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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGTATCCCAGTTAGCTTCTGGAAAACAGCCTGTTGGTACAACGGCTTACATGGGCAACATACAGTACTTGATGCAATGCAAATGTGGTGTAAATACAGgtatatagttgtatcttctggcaggctcctgttttagacagctgtatgccagtcatcactgtacgttatgtatatatatgcccattgctgggaagccattgatgttgagatgaatgccatagtgattcatttttccatgattatcgacag

Basic information

species Oryza sativa
transcript LOC_Os06g01390.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g01390.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G052389_T01 (Zea mays), 5'ss of exon 10
ACTGTATCCCAGTTAGCTTCTGGAAAACAGCCTGTTGGTACAACGGCTTACATGGGCAACATACAGTACTTGATGCAATGCAAATGTGGTGTAAATACAGgtatatagttgtatcttctggcaggctcctgttttagacagctgtatgccagtcatcactgtacgttatgtatatatatgcccattgctgggaagccattgatgttgagatgaatgccatagtgattcatttttccatgattatcgacag
|| || || ||||| || || || |||||||||||||| |||| ||| |||||||||||  | ||||| |||||||||||||||| || ||| | | ||||||  || || ||   |    ||   | || | | |   |   | | || |   ||     ||   | | | | ||   | ||||     ||   |  || |                                                
ACCGTTTCTCAGTTGGCATCCGGGAAACAGCCTGTTGGCACAATGGCCTACATGGGCAAAGTGCAGTATTTGATGCAATGCAAATCTGCTGTCAGTTCAGgtacgtatttataggctgacacacatttctctctcaagtacaaggaggctatatat-----tagcctgtatttgtaacagtccatgttctggcgactgttaacag---------------------------------------------

upper sequence: LOC_Os06g01390.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM5G864319_T01 (Zea mays), 5'ss of exon 10
ACTGTATCCCAGTTAGCTTCTGGAAAACAGCCTGTTGGTACAACGGCTTACATGGGCAACATACAGTACTTGATGCAATGCAAATGTGGTGTAAATACAGgtatatagttgtatcttctggcaggctcctgttttagacagctgtatgccagtcatcactgtacgttatgtatatatatgcccattgctgggaagccattgatgttgagatgaatgccatagtgattcatttttccatgattatcgacag
||  |||| || ||  | ||||||||||| ||||||||||||| |||||||||||||||  |||| ||  |||||||||||||||||| ||| || |||||||  || ||         ||| || ||   || ||        | | | |||  ||| | ||  ||   ||| | |       ||  || | |     | ||||    ||  |        | |||||| |||   ||| |  | ||||
ACCTTATCTCAATTGACATCTGGAAAACAACCTGTTGGTACAATGGCTTACATGGGCAATGTACAATATCTGATGCAATGCAAATGTGCTGTTAACACAGgtacttattta--------ggctggatc--attata--------ttttctagttctcagt-tatatttgatatttgttccaggcttcttgagga-----taatgtctgtattgactatggtataattcatgtttg-gtgact--caacag
















