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

gtaaatttctagtcttattctgtgcagtattgctcttctcaacttgatatggagtgcctgcatttctttactgtattgtgttcagaattttgtgtctgtttctttcaaaatggttccttattctcatttgaatttcgtttggcagATCATCTTCCCACTTATATACTCTTTGACAAGGCCACTGAAGTTGCACGATTCCCAGAAATCATGAATGAATCAAAAGTATTTGTGCCAAAAATTACAAA

Basic information

species Oryza sativa
transcript LOC_Os01g10340.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g10340.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM5G871861_T02 (Zea mays), 3'ss of exon 7
gtaaatttctagtcttattctgtgcagtattgctcttctcaacttgatatggagtgcctgcatttctttactgtattgtgttcagaattttgtgtctgtttctttcaaaatggttccttattctcatttgaatttcgtttggcagATCATCTTCCCACTTATATACTCTTTGACAAGGCCACTGAAGTTGCACGATTCCCAGAAATCATGAATGAATCAAAAGTATTTGTGCCAAAAATTACAAA
|||||||| | | |||  | |   | |  |   | ||  | | |  || ||    | ||| |  | |  |  |  |    |||||  || | ||      ||| ||||      |  | | |||    |  ||||| ||   |||||||||| |||||||| ||| | ||||||||||  ||||||||| | || || ||||||||||  | ||||||||||||||||||||||||| |||| ||
gtaaattttttgacttcattttatctgcttcattgtttaccatt--atctgtttgggctggagatttggagcgcttgaatttcagtcttatatgc-----tctatcaag-----tattaactcttgacttgatttctttgaacagATCATCTCCCCACTTACATATTGTTTGACAAGGTGACTGAAGTTTCTCGGTTTCCAGAAATCACAAGTGAATCAAAAGTATTTGTGCCAAAAGTTACTAA

upper sequence: LOC_Os01g10340.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM5G871861_T03 (Zea mays), 3'ss of exon 8
-----gtaaatttctagtcttattctgtgcagtattgctcttctcaacttgatatggagtgcctgcatttctttactgtattgtgttcagaattttgtgtctgtttctttcaaaatggttccttattctcatttgaatttcgtttggcagATCATCTTCCCACTTATATACTCTTTGACAAGGCCACTGAAGTTGCACGATTCCCAGAAATCATGAATGAATCAAAAGTATTTGTGCCAAAAATTACAAA
     |||||||| | | |||  | |   | |  |   | ||  | | |  || ||    | ||| |  | |  |  |  |    |||||  || | ||      ||| ||||      |  | | |||    |  ||||| ||   |||||||||| |||||||| ||| | ||||||||||  ||||||||| | || || ||||||||||  | ||||||||||||||||||||||||| |||| ||
gtggggtaaattttttgacttcattttatctgcttcattgtttaccatt--atctgtttgggctggagatttggagcgcttgaatttcagtcttatatgc-----tctatcaag-----tattaactcttgacttgatttctttgaacagATCATCTCCCCACTTACATATTGTTTGACAAGGTGACTGAAGTTTCTCGGTTTCCAGAAATCACAAGTGAATCAAAAGTATTTGTGCCAAAAGTTACTAA
















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|88506530|gb|CI434036.1|CI434036
EST:     TCTTGGGCATTTTCCAAATGCTGCAGCAAAGTTTGGAATATCCATGTGGG                         ATCATCTTCCCACTTATATACTCTTTGACAAGGCCACTGAAGTTGCACGAT
genomic: TCTTGGGCATTTTCCAAATGCTGCAGCAAAGTTTGGAATATCCATGTGGGgtaaatttct ... cgtttggcagATCATCTTCCCACTTATATACTCTTTGACAAGGCCACTGAAGTTGCACGAT
EST: gi|88513134|gb|CI440640.1|CI440640
EST:     GAATATCCATGTGGG                         ATCATCTTCCCACTTATATACTCTTTGACAAGGCCACTGAAGTTGCACGAT
genomic: GAATATCCATGTGGGgtaaatttct ... cgtttggcagATCATCTTCCCACTTATATACTCTTTGACAAGGCCACTGAAGTTGCACGAT
EST: gi|86259409|gb|CI008086.1|CI008086
EST:     TCTTGGGCATTTTCCAAATGCTGCAGCAAAGTTTGGAATATCCATGTGGG                         ATCATCTTCCCACTTATATACTCTTTGACAAGGCCACTGAAGTTGCACGAT
genomic: TCTTGGGCATTTTCCAAATGCTGCAGCAAAGTTTGGAATATCCATGTGGGgtaaatttct ... cgtttggcagATCATCTTCCCACTTATATACTCTTTGACAAGGCCACTGAAGTTGCACGAT

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: 56 (upstream exon), 57 (downstream exon)
Score: 19

ATACTCTAACAAGAACATTTCGTTTGGAATAATTGATCTTGGGCATTTTCCAAATGCTGCAGCAAAGTTTGGAATATCCATGTGGGgtaaatttct ... cgtttggcagATCATCTTCCCACTTATATACTCTTTGACAAGGCCACTGAAGTTGCACGATTCCCAGAAATCATGAATGAATCAAAAGTATTTGTGCCAAAAATTACAAA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtctgtttctttcaaaatggttccttattctcatttgaatttcgtttggcagATCATCTTCCCACTTATATACTCTTTGACAAGGCCACTGAAGTTGCACGATTCCCAGAAATCATGAATGAATCAAAAGTATTTGTGCCAAAAATTACAAA
                                          tttcgttt  CT-rich tract
                                   atttgaattt  TA-rich tract