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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaattttgattgattttatgacttttttgttgctacatgcactaatttcgttttgtaattcatgaatgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCAGAATCTTTATGTGGCATTGGTCCACCACCATTTCGTCAATTTGTTGAGT

Basic information

species Oryza sativa
transcript LOC_Os01g10150.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G045259_T02 (Zea mays), 3'ss of exon 9
--------------------gttaa--ttttgattgattttatgacttttttgttgctacatg------cactaatttcgt-tttgtaattcatgaatgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCAGAATCTTTATGTGGCATTGGTCCACCACCATTTCGTCAATTTGTTGAGT
                    | | |  ||||  ||  |  ||    |||||||||  ||  |       ||| |||||  | | ||| |||| | ||| || |||||||||||| |||||||||||||| ||||||||||||||||| || ||||| || ||| | ||||| ||  |||||| ||| || ||  | ||||||||||
gttagtgtagttgatgttctgctcacctttttcttactcctactctttttttgtttttatttaaatactcacaaattttttatctgttattcttcaatcaatttagGGAGAGAACAAAGGTTTTCTTGTCTGCAAGAAAAAGATGGCGACATCTCCGGAGTCTCTGTGTGGAATCTGTCCACAACCTTTCCGGAATTTTGTTGAGT

upper sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 9
gttaattttgattgattttatgacttttttgttgcta-catgcactaatttcgtt-ttgtaattcatgaatgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCAGAATCTTTATGTGGCATTGGTCCACCACCATTTCGTCAATTTGTTGAGT
|||| | ||  || |  |  | | |||  |  |  |   |      ||| |  || || | |||  |   |      ||||||| |||||||| |||||||| ||||||||||||||||| || ||||||||| |||| ||| || || |||| | ||||||||| ||||||||||| |
gttattattccttcaaatagtcattttagtactaatggtaaatgaaaatatgattcttatgatttttt--ttgttacagGGAGAAAATAAAGGGTTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCAGAAACTTTGTGTTGCTTTTGTCCTCAACCATTTCGACAATTTGTTGAAT

upper sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 9
gttaattttgattgattttatgacttttttgttg-ctacatgcactaatttcgttttgtaattcatgaatgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCAGAATCTTTATGTGGCATTGGTCCACCACCATTTCGTCAATTTGTTGAGT
|||| | ||| || |  |  | | |||  |  |   |  |      ||| |   | | ||    |    |      ||||||| |||||||| |||||||| ||||||||||||||||| || ||||||||| |||| ||| || || |||| | ||||||||| |||||||| || |
gttattattgtttcaaatagtcattttagtactaattgtaaatgaaaatatgactct-tatgaaactttttgttacagGGAGAAAATAAAGGGTTTCTTGTCTGCAAGAAAAAGATGGCCACGTCTCCAGAAACTTTGTGTTGCTTTTGTCCCCAACCATTTCGGCAATTTGTGGAAT

upper sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 9
gttaattttgattgattttatgacttttttgttgcta-catgcactaatttcgttttgtaattcatgaatgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCAGAATCTTTATGTGGCATTGGTCCACCACCATTTCGTCAATTTGTTGAGT
|||| | |||  | |  |  | | ||   |  |  |   | |    || |  | ||  ||    ||   |      ||||||| |||||||| |||||||| ||||||||||||||||| || ||||| ||| |||| ||| || |  |||| | ||||||||| ||||||||||| |
gttattattgtctcaaatagtcatttgagtactaatggtaagtcaaaaatatgattcttatgagattttttgttacagGGAGAAAATAAAGGATTTCTTGTCTGCAAGAAAAAGATGGCCACTTCTCCTGAAACTTTGTGTTGCTTGTGTCCTCAACCATTTCGGCAATTTGTTGAAT

upper sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 9
gttaattttgattgattttatgacttttttgttgctacatgcactaatttcgttttgtaattcatgaatgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCAGAATCTTTATGTGGCATTGGTCCACCACCATTTCGTCAATTTGTTGAGT------
||||  |||| || ||||  || |   |||  |  | ||  || ||| || || |    |||  |         ||||||||||| |||||||| |||||||||||||| |||||||| || || |||||| || | ||  || |  |||| | ||| |||||||| ||||| ||||      
gtta--tttgttttatttcctggcaactttccttgt-caatcattaacttggtct----atttgt---------tagggagagAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGTATGTGG

