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'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagctttggttcattggttgacgtcatgaattttcttttgtaataatttctcttatgtaatgcatgcgtttccttctttgcagTTGCTATATGGCCTCAGTAATGCAAGTTATGTTTTCAACTCATCCTTTTATATCACG

Basic information

species Oryza sativa
transcript LOC_Os01g08200.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g08200.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G107696_T02 (Zea mays), 3'ss of exon 10
-----gtagctttggttcattggttgacgtcatga----attttcttttgtaataatttctcttatgtaatgcatgcgtttccttctttgcagTTGCTATATGGCCTCAGTAATGCAAGTTATGTTTTCAACTCATCCTTTTATATCACG
      |   ||   ||| | |  |    |  |||    ||  |   |||||| || |  | |||  ||     |    || ||| ||| ||||||||||||||| ||| |||||||||| ||||||||||  |||||||| |||||| |
gtagcatgatttgacttcgtagaatactcttttgatctgataattccttgtaacaaatgat-ttagctatcatgt-ttctttcttttttacagTTGCTATATGGCTTCAATAATGCAAGTCATGTTTTCAATCCATCCTTTCATATCAAG
















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|58606193|gb|CK034226.1|CK034226
EST:     GAACTTTTATACGGCCCTGGTTATACTGGCCTTGTAAATCTTGGAAATAG                         TTGCTATATGGCCTCAGTAATGCAAGTTATGTTTTCAACTCATCCTTTTAT
genomic: GAACTTTTATACGGCCCTGGTTATACTGGCCTTGTAAATCTTGGAAATAGgtagctttgg ... ttctttgcagTTGCTATATGGCCTCAGTAATGCAAGTTATGTTTTCAACTCATCCTTTTAT
EST: gi|58663886|gb|CK052572.1|CK052572
EST:     GAACTTTTATACGGCCCTGGTTATACTGGCCTTGTAAATCTTGGAAATAG                         TTGCTATATGGCCT
genomic: GAACTTTTATACGGCCCTGGTTATACTGGCCTTGTAAATCTTGGAAATAGgtagctttgg ... ttctttgcagTTGCTATATGGCCT
EST: gi|29622184|gb|CB627195.1|CB627195
EST:     GAACTTTTATACGGCCCTGGTTATACTGGCCTTGTAAATCTTGGAAATAG                         TTGCTATATGGCCTCAGTAATGCAAGTTATGTTTTCAACTCATCCTTTTAT
genomic: GAACTTTTATACGGCCCTGGTTATACTGGCCTTGTAAATCTTGGAAATAGgtagctttgg ... ttctttgcagTTGCTATATGGCCTCAGTAATGCAAGTTATGTTTTCAACTCATCCTTTTAT
EST: gi|58693785|gb|CK082472.1|CK082472
EST:     GAACTTTTATACGGCCCTGGTTATACTGGCCTTGTAAATCTTGGAAATAG                         TTGCTATATGGCCTCAGTAATGCAAGTTATGTTTTCAACTCATCCTTTTAT
genomic: GAACTTTTATACGGCCCTGGTTATACTGGCCTTGTAAATCTTGGAAATAGgtagctttgg ... ttctttgcagTTGCTATATGGCCTCAGTAATGCAAGTTATGTTTTCAACTCATCCTTTTAT
EST: gi|33674839|gb|CF303078.1|CF303078
EST:     GAACTTTTATACGGCCCTGGTTATACTGGCCTTGTAAATCTTGGAAATAG                         TTGCTATATGGCCTCAGTAATGCAAGTTATGTTTTCAACTCATCCTTTTAT
genomic: GAACTTTTATACGGCCCTGGTTATACTGGCCTTGTAAATCTTGGAAATAGgtagctttgg ... ttctttgcagTTGCTATATGGCCTCAGTAATGCAAGTTATGTTTTCAACTCATCCTTTTAT
EST: gi|58661919|gb|CK050599.1|CK050599
EST:     GAACTTTTATACGGCCCTGGTTATACTGGCCTTGTAAATCTTGGAAATAG                         TTGCTATATGGCCTCAGTAATGCAAGTTATGTTTTCAACTCATCCTTTTAT
genomic: GAACTTTTATACGGCCCTGGTTATACTGGCCTTGTAAATCTTGGAAATAGgtagctttgg ... ttctttgcagTTGCTATATGGCCTCAGTAATGCAAGTTATGTTTTCAACTCATCCTTTTAT

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: 71 (upstream exon), 57 (downstream exon)
Score: 30

ACAACACAAATTATGACTGGAATAGAATACAAGAAAGTGGCAAAGATGCCGAACTTTTATACGGCCCTGGTTATACTGGCCTTGTAAATCTTGGAAATAGgtagctttgg ... ttctttgcagTTGCTATATGGCCTCAGTAATGCAAGTTATGTTTTCAACTCATCCTTTTATATCACG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattttcttttgtaataatttctcttatgtaatgcatgcgtttccttctttgcagTTGCTATATGGCCTCAGTAATGCAAGTTATGTTTTCAACTCATCCTTTTATATCACG
                                    tgcgtttccttcttt  CT-rich tract
       ttttgtaataatttct  TA-rich tract