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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACGTCTACAGTTTTGGAGTTTTGCTACTTGAAATACTAAGCGGAAAACGACCTACTGATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGGgtatgtatgacctttatgtccttccatttcatatccacagttttctgatatgaattacgtatgccttcaattgatttaatgtattcttgaaataatctacttgctctgtggcag

Basic information

species Oryza sativa
transcript LOC_Os03g16010.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g16010.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM5G886952_T01 (Zea mays), 5'ss of exon 13
TGACGTCTACAGTTTTGGAGTTTTGCTACTTGAAATACTAAGCGGAAAACGACCTACTGATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGGgtatgtatgacctttatgtccttccatttcatatccacagttttctgatatgaattacgta-tgccttcaattgatttaatgtattcttgaaataatctacttgctctgtggcag
||| |||||||||||||| |||||| |||| |||||||| || ||||| || |||||||||||||| || ||||| |||||| | |||||||||||||||||||||          ||  |    |||| |  ||             || |  || | || |  |||| || || ||   |||  || ||||  |||  ||||   | ||||||
TGATGTCTACAGTTTTGGGGTTTTGGTACTCGAAATACTCAGTGGAAAGCGGCCTACTGATGCATCCTTCATTGAGAAGGGACTAAACATTGTTGGATGGgtatgtcc--------tgctcgattattttaattct------------taaggcttgcatactttcttctatcgagttggagtaacct-gaaaggatcatcttgtcttttggcag

upper sequence: LOC_Os03g16010.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G479243_T01 (Zea mays), 5'ss of exon 13
TGACGTCTACAGTTTTGGAGTTTTGCTACTTGAAATACTAAGCGGAAAACGACCTACTGATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGGgtatgtatgacctttatgtccttccatttcatatccacagttttc------------tgatatgaatt----acgtatg-ccttcaattgatttaatgtattctt----gaaataatctacttgct-ctgtggcag
 || |||||||||||||| ||| || ||||||||||||| |||||||| || ||||| |||||||| || ||||| |||||||| |||||||||||||||||||||    |  ||||| |||||| ||| |||| |||  || ||            | || | ||||     ||| || ||||| || || ||   |||  ||     ||||  |||  ||||    | ||||||
CGATGTCTACAGTTTTGGGGTTCTGGTACTTGAAATACTCAGCGGAAAGCGGCCTACGGATGCATCCTTCATTGAGAAGGGATTAAACATTGTTGGATGGgtatgtc---ctgttatgaccttccctttgatatgcacccttgtcataagggctccattattttaattctaagcgtgtgaccttctatcgagttggggtaacctgaaaggaaaggatcatcttgtcgttttggcag

upper sequence: LOC_Os03g16010.1 (Oryza sativa), 5'ss of exon 13
lower sequence: Vv02s0087g00170.t01 (Vitis vinifera), 5'ss of exon 13
TGACGTCTACAGTTTTGGAGTTTTGCTACTTGAAATACTAAGCGGAAAACGACCTACTGATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGGgtatgtatgacctttatgtccttccatttcatatccacagttttctgatatgaattacgtatgccttcaattgatttaatgtattc--ttgaaataatctacttgctctgtggcag
 ||| | || |||||||| ||| || | |||||| || |    || || ||||| |||||||| || || |||||||||||  | ||||||||||| ||||||||| |      ||||    |  |  |  | |    || ||  | |  | |  |     | | |     | ||||   |||  |  ||   |||||  ||              
CGACATTTATAGTTTTGGGGTTCTGATGCTTGAAGTATTGGCTGGGAAGCGACCCACTGATGCTTCGTTCATTGAAAAGGGCCTCAACATTGTTGGCTGGgtatgtctccttgctatgcttgttaagat--tgttttaagcttatttaccttatatcttctttcatcaggatcatttccggtaaccaattatcataattcac--------------

