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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttgatccagtgatcaatacatgttccacaaacaattgaagaaagagtttgacatatttttctcatatttccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGATTCTGTCACGCATCATAGATGGGACACTCAGTTATGATAGAAATGGTTT

Basic information

species Oryza sativa
transcript LOC_Os01g08700.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g08700.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM5G844173_T01 (Zea mays), 3'ss of exon 4
gtaatttgatccagtgatcaatacatgttccacaaacaattgaagaaagagtttgacatatttttctcatatt-----tccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGATTCTGTCACGCATCATAGATGGGACACTCAGTTATGATAGAAATGGTTT
|||||   | |   | ||  |||  || |    |   |||| |||||||| | |||||  ||| | | |  |      | ||||||||||||||||||||||||| |||||||| ||||||||||| ||||| ||||| |||| ||||||||||||||||||  | ||||||||  |||||  
gtaatacaaacttcttatggataattgct----aggaaattcaagaaagaatctgacaagtttcttttacttgcactgtacagCAACTTTTGTTCTTCATCATCCGGAGCATGGTCATGCAGTTGTACATCCAATTCTTTCACCCATCATAGATGGGACACTGTGCTATGATAGGCATGGTCC

upper sequence: LOC_Os01g08700.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G107101_T05 (Zea mays), 3'ss of exon 5
gtaatttgatccagtgatcaatacatgttccacaaacaattgaagaaagagtttgacatatttttctca----tatt-tccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGATTCTGTCACGCATCATAGATGGGACACTCAGTTATGATAGAAATGGTTT
|||||   | |   | ||  | |  |||    ||   || | |||||||| | | ||||||  || | |     ||| | ||||||||||||||||||||||||| |||||||| ||||||||||  ||||| ||||| |||||||||||||||||||| ||  | ||||||||| |||||  
gtaatacaaactccttatggacaattgt----caggaaactcaagaaagaatctaacatatcatttttaattgcattgtacagCAACTTTTGTTCTTCATCATCCGGAGCATGGTCATGCAGTTGCACATCCAATTCTTTCACGCATCATAGATGGGACGCTGTGCTATGATAGACATGGTCC

upper sequence: LOC_Os01g08700.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA10G36600.1 (Glycine max), 3'ss of exon 4
------------------------------------------gtaatttga-tccagtgatcaatacatgttccacaaacaattgaagaaagagtttgacatatttttctcatatttccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGATTCTGTCACGCATCATAGATGGGACACTCAGTTATGATAGAAATGGTTT
                                            ||  | | |   || | ||  |  | || |      | ||| |  ||    || |  | |||  |   ||  || ||| || ||||| ||||||||||| |||||||| ||||||||||||| ||| ||| | ||| | || || ||||| |||||    |||||||    | ||  
gtatttatgctctatcccatgtcagtttaacttatgattgactcaacataaatatggttaccatgatttatttctattttatttgtaataacttctttatgt-tttcacatgtaaatctagCGACATTTGTCCTTCATCATCCAGAGCATGGGCATGCAGTTGTGCTTCCAATTATTTCATGTATTATTGATGGTACACTAGTCTATGATAAGGCTAGTCC

upper sequence: LOC_Os01g08700.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA09G07240.1 (Glycine max), 3'ss of exon 4
----------------------------------gtaatt-tgatccagtgatcaatacatgttccacaaacaattgaagaaagagtttgacatattt-ttctcatatt--tccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGATTCTGTCACGCATCATAGATGGGACACTCAGTTATGATAGAAATGGTTT--------------------------
                                    |||| ||||  | | | || || |  |   || |    |||   ||| |  |  |  ||||  ||| ||| |   ||||||     |||||||||||||||| ||||| || ||||||||||||| ||| ||| | ||| | || || ||||| || ||    |||||||  | | ||                            
gtatagggtatttttgctttacttagtattagtttcaattatgatttactcaacagta-acttatgactatttcttgtccaaataact-aatttattcattcacatgtacatccagcggtacttgttcttcatcatccagagCACGGGCATGCAGTTGTGCTTCCAATTATTTCATGTATTATTGATGGTACGCTGGACTATGATAAGACTAGTCCTCCATTTGCTTCTTTCATTTCTTTAG

