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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttacgaaaccatcttattcgtgcgtatgtattcttattggcgaactttaggcttgtaatcctttcctatacataaatattttctgcatgtgaattgtcagGTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGACAGAAG

Basic information

species Oryza sativa
transcript LOC_Os08g14440.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g14440.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G120579_T02 (Zea mays), 3'ss of exon 5
ttacgaaaccatcttattcgtgcgtatgtattcttattggcgaacttt-aggcttgtaatcctttcctatacataaatattttctgcatgtgaattgtcagGTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGACAGAAG
| |  |||    ||     || | | | ||   ||||    |    |  || |||| || ||||  ||  | ||||| ||| |   | |||  |||   ||||||||||||| ||||||||||||||||| || ||||||||||||||||| |||||
tgatcaaattg-ctgccaagtacatctttagaattatgtatggttctggagacttgaaaaccttcactggatataaacattgttcacttgtacattcgtagGTTGATGTGGATATAGCAACCCACATAGATATCTATGATGATGGCCCTGAAAGAAG

upper sequence: LOC_Os08g14440.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA07G02580.1 (Glycine max), 3'ss of exon 6
ttacgaaaccatcttattcgtgcgtatgtattcttattggcgaact---ttaggcttgtaatcctttcctatacataaatattttctgcatgtgaattgtcagGTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGACAGAAG
|   ||||  |  | ||  || | | ||  | || |||| |  |||   || | | | || |   || ||  |  |  ||||||| |  || |    ||||||||||| || |||||||||||||||||| |||| | |||||||||||| ||  ||||
tattgaaaatacatcatgtgttcatctgattactaattgtcagactatattggtcctctactatcttgcttaaactttatattttgttaatat---ctgtcagGTTGACGTAGACATAGCAACCCACATAAACATTTCTGATGATGGCCCAGATCGAAG

upper sequence: LOC_Os08g14440.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA08G23440.1 (Glycine max), 3'ss of exon 6
-ttacgaaaccatcttattcgtgcgtatgtattcttattggcgaacttta--ggcttgtaat--cctttcctatacataaatattttctgcatgtgaattgtcagGTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGACAGAAG
 |    |||  |  | ||   | ||| ||  | || |||| |  ||| ||  ||     ||    ||| | ||||| | | |||||  |  || |    ||||||||||| || |||||||||||||||||| |||| | ||||||| |||| || |||||
atattaaaaatacatcatgtattcgtctgattactaattgtcagactatattggtcctcaacaatcttgcttatacttta-tatttgtta-atat---ctgtcagGTTGACGTAGACATAGCAACCCACATAAACATTTCTGATGATTGCCCAGATAGAAG

upper sequence: LOC_Os08g14440.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv09s0018g01780.t01 (Vitis vinifera), 3'ss of exon 6
ttacgaaaccatcttattcgtgcgtatgtattcttattggcgaactttaggcttgtaatcctttcctatacataaatatttt-ctgcatgtgaatt-gtcagGTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGACAGAAG
     | ||   |   |   |||  ||| |  | | ||      |||||    ||  ||    |  |  |  ||  | || |  ||  | ||  ||  ||||||||||||||||||||| |||||||||    |  |||||||||| |||||| ||||
--ctcagacttgcacttcgttgctgatgcaaacattttctttccctttaaagatggcatttacttatccatgtacttcttctgttgtgtttggcttcatcagGTTGATGTGGACATAGCGACCCACATAAGTGTTAATGATGATGGTCCTGACCGAAG

