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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGCAGTGACACCATTATCTCAATCAGATGCTGTCGATCTGGTTAAGGACGTTTTTGCATCAGCCACAGAACGAGACATATACACTgtatgatgatttaaatctctttggttgctcgaagttaatcactagtggccaactaaacagtattgattcaaattctaattttgttccatgaattttgcag

Basic information

species Oryza sativa
transcript LOC_Os08g41730.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g41730.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G124417_T01 (Zea mays), 5'ss of exon 5
GATGCAGTGACACCATTATCTCAATCAGATGCTGTCGATCTGGTTAAGGACGTTTTTGCATCAGCCACAGAACGAGACATATACACTgtatgatgatttaaatctctttgg--ttgctcgaagttaatcac--tagtggccaactaaacagtattgattcaaattctaattttgttccatgaattttgcag
|||||||||||||| || ||| |||| ||||| || |||||||| ||||||||||| ||||||||||| ||||||||||||||||||||||| || |||   |    |||   || |  ||  ||| |     |  ||   | |||||   |  ||| || |||   | | |||||||||||| |||||||
GATGCAGTGACACCCTTGTCTGAATCTGATGCGGTTGATCTGGTGAAGGACGTTTTCGCATCAGCCACTGAACGAGACATATACACTgtatgttgcttttcctgcacttgagatttccagagattactagtgatgatgattatctaaat--ttctgaatccaat---attgttgttccatgaaatttgcag
















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|88255892|gb|CI353763.1|CI353763
EST:     ATCTGGTTAAGGACGTTTTTGCATCAGCCACAGAACGAGACATATACACT                         GGAGATAAACTGGAGATTGTTGTCATCAACAGCGCCGGCTCTCACCGTGAG
genomic: ATCTGGTTAAGGACGTTTTTGCATCAGCCACAGAACGAGACATATACACTgtatgatgat ... aattttgcagGGAGATAAACTGGAGATTGTTGTCATCAACAGCGCCGGCTCTCACCGTGAG
EST: gi|86528394|gb|CI168600.1|CI168600
EST:     ATCTGGTTAAGGACGTTTTTGCATCAGCCACAGAATGAGACATATACACT                         GGAGATAAACTGGAGATTGTTGTCATCAACAGCGCCGGCTCTCACCGTGAG
genomic: ATCTGGTTAAGGACGTTTTTGCATCAGCCACAGAACGAGACATATACACTgtatgatgat ... aattttgcagGGAGATAAACTGGAGATTGTTGTCATCAACAGCGCCGGCTCTCACCGTGAG
EST: gi|86528608|gb|CI168814.1|CI168814
EST:     ATCTGGTTAAGGACGTTTTTGCATCAGCCACAGAATGAGACATATACACT                         GGAGATAAACTGGAGATTGTTGTCATCAACAGCGCCGGCTCTCACCGTGAG
genomic: ATCTGGTTAAGGACGTTTTTGCATCAGCCACAGAACGAGACATATACACTgtatgatgat ... aattttgcagGGAGATAAACTGGAGATTGTTGTCATCAACAGCGCCGGCTCTCACCGTGAG

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: 14 (upstream exon), 65 (downstream exon)
Score: 2

GATGCAGTGACACCATTATCTCAATCAGATGCTGTCGATCTGGTTAAGGACGTTTTTGCATCAGCCACAGAACGAGACATATACACTgtatgatgat ... aattttgcagGGAGATAAACTGGAGATTGTTGTCATCAACAGCGCCGGCTCTCACCGTGAGTTCATTGAGCTAAGGAAGGATTAGCGTGGGATACTATCAAACCACCTCG




<











<


<