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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactagttttgcatgttttgtttggattctgtttcccccttcatgtgatagttgcctattctcttaatgttaaatttattgcaatgatttccattgaatctttttccctcattgcagGAGAGTGACATCAAGTGGGCTTCCCGTTGGGACACCTATCTGTTGATGACTGATGATCAGATTCACTGGTTTTCTATTGTCAACTCTCTCATGATCGTGC

Basic information

species Oryza sativa
transcript LOC_Os09g38530.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g38530.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G039811_T01 (Zea mays), 3'ss of exon 6
gtactagttttgcatgttttgtttggattctgtttcccccttcatgtgatagttgcctattctcttaatgttaaatttattgcaatgatttccattgaatctttttccctcattgcagGAGAGTGACATCAAGTGGGCTTCCCGTTGGGACACCTATCTGTTGATGACTGATGATCAGATTCACTGGTTTTCTATTGTCAACTCTCTCATGATCGTGC
|||| ||  |   || |      ||  |  | |  |    || |  || | || |  || ||| | |||||| |   ||| |  |||||||| || ||| ||   |      |||||||||||||| ||||||||||| || |||||||||||||| |||||||||||||||||||||||||| |||||||||||||| |||||||||||||||||||
gtacgagactgagat-taagaactgcttagtttaactttgtttagctgct-gtagtgtactctttgaatgttta---tat-gtgatgatttc-atggaacctcaatt-----ttgcagGAGAGTGAGATCAAGTGGGCATCACGTTGGGACACCTACCTGTTGATGACTGATGATCAGATTCATTGGTTTTCTATTGTGAACTCTCTCATGATCGTGC

upper sequence: LOC_Os09g38530.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G006117_T03 (Zea mays), 3'ss of exon 2
gtactagttttgcatgttttgtttggattctgtttcccccttcatgtgatagttgcctattctcttaatgttaaatttattgcaatgatttccattgaatctttttccctcattgcagGAGAGTGACATCAAGTGGGCTTCCCGTTGGGACACCTATCTGTTGATGACTGATGATCAGATTCACTGGTTTTCTATTGTCAACTCTCTCATGATCGTGC
|||| ||  | | || |     |||  |  | |  |    || |  || ||||    || ||| | ||||||   | | |||  |||||||  || |||   ||   |    || ||||||||||| ||||||||||| || || ||||||||||| ||||||||||| ||||||||||||||||||||||||||||| |||||||||||||||||||
gtacaagactgggat-taagaattgcttattttaactttgtttagctgctagtg---tactctttgaatgtt---tcttttgtcatgattttaatggaac--ttccactaattttcagGAGAGTGAGATCAAGTGGGCGTCACGCTGGGACACCTACCTGTTGATGACCGATGATCAGATTCACTGGTTTTCTATTGTGAACTCTCTCATGATCGTGC

upper sequence: LOC_Os09g38530.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA06G06460.1 (Glycine max), 3'ss of exon 6
gtactagttttgcatgttttgtttggattctgtttcccccttcatgtgatagttgcctattctcttaatgttaaatttattgcaatgatttccattgaatctttttccctcat-tgcagGAGAGTGACATCAAGTGGGCTTCCCGTTGGGACACCTATCTGTTGATGACTGATGATCAGATTCACTGGTTTTCTATTGTCAACTCTCTCATGATCGTGC
             |  |    |    ||  | |||     ||  | |||||       ||| |      | |  |||| ||   ||   | | |||    |||| ||    |  | |||||||||||| | |||||||||||  | |||||  | ||| || | |||| ||||||||| || |||||||| |||||||| |||||  | ||||| || |
-------------aactaacatcctcatcttttttttttgttgttatgataaaatgtgattat----gggctgtatttcttattat--ctgctattttgcctttgtctggtaccttcagGAGAGTGACGTGAAGTGGGCTTCAAGATGGGATGCTTATTTGCTAATGAATGATGATCAAATCCACTGGTTCTCTATTGTTAACTCATTAATGATTGTTC

