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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTTCGACATGCGGCACATGTTCTCTTCGATAGAAAAATTGAAGGATCAGTTGATTTCAGAATCTTACGAAATTCAGATTTTCGTGAGGTTACACTGGAGgtgaattcatcctgcatcatgttggcctgctttcaattctctcttaagcatgattcaagtggccttagattaattttgtataacgtgtgttgtgttaatgcacag

Basic information

species Oryza sativa
transcript LOC_Os03g53750.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g53750.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G171998_T01 (Zea mays), 5'ss of exon 8
CTTTCGACATGCGGCACATGTTCTCTTCGATAGAAAAATTGAAGGATCAGTTGATTTCAGAATCTTACGAAATTCAGATTTTCGTGAGGTTACACTGGAGgtgaattcat--cctgcatcatgttggcctgctttcaattctctcttaagcatgattcaagtggccttagattaattttgtataacgtgtgttgtgttaatgcacag
||||||  |||  ||||||||  | | | | ||| |||| || ||  |  |||| ||||||||| | ||||||||||||||||||||  ||||||||||||| || ||||  |||  || ||  |||    |    |||| || | ||        |  ||||   ||  ||  ||      || |   || || ||       |||
CTTTCGCTATGTAGCACATGTAATTTACAAGAGAGAAATAGAGGGTCCTCTTGACTTCAGAATCCTCCGAAATTCAGATTTTCGTGAAATTACACTGGAGgtaaactcattcccttgatgatcatggaaaaccagtaattttcacctag------cttgagtga--ttgtatgtataacaattagcaaatgctgcgtgtgctagcag

upper sequence: LOC_Os03g53750.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G456690_T01 (Zea mays), 5'ss of exon 8
CTTTCGACATGCGGCACATGTTCTCTTCGATAGAAAAATTGAAGGATCAGTTGATTTCAGAATCTTACGAAATTCAGATTTTCGTGAGGTTACACTGGAGgtgaattcatcctgcatcatgttggcctgctttcaattctctcttaagcatgattcaagtggccttagattaattttgtataacgtgtgttgtgttaatgcacag
||||||  |||  ||| ||||  | | | | ||| |||| || ||  |  |||| |||||||||||  |||||||||||||||||||  ||||| ||||||| |  |||| |  | | |||   | | |       ||   | ||   | |   |  ||||    ||  |  ||      || |   || || ||       |||
CTTTCGCTATGGAGCAAATGTAATTTACAAAAGAGAAATAGAGGGTCCTCTTGACTTCAGAATCTTGAGAAATTCAGATTTTCGTGAAATTACATTGGAGgtaacctcattcc-cttgatggatggcagaaaatcgttaattattttacctagctggagtga--atatgtgtataacaattagcaaatgctgcgtgtgcttgcag
















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|29638417|gb|CB643426.1|CB643426
EST:     TTGATTTCAGAATCTTACGAAATTCAGATTTTCGTGAGGTTACACTGGAG                         GTGGAGGGCAAACCTGTTCTTAAGTTTGCACTTTGTTATGGATTCAGAAAT
genomic: TTGATTTCAGAATCTTACGAAATTCAGATTTTCGTGAGGTTACACTGGAGgtgaattcat ... taatgcacagGTGGAGGGCAAACCTGTTCTTAAGTTTGCACTTTGTTATGGATTCAGAAAT
EST: gi|29667391|gb|CB663666.1|CB663666
EST:     TTGATTTCAGAATCTTACGAAATTCAGATTTTCGTGAGGTTACACTGGAG                         GTGGAGGGCAAACCTGTTCTTAAGTTTGCACTTTGTTATGGATTCAGAAAT
genomic: TTGATTTCAGAATCTTACGAAATTCAGATTTTCGTGAGGTTACACTGGAGgtgaattcat ... taatgcacagGTGGAGGGCAAACCTGTTCTTAAGTTTGCACTTTGTTATGGATTCAGAAAT
EST: gi|29667390|gb|CB663665.1|CB663665
EST:     TTGATTTCAGAATCTTACGAAATTCAGATTTTCGTGAGGTTACACTGGAG                         GTGGAGGGCAAACCTGTTCTTAAGTTTGCACTTTGTTATGGATTCAGAAAT
genomic: TTGATTTCAGAATCTTACGAAATTCAGATTTTCGTGAGGTTACACTGGAGgtgaattcat ... taatgcacagGTGGAGGGCAAACCTGTTCTTAAGTTTGCACTTTGTTATGGATTCAGAAAT
EST: gi|218489808|gb|FG954312.1|FG954312
EST:     TTGATTTCAGAATCTTACGAAATTCAGATTTTCGTGAGGTTACACTGGAG                         GTGGAGGGCAAACCTG
genomic: TTGATTTCAGAATCTTACGAAATTCAGATTTTCGTGAGGTTACACTGGAGgtgaattcat ... taatgcacagGTGGAGGGCAAACCTG

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: 62 (upstream exon), 50 (downstream exon)
Score: 12

CTTTCGACATGCGGCACATGTTCTCTTCGATAGAAAAATTGAAGGATCAGTTGATTTCAGAATCTTACGAAATTCAGATTTTCGTGAGGTTACACTGGAGgtgaattcat ... taatgcacagGTGGAGGGCAAACCTGTTCTTAAGTTTGCACTTTGTTATGGATTCAGAAATCTGCAGAACATTATTAGGAAGATTAAGATGGGAAAATGCGAATATCACT




<











<


<