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|58672794|gb|CK061480.1|CK061480
EST:     ATGGTGCAACATACAGTACTTGATGCAATGCAAATGTGGTGTAAATACAG                         CTGAAGATTGGCTAAATCCTGCTGCCATACGAGAGGTATTTGAAGCTCGGG
genomic: ATGG-GCAACATACAGTACTTGATGCAATGCAAATGTGGTGTAAATACAGgtatatagtt ... ttatcgacagCTGAAGATTGGCTAAATCCTGCTGCCATACGAGAGGTATTTGAAGCTCGGG
EST: gi|58670583|gb|CK059269.1|CK059269
EST:     CATGGGCAACATACAGTACTTGATGCAATGCAAATGTGGTGTAAATACAG                         CTGAAGATTGGCTAAATCCTGCTGCCATACGAGAGGTATTTGAAGCTCGGG
genomic: CATGGGCAACATACAGTACTTGATGCAATGCAAATGTGGTGTAAATACAGgtatatagtt ... ttatcgacagCTGAAGATTGGCTAAATCCTGCTGCCATACGAGAGGTATTTGAAGCTCGGG
EST: gi|218498819|gb|FG964003.1|FG964003
EST:     CATGGGCAACATACAGTACTTGATGCAATGCAAATGTGGTGTAAATACAG                         CTGAAGATTGGCTAAATCCTGCTGCCATACGAGAGGTATTTGAAGCTCGGG
genomic: CATGGGCAACATACAGTACTTGATGCAATGCAAATGTGGTGTAAATACAGgtatatagtt ... ttatcgacagCTGAAGATTGGCTAAATCCTGCTGCCATACGAGAGGTATTTGAAGCTCGGG
EST: gi|29641670|gb|CB646677.1|CB646677
EST:     CATGGGCAACATACAGTACTTGATGCAATGCAAATGTGGTGTAAATACAG                         CTGAAGATTGGCTAAATCCTGCTGCCATACGAGAGGTATTTGAAGCTCGGG
genomic: CATGGGCAACATACAGTACTTGATGCAATGCAAATGTGGTGTAAATACAGgtatatagtt ... ttatcgacagCTGAAGATTGGCTAAATCCTGCTGCCATACGAGAGGTATTTGAAGCTCGGG
EST: gi|58652726|gb|CK041406.1|CK041406
EST:     CATGGGCAACATACAGTACTTGATGCAATGCAAATGTGGTGTAAATACAG                         CTGAAGATTGGCTAAATCCTGCTGCCATACGAGAGGTATTTGAAGCTCGG
genomic: CATGGGCAACATACAGTACTTGATGCAATGCAAATGTGGTGTAAATACAGgtatatagtt ... ttatcgacagCTGAAGATTGGCTAAATCCTGCTGCCATACGAGAGGTATTTGAAGCTCGG
EST: gi|27410222|gb|CA923292.1|CA923292
EST:     GATGCAATGCAAATGTGGTGTAAATACAG                         CTGAAGATTGGCTAAATCCTGCTGCCATACGAGAGGTATTTGAAGCTCGGG
genomic: GATGCAATGCAAATGTGGTGTAAATACAGgtatatagtt ... ttatcgacagCTGAAGATTGGCTAAATCCTGCTGCCATACGAGAGGTATTTGAAGCTCGGG
EST: gi|58598568|gb|CK009096.1|CK009096
EST:     CATGGGCAACATACAGTACTTGATGCAATGCAAATGTGGTGTAAATACAG                         CTGAAGATTGGCTAAATCCTGCTGCCATACGAGAGGTATTTGAAGCTCGGG
genomic: CATGGGCAACATACAGTACTTGATGCAATGCAAATGTGGTGTAAATACAGgtatatagtt ... ttatcgacagCTGAAGATTGGCTAAATCCTGCTGCCATACGAGAGGTATTTGAAGCTCGGG
EST: gi|87023655|gb|CI286406.1|CI286406
EST:     CATGGGCAACATACAGTACTTGATGCAATGCAAATGTGGTGTAAATACAG                         CTGAAGATTGGCTAAATCCTGCTGCCATACGAGAGGTATTTGAAGCTCGGG
genomic: CATGGGCAACATACAGTACTTGATGCAATGCAAATGTGGTGTAAATACAGgtatatagtt ... ttatcgacagCTGAAGATTGGCTAAATCCTGCTGCCATACGAGAGGTATTTGAAGCTCGGG

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 1 RNA-Seqlibrary.


Block sizes: 73 (upstream exon), 73 (downstream exon)
Score: 48

ACTGTATCCCAGTTAGCTTCTGGAAAACAGCCTGTTGGTACAACGGCTTACATGGGCAACATACAGTACTTGATGCAATGCAAATGTGGTGTAAATACAGgtatatagtt ... ttatcgacagCTGAAGATTGGCTAAATCCTGCTGCCATACGAGAGGTATTTGAAGCTCGGGCTCTCAGGATGGCGGTGAATTGTGCCCAGAACATAAACAAGGCGCCAAG




<











<


<