upper sequence: LOC_Os09g38530.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA17G34020.1 (Glycine max), 3'ss of exon 6
gtactagttttgcatgttttgtttggattctgtttcccccttcatgtgatagttgcctattctcttaatgttaaatttattgcaatgatttccattgaatctttttccctcattgcagGAGAGTGACATCAAGTGGGCTTCCCGTTGGGACACCTATCTGTTGATGACTGATGATCAGATTCACTGGTTTTCTATTGTCAACTCTCTCATGATCGTGC
       | |||  | ||   |     |   ||   |  | || |          | ||||||| |  |  | |  || ||    |||  | | || |  | ||| ||  |||| |||||||||||  | |||||||||||  | |||||  ||||| || |||||| |||||| || ||||||||||| || ||||| |||||  | ||||| || |
-------tattgtttcttccatccaagtggagtcatcttcctcttcct----cctcttattctcatctttgtcatcttctt----tgacctgctttta--cctttgcctacatt-cagGAGAGTGATGTGAAGTGGGCTTCAAGATGGGATGCCTATTTGCTGATGAGTGATGACCAAATTCACTGGTTCTCAATTGTGAACTCATTGATGATTGTTC

upper sequence: LOC_Os09g38530.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT5G25100.1 (Arabidopsis thaliana), 3'ss of exon 6
gtactagttttgcatgttttgtttggattctgtttcccccttcatgtgatagttgcctattctcttaatgttaaatttattgcaatgatttccattgaatctttttccctcat---tgcagGAGAGTGACATCAAGTGGGCTTCCCGTTGGGACACCTATCTGTTGATGACTGATGATCAGATTCACTGGTTTTCTATTGTCAACTCTCTCATGATCGTGC
           ||| ||| |  || ||  ||  |       |||   |||||||   | ||      ||  ||  | | || |  |  |  |  ||     |||| | || ||   | ||||| |||||  | |||||||| ||  | |||||  | ||||| |||||||  ||  |||| ||||||||||||||||||||||||||||| |||||||| |
-----------gcaagttcttgtttga--ctaatcagtttatcaccagatagttttgtcttagtgagatactat-tgtgttcctgttctcactgttttgatttttgcgctgatgtcttcagGAAAGTGAAGTGAAGTGGGCGTCTAGATGGGATGCTTATCTTTTGATGAGCGACAATCAAATTCACTGGTTTTCTATTGTCAACTCTCTTATGATCGTCC

upper sequence: LOC_Os09g38530.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv11s0037g00210.t01 (Vitis vinifera), 3'ss of exon 6
gtactagttttgcatgttttgtt-tggattctgtttcccccttcatgtgatagttgcctattctcttaatgttaaatttattgcaatgatttccattgaatctttttccctcattgcagGAGAGTGACATCAAGTGGGCTTCCCGTTGGGACACCTATCTGTTGATGACTGATGATCAGATTCACTGGTTTTCTATTGTCAACTCTCTCATGATCGTGC
    ||      |||  ||| |  |  ||  || ||   || | |      |  ||  | | ||        | |  ||  || | || |          || | | |      |||||||||||||  | || ||||| || || ||||| ||||| ||  ||||| | |||||||| |||||||||||||| |||||||| ||| | ||||| || |
---gtaagaccacatactttataataaataatgattttgccatta------acctgtgtgtactacaggcaatgatattcctgtattgct---------gtcatgtgcttggtatgcagGAGAGTGATGTGAAATGGGCCTCTCGATGGGATACCTACCTTCTGATGGCCGATGATCAAATTCACTGGTTTTCAATTGTCAATTCTTTGATGATTGTTC

