTTGCTCGTCCTACGgtaagaatgc ... cttgtctcagGATCCTCAAGTTGTTACTGGTTCACATGATACAACTATTAAATTCTGGGATCTTGTAGCTG


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 78

GTGTGGGACATCAGAACAAAAGCACATGTTTCTGCTTTAACAGGGCATGACAACACTGTCTGTTCAGTGTTTGCTCGTCCTACGgtaagaatgc ... cttgtctcagGATCCTCAAGTTGTTACTGGTTCACATGATACAACTATTAAATTCTGGGATCTTGTAGCTG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 104

GTGTGGGACATCAGAACAAAAGCACATGTTTCTGCTTTAACAGGGCATGACAACACTGTCTGTTCAGTGTTTGCTCGTCCTACGgtaagaatgc ... cttgtctcagGATCCTCAAGTTGTTACTGGTTCACATGATACAACTATTAAATTCTGGGATCTTGTAGCTG


Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 75

GTGTGGGACATCAGAACAAAAGCACATGTTTCTGCTTTAACAGGGCATGACAACACTGTCTGTTCAGTGTTTGCTCGTCCTACGgtaagaatgc ... cttgtctcagGATCCTCAAGTTGTTACTGGTTCACATGATACAACTATTAAATTCTGGGATCTTGTAGCTG