upper sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT2G25760.1 (Arabidopsis thaliana), 3'ss of exon 9
gttaattttgattgattttatgacttttttgttgctacatgcactaatttcgttttgtaattcatgaatgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCAGAATCTTTATGTGGCATTGGTCCACCACCATTTCGTCAATTTGTTGAGT
|||       | | |  ||||   |||| | |     ||        | ||  |   ||| |           |||||||||||| |||||||| |||||||||||||| |||||||| || || |||||| || | ||  || |  |||| | ||| |||||||| ||||| ||||
gttggggac-actaaagttatttgttttatttcctggcaactttccttgtcaatcattaacttggtctatttgttagGGAGAGAACAAAGGTTTCCTTGTTTGCAAGAAGAAGATGGCCACTTCCCCAGAAACTCTTTGCTGCTTCTGTCCCCAACCTTTTCGTCAGTTTGTCGAGT

upper sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv09s0002g03680.t01 (Vitis vinifera), 3'ss of exon 9
------------------------------------------------gttaattttgattgattttatgacttttttgttgctacatgcactaatttcgttttgtaattcatgaa----tgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCAGAATCTTTATGTGGCATTGGTCCACCACCATTTCGTCAATTTGTTGAGT
                                                   | ||  |||  | ||| |  ||| | |     |  |     | | ||  |||| |  ||| | ||       |  ||||||||||| || || || |||||||||||||| ||||||||||| ||||| ||| || | ||| || |  |||||   || ||  | || |||||||| |
gttggctccattcgaagttccgataaaatttgttccttctcttcaatttgaagttccgataaaatttgttccttgtcttcctttcaagtttttgacttgatttttttgttcttaaaatcccatatatagGGAGAGAACAAGGGGTTCCTTGTTTGCAAGAAGAAGATGGCAACATCTCCGGAAGCTCTGTGTTGCTTCTGTCCAATGCCTTTCAGACAGTTTGTTGAAT

upper sequence: LOC_Os01g10150.1 (Oryza sativa), 3'ss of exon 9
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 9
gttaattttgattgattttatgacttttttgttgctacatgcactaatttcgttttgtaattcatgaatgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCAGAATCTTTATGTGGCATTGGTCCACCACCATTTCGTCAATTTGTTGAGT
||| |   |     |  |||       |||  |  ||  ||      |      || | |  ||  |      |||||||||||||||||| |  ||||||||||| || ||||||||||| ||||||||| |||| ||| || || |||| |  || ||||| || |||||||| |
gttgacagtttccaaacttaaataggattttcttttatgtgattctgtacatcattctgaaccaacagcttctttagGGAGAGAATAAAGGGTACCTTGTTTGCAAAAAGAAGATGGCAACATCTCCAGAAGCTTTGTGTTGCTTTTGTCCTCAGCCTTTTCGGCAGTTTGTTGAAT

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|58696276|gb|CK084963.1|CK084963
EST:     CACACTTATTTTCCTTCTCCGTGGCCGCCTGCCTTGTGCAAGGATTCCAG                         TGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCA
genomic: CACACTTATTTTCCTTCTCCGTGGCCGCCTGCCTTG-GCAAGGATTCCAGgttaattttg ... atgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCA
EST: gi|88573975|gb|CI665744.1|CI665744
EST:     ACACACTTATTTTCCTTCTCCGTGGCCGCCTGCCTTGGCAAGGATTCCAG                         GGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTC
genomic: ACACACTTATTTTCCTTCTCCGTGGCCGCCTGCCTTGGCAAGGATTCCAGgttaattttg ... atgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTC
EST: gi|29645031|gb|CB650038.1|CB650038
EST:     ACACACTTATTTTCCTTCTCCGTGGCCGCCTGCCTTGGCAAGGATTCCAG                         GGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCA
genomic: ACACACTTATTTTCCTTCTCCGTGGCCGCCTGCCTTGGCAAGGATTCCAGgttaattttg ... atgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCA
EST: gi|29670785|gb|CB667060.1|CB667060
EST:     ACACACTTATTTTCCTTCTCCGTGGCCGCCTGCCTTGGCAAGGATTCCAG                         GGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCA
genomic: ACACACTTATTTTCCTTCTCCGTGGCCGCCTGCCTTGGCAAGGATTCCAGgttaattttg ... atgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttttttgttgctacatgcactaatttcgttttgtaattcatgaatgaacttagGGAGAGAATAAAGGTTTTCTTGTTTGCAAGAAAAAGATGGCAACCTCTCCAGAATCTTTATGTGGCATTGGTCCACCACCATTTCGTCAATTTGTTGAGT
                   cactaat  putative branch site (score: 2)
                              ttttgtaatt  TA-rich tract