upper sequence: LOC_Os09g38530.1 (Oryza sativa), 3'ss of exon 6
lower sequence: PP1S137_209V6.1 (Physcomitrella patens), 3'ss of exon 7
-------------------------------------------------------------gtactagttttgcatgttttgtttggattctgtttcccccttcatgtgata-gttgcctattctcttaatgt--taaatttattgcaatgatttccattgaatctttt----tccctcat----tgcagGAGAGTGACATCAAGTGGGCTTCCCGTTGGGACACCTATCTGTTGATGACTGATGATCAGATTCACTGGTTTTCTATTGTCAACTCTCTCATGATCGTGC
                                                              || | |  |  | | |   | ||  | ||  ||      ||  |||   | ||   ||| |     | |||   ||  | |||  |     | | |   || |  ||    | | |  |    ||||||| ||||||||||||||||| || || ||||| || ||| |||||||||| |||||||| ||||| ||||| || ||||| ||||| |||||||| || |
gtgggtgattacttcagtacttccttttgctattacacaacttcgacaatcacttgaattgttatttgcctctcgtttcgggatttaagtcgtttgaagattttttgtagaatgtcagctactagtcaagtgtatcaagatcattctagcttctccaacccaagcacttggcttgctttgtgctgtgcagGAAAGTGACATCAAGTGGGCATCTCGCTGGGATACATATTTGTTGATGACAGATGATCAAATTCATTGGTTCTCCATTGTTAACTCCCTCATGATTGTCC

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|29627738|gb|CB632749.1|CB632749
EST:     AGGTCGAAGCTGGCAAAGAAATCATATTCACCTATGATGTTCGCTTTGAG                         GAGAGTGACATCAAGTGGGCTTCCCGTTGGGACACCTATCTGTTGATGACT
genomic: AGGTCGAAGCTGGCAAAGAAATCATATTCACCTATGATGTTCACTTTGAGgtactagttt ... ctcattgcagGAGAGTGACATCAAGTGGGCTTCCCGTTGGGACACCTATCTGTTGATGACT
EST: gi|29646687|gb|CB651694.1|CB651694
EST:     AGGTCGAAGCTGGCAAAGAAATCATATTCACCTATGATGTTCACTTTGAG                         GAGAGTGACATCAAGTGGGCTTCCCGTTGGGACACCTATCTGTTGATGACT
genomic: AGGTCGAAGCTGGCAAAGAAATCATATTCACCTATGATGTTCACTTTGAGgtactagttt ... ctcattgcagGAGAGTGACATCAAGTGGGCTTCCCGTTGGGACACCTATCTGTTGATGACT
EST: gi|29630499|gb|CB635508.1|CB635508
EST:     AGGTCGAAGCTGGCAAAGAAATCATATTCACCTATGATGTTCGCTTTGAG                         GAGAGTGACATCAAGTGGGCTTCCCGTTGGGACACCTATCTGTTGATGACT
genomic: AGGTCGAAGCTGGCAAAGAAATCATATTCACCTATGATGTTCACTTTGAGgtactagttt ... ctcattgcagGAGAGTGACATCAAGTGGGCTTCCCGTTGGGACACCTATCTGTTGATGACT
EST: gi|29627339|gb|CB632350.1|CB632350
EST:     AGGTCGAAGCTGGCAAAGAAATCATATTCACCTATGATGTTCGCTTTGAG                         GAGAGTGACATCAAGTGGGCTTCCCGTTGGGACACCTATCTGTTGATGACT
genomic: AGGTCGAAGCTGGCAAAGAAATCATATTCACCTATGATGTTCACTTTGAGgtactagttt ... ctcattgcagGAGAGTGACATCAAGTGGGCTTCCCGTTGGGACACCTATCTGTTGATGACT

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), 61 (downstream exon)
Score: 38

ATGTGACCCTCATGCTAACAAGCTTGTAACAAGTTCTGACTCTCCTCAGGAGGTCGAAGCTGGCAAAGAAATCATATTCACCTATGATGTTCACTTTGAGgtactagttt ... ctcattgcagGAGAGTGACATCAAGTGGGCTTCCCGTTGGGACACCTATCTGTTGATGACTGATGATCAGATTCACTGGTTTTCTATTGTCAACTCTCTCATGATCGTGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaatgttaaatttattgcaatgatttccattgaatctttttccctcattgcagGAGAGTGACATCAAGTGGGCTTCCCGTTGGGACACCTATCTGTTGATGACTGATGATCAGATTCACTGGTTTTCTATTGTCAACTCTCTCATGATCGTGC
 tcttaat  putative branch site (score: 38)
                                    tctttttccctcattg  putative PPT
       ttaaatttattgcaat  TA-rich tract