upper sequence: LOC_Os01g08700.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv18s0157g00020.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------------------gtaatttgatccagtgatc---aatacatgttccacaaacaattgaagaaagagtttgacatatttttctcatatttccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGATTCTGTCACGCATCATAGATGGGACACTCAGTTATGATAGAAATGGTTT
                                    | || | |   | |  ||   ||||    ||   | | ||| || | |  || ||    ||| ||       |||| ||||||| ||||||||||||||||| || ||||| ||||| || || | ||| ||| | ||  | ||||| ||||| |||||    ||||||||   |  |  
gtattcatgtttttcaatgttgatatacctaaaaattgatataagttattattccctaatatgaatttt-ctatcaactgcatagtgacttccttataattaaaatcaattttcagCAACGTTTGTTCTTCATCATCCGGAACATGGGCATGCTGTCGTTCTTCCAATTATTTCGTGTATCATTGATGGTACACTGGTGTATGATAGGTGTACTCC

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|29667209|gb|CB663484.1|CB663484
EST:     GATGAAGTATTAG                         CAACTTTTGTTCTTCATCATCNTGAGCATGGCCATGCAGTTGTGCATCCGA
genomic: GATGAAGTATTAGgtaatttgat ... atatttccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
EST: gi|29642016|gb|CB647023.1|CB647023
EST:     TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAG                         CAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
genomic: TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAGgtaatttgat ... atatttccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
EST: gi|29636922|gb|CB641931.1|CB641931
EST:     TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAG                         CAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
genomic: TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAGgtaatttgat ... atatttccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
EST: gi|88369882|gb|CI680559.1|CI680559
EST:     TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAG                         CAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
genomic: TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAGgtaatttgat ... atatttccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
EST: gi|29646260|gb|CB651267.1|CB651267
EST:     TCAAAGTTGCTATCCATCAAAAGAAAAGCGCNTTGTAGATGAAGTATTAG                         CAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
genomic: TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAGgtaatttgat ... atatttccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
EST: gi|29636923|gb|CB641932.1|CB641932
EST:     ATCCATCAAAAGAAAAGCGCCTGGTAGATGAAGTATTAG                         CAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
genomic: ATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAGgtaatttgat ... atatttccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
EST: gi|88587781|gb|CI705554.1|CI705554
EST:     TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAG                         CAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
genomic: TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAGgtaatttgat ... atatttccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
EST: gi|88361618|gb|CI680183.1|CI680183
EST:     TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAG                         CAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
genomic: TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAGgtaatttgat ... atatttccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
EST: gi|88369175|gb|CI680281.1|CI680281
EST:     TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAG                         CAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
genomic: TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAGgtaatttgat ... atatttccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
EST: gi|58590243|gb|CF988551.1|CF988551
EST:     CAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAG                         CAGCGGTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
genomic: CAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAGgtaatttgat ... atatttccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
EST: gi|88454127|gb|CI694894.1|CI694894
EST:     TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAG                         CAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
genomic: TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAGgtaatttgat ... atatttccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA

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: 72 (upstream exon), 75 (downstream exon)
Score: 104

CTAATTCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAGgtaatttgat ... atatttccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGATTCTGTCACGCATCATAGATGGGACACTCAGTTATGATAGAAATGGTTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgttccacaaacaattgaagaaagagtttgacatatttttctcatatttccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGATTCTGTCACGCATCATAGATGGGACACTCAGTTATGATAGAAATGGTTT
                           gtttgac  putative branch site (score: 104)
                                     tttttctcatatttcc  putative PPT
                                  atatttttctcatatt  TA-rich tract