Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCATGATGTTAAGAACACGGCTATTATGGGGAAGATTCGGTATGCATGATCAGCACCAGGATTGGCGACTCGACGTTGACAACATGACATATGAGgtaccctcccatgcccaatatgtgcaacccaaaaaaaaaaactttttagtacattaccatcacaaattctccttcatccacccattgttcaatttgatag

Basic information

species Oryza sativa
transcript LOC_Os05g47670.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g47670.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G061663_T02 (Zea mays), 5'ss of exon 2
ATCATGATGTTAAGAACACGGCTATTATGGGGAAGATTCGGTATGCATGATCAGCACCAGGATTGGCGACTCGACGTTGACAACATGACATATGAGgtaccctcccatgcccaatatgtgcaacccaaaaaaaaaaactttttagtacattaccatcacaaattctccttcatccacccattgttcaatttgatag
   ||||||||    ||| || | |||| ||||||| | |||||  |||||||| | ||||||||||| ||||| || |||||||||||||||||||||||||||||  |  ||||     | | |  |  |||| |              | ||  | | ||| | | ||| |    |||    ||         
---ATGATGTTCCAGACAAGGATGTTATTGGGAAGAATGGGTATTTATGATCAGTATCAGGATTGGCGCCTCGATGTCGACAACATGACATATGAGgtaccctccca--ctgaatagcaatagcacgtagtaaaataa-------------aacagaaaagattttacctcaccatttcatatcgcag--------
















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|112786871|gb|EE591602.1|EE591602
EST:     ATGATCAGCACCAGGATTGGCGACTCGACGTTGACAACATGACATATGAG                         GAGCTGCTGGATCTTGAAGACAGAATTGGGTATGTAAGCACAGGGTTGCAT
genomic: ATGATCAGCACCAGGATTGGCGACTCGACGTTGACAACATGACATATGAGgtaccctccc ... aatttgatagGAGCTGCTGGATCTTGAAGACAGAATTGGGTATGTAAGCACAGGGTTGCAT
EST: gi|38474313|gb|CF958445.1|CF958445
EST:     CCAGGA-TGGCGACTCGACG-TGACAACATGACATATCGAG                         GAGCTGCTGGATCTTGAAGACAGAATTGGGTATGTAAGCACAGGGTTGCA
genomic: CCAGGATTGGCGACTCGACGTTGACAACATGACATAT-GAGgtaccctccc ... aatttgatagGAGCTGCTGGATCTTGAAGACAGAATTGGGTATGTAAGCACAGGGTTGCA
EST: gi|29662570|gb|CB658845.1|CB658845
EST:     ATGATCAGCACCAGGATTGGCGACTCGACGTTGACAACATGACATATGAG                         GAGCTGCTGGATCTTGAAGACAGAATTGGGTATGTAAGCACAGGGTTGCAT
genomic: ATGATCAGCACCAGGATTGGCGACTCGACGTTGACAACATGACATATGAGgtaccctccc ... aatttgatagGAGCTGCTGGATCTTGAAGACAGAATTGGGTATGTAAGCACAGGGTTGCAT
EST: gi|87026428|gb|CI252382.1|CI252382
EST:     ATGATCAGCACCAGGATTGGCGACTCGACGTTGACAACATGACATATGAG                         GAGCTGCTGGATCTTGAAGACAGAATTGGGTATGTAAGCCCAGGGTTGCAT
genomic: ATGATCAGCACCAGGATTGGCGACTCGACGTTGACAACATGACATATGAGgtaccctccc ... aatttgatagGAGCTGCTGGATCTTGAAGACAGAATTGGGTATGTAAGCACAGGGTTGCAT
EST: gi|86494294|gb|CI136927.1|CI136927
EST:     ATGATCAGCACCAGGATTGGCGACTCGACGTTGACAACATGACATATGAG                         GAGCTGCTGGATCTTGAAGACAGAATTGGGTATGTAAGCACAGGGTTGCAT
genomic: ATGATCAGCACCAGGATTGGCGACTCGACGTTGACAACATGACATATGAGgtaccctccc ... aatttgatagGAGCTGCTGGATCTTGAAGACAGAATTGGGTATGTAAGCACAGGGTTGCAT
EST: gi|29659759|gb|CB656034.1|CB656034
EST:     ATGATCAGCACCAGGATTGGCGACTCGACGTTGACAACATGACATATGAG                         GAGCTGCTGGATCTTGAAGACAGAATTGGGTATGTAAGCACAGGGTTGCAT
genomic: ATGATCAGCACCAGGATTGGCGACTCGACGTTGACAACATGACATATGAGgtaccctccc ... aatttgatagGAGCTGCTGGATCTTGAAGACAGAATTGGGTATGTAAGCACAGGGTTGCAT
EST: gi|27545904|gb|CA764245.2|CA764245
EST:     GATCAGCACCAGGATTGGCGACTCGACGCTGACAACATGACATATGAG                         GAGCTGCTGGATCTTGAAGACAGAATTGGGTATGTAAGCACAGGGTTGCAT
genomic: GATCAGCACCAGGATTGGCGACTCGACGTTGACAACATGACATATGAGgtaccctccc ... aatttgatagGAGCTGCTGGATCTTGAAGACAGAATTGGGTATGTAAGCACAGGGTTGCAT

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: 69 (upstream exon), 50 (downstream exon)
Score: 26

ATCATGATGTTAAGAACACGGCTATTATGGGGAAGATTCGGTATGCATGATCAGCACCAGGATTGGCGACTCGACGTTGACAACATGACATATGAGgtaccctccc ... aatttgatagGAGCTGCTGGATCTTGAAGACAGAATTGGGTATGTAAGCACAGGGTTGCATGACGATGAAATCGCTCGCAGCCTTAGGATGGTCAAGTATTCAGCATTCA




<











<


<