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|27578238|gb|CB000933.1|CB000933
EST:     GCCAATTGGCTCTGGGTGCAACTTTTGGTCCAGAGCCCCCTACAGAACTG                         GTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGAC
genomic: GCCAATTGGCTCTGGGTGCAACTTTTGGTCCAGAGCCCCCTACAGAACTGgtactagctt ... gaattgtcagGTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGAC
EST: gi|29663445|gb|CB659720.1|CB659720
EST:     ACTTTTGGTCCAGAGCCCCCTACAGAACTG                         GTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGAC
genomic: ACTTTTGGTCCAGAGCCCCCTACAGAACTGgtactagctt ... gaattgtcagGTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGAC
EST: gi|29689080|gb|CB685355.1|CB685355
EST:     CTTTTGGTCCAGAGCCCCCTACAGAACTG                         GTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGAC
genomic: CTTTTGGTCCAGAGCCCCCTACAGAACTGgtactagctt ... gaattgtcagGTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGAC
EST: gi|29663096|gb|CB659371.1|CB659371
EST:     GCCAATTGGCTCTGGGTGCAACTTTTGGTCCAGAGCCCCCTACAGAACTG                         GTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGAC
genomic: GCCAATTGGCTCTGGGTGCAACTTTTGGTCCAGAGCCCCCTACAGAACTGgtactagctt ... gaattgtcagGTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGAC
EST: gi|38479507|gb|CF963616.1|CF963616
EST:     GCCAATTGGCTCTGGGTGCAACTTTTGGTCCAGAGCCCCCTACAGAACTG                         GTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGAC
genomic: GCCAATTGGCTCTGGGTGCAACTTTTGGTCCAGAGCCCCCTACAGAACTGgtactagctt ... gaattgtcagGTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGAC
EST: gi|29688167|gb|CB684442.1|CB684442
EST:     GCCAATTGGCTCTGGGTGCAACTTTTGGTCCAGAGCCCCCTACAGAACTG                         GTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGAC
genomic: GCCAATTGGCTCTGGGTGCAACTTTTGGTCCAGAGCCCCCTACAGAACTGgtactagctt ... gaattgtcagGTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGAC
EST: gi|58654305|gb|CK042985.1|CK042985
EST:     GCCAATTGGCTCTGGGTGCAACTTTTGGTCCAGAGCCCCCTACAGAACTG                         GTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGAC
genomic: GCCAATTGGCTCTGGGTGCAACTTTTGGTCCAGAGCCCCCTACAGAACTGgtactagctt ... gaattgtcagGTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGAC
EST: gi|88545940|gb|CI475543.1|CI475543
EST:     CCCCCTACAGAACTG                         GTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGAC
genomic: CCCCCTACAGAACTGgtactagctt ... gaattgtcagGTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGAC
EST: gi|58693125|gb|CK081812.1|CK081812
EST:     GCCAATTGGCTCTGGGTGCAACTTNTGGTCCAGAGGCCCCTACAGAACTG                         GTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGAC
genomic: GCCAATTGGCTCTGGGTGCAACTTTTGGTCCAGAGCCCCCTACAGAACTGgtactagctt ... gaattgtcagGTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGAC
EST: gi|29625507|gb|CB630518.1|CB630518
EST:     GCCAATTGGCTCTGGGTGCAACTTTTGGTCCAGAGCCCCCTACAGAACTG                         GTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGAC
genomic: GCCAATTGGCTCTGGGTGCAACTTTTGGTCCAGAGCCCCCTACAGAACTGgtactagctt ... gaattgtcagGTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGAC
EST: gi|29656672|gb|CB652947.1|CB652947
EST:     TTGGTCCAGAGCCCCCTACAGAACTG                         GTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGAC
genomic: TTGGTCCAGAGCCCCCTACAGAACTGgtactagctt ... gaattgtcagGTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGAC
EST: gi|58587293|gb|CF985601.1|CF985601
EST:     GCCAATTGGCTCTGGGTGCAACTTTTGGTCCAGAGCCCCCTACAGAACTG                         GTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGAC
genomic: GCCAATTGGCTCTGGGTGCAACTTTTGGTCCAGAGCCCCCTACAGAACTGgtactagctt ... gaattgtcagGTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGAC
EST: gi|29663151|gb|CB659426.1|CB659426
EST:     GCAACTTTTGGTCCAGAGCCCCCTACAGAACTG                         GTTGATGTGGACATAGCAACCCCCATAGACATATATGATGATGGCCCTGAC
genomic: GCAACTTTTGGTCCAGAGCCCCCTACAGAACTGgtactagctt ... gaattgtcagGTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGAC
EST: gi|29667075|gb|CB663350.1|CB663350
EST:     GCCAATTGGCTCTGGGTGCAACTTTTGGTCCAGAGCCCCCTACAGAACTG                         GTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGAC
genomic: GCCAATTGGCTCTGGGTGCAACTTTTGGTCCAGAGCCCCCTACAGAACTGgtactagctt ... gaattgtcagGTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGAC
EST: gi|58664474|gb|CK053160.1|CK053160
EST:     GCCAATTGGCTCTGGGTGCAACTTTTGGTCCAGAGCCCCCTACAGAACTG                         GTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGAC
genomic: GCCAATTGGCTCTGGGTGCAACTTTTGGTCCAGAGCCCCCTACAGAACTGgtactagctt ... gaattgtcagGTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGAC
EST: gi|29685178|gb|CB681453.1|CB681453
EST:     GGGTGCAACTTTTGGTCCAGAGCCCCCTACAGAACTG                         GTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGAC
genomic: GGGTGCAACTTTTGGTCCAGAGCCCCCTACAGAACTGgtactagctt ... gaattgtcagGTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGAC

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: 74 (upstream exon), 73 (downstream exon)
Score: 151

GAAGCTAGCAGCCAATTGGCTCTGGGTGCAACTTTTGGTCCAGAGCCCCCTACAGAACTGgtactagctt ... gaattgtcagGTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGACAGAAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaggcttgtaatcctttcctatacataaatattttctgcatgtgaattgtcagGTTGATGTGGACATAGCAACCCACATAGACATATATGATGATGGCCCTGACAGAAG
                tttcctatacataaat  TA-rich tract