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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_Os01g08700.1
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|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|29642016|gb|CB647023.1|CB647023
EST:     TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAG                         CAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
genomic: TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAGgtaatttgat ... atatttccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
EST: gi|88454127|gb|CI694894.1|CI694894
EST:     TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAG                         CAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA
genomic: TCAAAGTTGCTATCCATCAAAAGAAAAGCGCCTTGTAGATGAAGTATTAGgtaatttgat ... atatttccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgttccacaaacaattgaagaaagagtttgacatatttttctcatatttccagCAACTTTTGTTCTTCATCATCCTGAGCATGGCCATGCAGTTGTGCATCCGATTCTGTCACGCATCATAGATGGGACACTCAGTTATGATAGAAATGGTTT
                           gtttgac  putative branch site (score: 4)
                                     tttttctcatatttcc  putative PPT
                                  atatttttctcatatt  TA-rich tract