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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGAGTTTTCACCCTTTTATTTATCATAGCAAACGTTTCTACACTGTTCTACTCTGGCGCAGGGTGCTGGCCTTTTTAGTTgtaagtggctgtcccatgtcttttaacttatctctgcaaccattataatcatgatgtaacaatgatgtttttcttttctttcctctag

Basic information

species Oryza sativa
transcript LOC_Os01g63060.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g63060.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G169293_T01 (Zea mays), 5'ss of exon 5
TGGAGTTTTCACCCTTTTATTTATCATAGCAAACGTTTCTACACTGTTCTACTCTGGCGCAGGGTGCTGGCCTTTTTAGTTgtaagtggctgtcccatgtcttttaacttatctctgcaaccattataatcatgatgtaacaatgatgtttttcttttctttcctctag
||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||| ||||||||||| ||| |||| ||||||         ||    || |  ||   | || |   ||| ||  |||| |  |||||    ||  | ||  | | |  || ||
TGGAGTTTTCACCCTTTTATTTATCATAGCAAACGTTTCTACACTGTTCTACTATGGCGAAGGGTGCTGGCATTTCTAGTGgtaagt------ttgattatcttaactttgattgtgtatagattgtatccatgtttcaacaa----gtgatcctagtttcttgtccag

upper sequence: LOC_Os01g63060.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G004949_T01 (Zea mays), 5'ss of exon 3
TGGAGTTTTCACCCTTTTATTTATCATAGCAAACGTTTCTACACTGTTCTACTCTGGCGCAGGGTGCTGGCCTTTTTAGTTgtaagt--ggctgtcccatgtcttttaacttatct-ctgcaaccattataatcatgatgtaacaatgatgtttttcttttctttcctctag
|||||||||||||||||| ||||||| |||||||| || |||||||||||||| ||||| ||||||||||| ||| |||| ||||||  |  ||| | |  | |  |    |||    || | ||||  |     | | |||   || ||  |||  | | |          
TGGAGTTTTCACCCTTTTGTTTATCACAGCAAACGCTTTTACACTGTTCTACTATGGCGTAGGGTGCTGGCATTTCTAGTGgtaagtttgattgttctaactttgatggtgtatagattgtatccatgtt-----tcacgtagtgatcatagtttcttgtccag--------
















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|33675715|gb|CF303954.1|CF303954
EST:     AACGTTTCTACACTGTTCTACTCTGGCGCAGGGTGCTGGCCTTTTTAGTT                         GCTTCACAATTTTTGCGGATTATTACTTTCTATTCCACTCAGCTCCCAGGT
genomic: AACGTTTCTACACTGTTCTACTCTGGCGCAGGGTGCTGGCCTTTTTAGTTgtaagtggct ... tttcctctagGCTTCACAATTTTTGCGGATTATTACTTTCTATTCCACTCAGCTCCCAGGT
EST: gi|2312423|gb|C28578.1|C28578
EST:     AACGTTTCTACACTGTTCTACTCTGGCGCAGGGTGCTGGCCTTTTTAGTT                         GCTTCACAATTTTTGCGGATTATTACTTTCTATTCCACTCAGCTCCCAGGT
genomic: AACGTTTCTACACTGTTCTACTCTGGCGCAGGGTGCTGGCCTTTTTAGTTgtaagtggct ... tttcctctagGCTTCACAATTTTTGCGGATTATTACTTTCTATTCCACTCAGCTCCCAGGT
EST: gi|29646376|gb|CB651383.1|CB651383
EST:     AACGTTTCTACACTGTTCTACTCTGGCGCAGGGTGCTGGCCTTTTTAGTT                         GCTTCACAATTTTTGCGGATTATTACTTTCTATTCCACTCAGCTCCCAGGT
genomic: AACGTTTCTACACTGTTCTACTCTGGCGCAGGGTGCTGGCCTTTTTAGTTgtaagtggct ... tttcctctagGCTTCACAATTTTTGCGGATTATTACTTTCTATTCCACTCAGCTCCCAGGT
EST: gi|300215948|gb|HO088574.1|HO088574
EST:     AACGTTTCTACACTGTTCTACTCTGGCGCAGGGTGCTGGCCTTTTTAGTT                         GCTTCACAATTTTTGCGGATTATTACTTTCTATTCCACTCAGCTCCCAGGT
genomic: AACGTTTCTACACTGTTCTACTCTGGCGCAGGGTGCTGGCCTTTTTAGTTgtaagtggct ... tttcctctagGCTTCACAATTTTTGCGGATTATTACTTTCTATTCCACTCAGCTCCCAGGT
EST: gi|117231357|gb|CT842216.1|CT842216
EST:     AACGTTTCTACACTGTTCTACTCTGGCGCAGGGTGCTGGCCTTTTTAGTT                         GCTTCACAATTTTTGCGGATTATTACTTTCTATTCCACTCAGCTCCCAGGT
genomic: AACGTTTCTACACTGTTCTACTCTGGCGCAGGGTGCTGGCCTTTTTAGTTgtaagtggct ... tttcctctagGCTTCACAATTTTTGCGGATTATTACTTTCTATTCCACTCAGCTCCCAGGT

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: 63 (upstream exon), 68 (downstream exon)
Score: 7

TGGAGTTTTCACCCTTTTATTTATCATAGCAAACGTTTCTACACTGTTCTACTCTGGCGCAGGGTGCTGGCCTTTTTAGTTgtaagtggct ... tttcctctagGCTTCACAATTTTTGCGGATTATTACTTTCTATTCCACTCAGCTCCCAGGTCCAAATTATCACTGTCGGGAG




<











<


<