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|25806103|gb|CA762064.1|CA762064
EST:     GACCTACTGATGCATCATTTATTGAGAAGGGATTGAACATTGTTGGATGG                         TTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
genomic: GACCTACTGATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGGgtatgtatga ... tctgtggcagTTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
EST: gi|29629427|gb|CB634436.1|CB634436
EST:     GACCTACTGATGCATCATTTATTGAGAAGGGATTGAACATTGTTGGATGG                         TTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
genomic: GACCTACTGATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGGgtatgtatga ... tctgtggcagTTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
EST: gi|86872630|gb|CI325254.1|CI325254
EST:     AACATTGTTGGATGG                         TTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
genomic: AACATTGTTGGATGGgtatgtatga ... tctgtggcagTTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
EST: gi|86477546|gb|CI120179.1|CI120179
EST:     GACCTACTGATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGG                         TTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
genomic: GACCTACTGATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGGgtatgtatga ... tctgtggcagTTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
EST: gi|396941397|gb|HO188606.1|HO188606
EST:     GACCTACTGATGCATCATTTATTGAGAAGGGATTGAACATTGTTGGATGG                         TTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
genomic: GACCTACTGATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGGgtatgtatga ... tctgtggcagTTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
EST: gi|88262097|gb|CI365673.1|CI365673
EST:     CATCA-TTAGTGAAAAGGGATTGAACATTGTTGGAT-G                         TTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
genomic: CATCATTTATTGAAAAGGGATTGAACATTGTTGGATGGgtatgtatga ... tctgtggcagTTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
EST: gi|89184716|gb|CI007141.1|CI007141
EST:     GACCTACTGATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGG                         TTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
genomic: GACCTACTGATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGGgtatgtatga ... tctgtggcagTTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
EST: gi|87029284|gb|CI276552.1|CI276552
EST:     GACCTACTGATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGG                         TTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
genomic: GACCTACTGATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGGgtatgtatga ... tctgtggcagTTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
EST: gi|88994832|gb|CI036413.1|CI036413
EST:     GACCTACTGATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGG                         TTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
genomic: GACCTACTGATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGGgtatgtatga ... tctgtggcagTTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
EST: gi|29625253|gb|CB630264.1|CB630264
EST:     GACCTACTGATGCATCATTTATTGAGAAGGGATTGAACATTGTTGGATGG                         TTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
genomic: GACCTACTGATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGGgtatgtatga ... tctgtggcagTTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
EST: gi|14981452|gb|BI306130.1|BI306130
EST:     GACCTACTGATGCATCATTTATTGAGAAGGGATTGAACATTGTTGGATGG                         TTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
genomic: GACCTACTGATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGGgtatgtatga ... tctgtggcagTTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
EST: gi|89185140|gb|CI050874.1|CI050874
EST:     GACCTACTGATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGG                         TTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
genomic: GACCTACTGATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGGgtatgtatga ... tctgtggcagTTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
EST: gi|38482222|gb|CF966274.1|CF966274
EST:     GACCTACTGATGCATCATTTATGGAGAAGGGATTGAACATTGTTGGATGG                         TTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
genomic: GACCTACTGATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGGgtatgtatga ... tctgtggcagTTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
EST: gi|86839146|gb|CI331442.1|CI331442
EST:     TTGAACATTGTT-GATGG                         TTGAATTTCCTGGTC-GTGAGAATC-GGAGAGGGAAATTGTCCATCCATAT
genomic: TTGAACATTGTTGGATGGgtatgtatga ... tctgtggcagTTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
EST: gi|88844028|gb|CI001085.1|CI001085
EST:     GACCTACTGATTCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGG                         TTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
genomic: GACCTACTGATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGGgtatgtatga ... tctgtggcagTTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
EST: gi|29629424|gb|CB634433.1|CB634433
EST:     GACCTACTGATGCATCATTTATTGAGAAGGGATTGAACATTGTTGGATGG                         TTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
genomic: GACCTACTGATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGGgtatgtatga ... tctgtggcagTTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
EST: gi|29614510|gb|CB619523.1|CB619523
EST:     GACCTACTGATGCATCATTTATTGAGAAGGGATTGAACATTGTTGGATGG                         TTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
genomic: GACCTACTGATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGGgtatgtatga ... tctgtggcagTTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
EST: gi|88959662|gb|CI002272.1|CI002272
EST:     GATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGG                         TTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
genomic: GATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGGgtatgtatga ... tctgtggcagTTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
EST: gi|88995929|gb|CI037220.1|CI037220
EST:     GACCTACTGATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGG                         TTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
genomic: GACCTACTGATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGGgtatgtatga ... tctgtggcagTTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
EST: gi|88994853|gb|CI036434.1|CI036434
EST:     GACCTACTGATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGG                         TTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
genomic: GACCTACTGATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGGgtatgtatga ... tctgtggcagTTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
EST: gi|86479170|gb|CI121803.1|CI121803
EST:     GACCTACTGATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGG                         TTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
genomic: GACCTACTGATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGGgtatgtatga ... tctgtggcagTTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
EST: gi|88844027|gb|CI001084.1|CI001084
EST:     GACCTACTGATTCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGG                         TTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
genomic: GACCTACTGATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGGgtatgtatga ... tctgtggcagTTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
EST: gi|88967913|gb|CI098155.1|CI098155
EST:     TTATTGAAAAGGGATTGAACATTGTTGGATGG                         TTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
genomic: TTATTGAAAAGGGATTGAACATTGTTGGATGGgtatgtatga ... tctgtggcagTTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
EST: gi|86827581|gb|CI272895.1|CI272895
EST:     GACCTACTGATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGG                         TTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT
genomic: GACCTACTGATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGGgtatgtatga ... tctgtggcagTTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATAT

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: 73 (upstream exon), 75 (downstream exon)
Score: 40

TGACGTCTACAGTTTTGGAGTTTTGCTACTTGAAATACTAAGCGGAAAACGACCTACTGATGCATCATTTATTGAAAAGGGATTGAACATTGTTGGATGGgtatgtatga ... tctgtggcagTTGAATTTCCTGGTCGGTGAGAATCGGGAGAGGGAAATTGTCGATCCATATTGTGAGGGAGTGCAGATTGAGACCTTGGATGCTCTACTTTCTCTTGCTA




<











<


<