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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggccatttctttttatcataaactattagtcacttggagtaactagtgagtatatcatattatctcaaaaaaaaaaatctttcagGCATTTGATCAGCAGCAACAAGATTTAATTGATGCAGCATCAAAAGCTTTATCATATAGACAAGATATTATTGAGGAAAACATCCGTCTGGCATATGCAG

Basic information

species Oryza sativa
transcript LOC_Os01g01800.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g01800.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G036206_T01 (Zea mays), 3'ss of exon 6
gtaggccatttctttttatcataaactattagtcacttggagtaactagtgagtatatcatattatctcaaaaaaaaaaatctttcagGCATTTGATCAGCAGCAACAAGATTTAATTGATGCAGCATCAAAAGCTTTATCATATAGACAAGATATTATTGAGGAAAACATCCGTCTGGCATATGCAG
||| |   || | |||||||  ||   | || |  |||||       |||| || |||||| | |||| || |         |||||||||||||| |||||||| || ||||||||||||||||| ||||||||||| ||||| || ||||||||||||||||||||||| |||||  | |||||  
gtaagatgtt-cattttatcgaaagagaataattccttgg-------agtgtgtctatcatctcatcttaatagttg----ttttcagGCATTTGACCAGCAGCAGCATGATTTAATTGATGCAGCTTCAAAAGCTTTGTCATACAGGCAAGATATTATTGAGGAAAACATTCGTCTCACGTATGCGT

upper sequence: LOC_Os01g01800.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA10G31880.1 (Glycine max), 3'ss of exon 7
--------------------------------------gtaggccatttctttttatcataaactattagtcacttggagtaactagtgagtatatcatattatctcaaaaaaaaaaatctttcagGCATTTGATCAGCAGCAACAAGATTTAATTGATGCAGCATCAAAAGCTTTATCATATAGACAAGATATTATTGAGGAAAACATCCGTCTGGCATATGCAG
                                       || ||   || | | | |   |   |     | | |||    | ||  ||   | || | || || |  || |       ||   |||| ||||||||||||||||| ||  |  | ||||| ||||||||||||||||||||  ||||||| || ||||| ||||| || |||||  |||||||| 
gtatgcatgaaattttgtcaaagtctttgtgaaattccttaagcatcttttatgttttgcacttttccttttatttgattgagcttctgctcaaat-aaataatttgtaatattg----ctgctagGCCTTTGATCAGCAGCAACAGGACCTTGTAGATGCTGCATCAAAAGCTTTATCATACCGACAAGACATAATTGAAGAAAATATACGTCTTACATATGCAT

upper sequence: LOC_Os01g01800.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA20G35770.1 (Glycine max), 3'ss of exon 8
--------------------------------------gtaggccatttctttttatcataaactattagtcacttggagtaactagtgagtatatcatattatctcaaaaaaaaaaatctttcagGCATTTGATCAGCAGCAACAAGATTTAATTGATGCAGCATCAAAAGCTTTATCATATAGACAAGATATTATTGAGGAAAACATCCGTCTGGCATATGCAG
                                       || ||   || | | | |   |   |       | ||||   | ||  ||   | || | || || |  || |       ||   |||| ||||||||||||||||| ||  |  | ||||| ||||||||||||||||||||  ||||||| || ||||| ||||| || |||||  |||||||| 
gtatgcatgaaattttgttgaaatctttgtgaaattccttaagcatcttttgtgttttgcatttttccttatatttggttgagcttctgctcaaat-aaataatttgtaatattg----ctgctagGCCTTTGATCAGCAGCAACAGGACCTTGTAGATGCTGCATCAAAAGCTTTATCATACCGACAAGACATAATTGAAGAAAATATACGTCTTACATATGCAT

upper sequence: LOC_Os01g01800.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT5G08440.2 (Arabidopsis thaliana), 3'ss of exon 6
gtaggccatttctttt---tatcataaactattagtcacttgga---gtaactagtgagtatatcatattatctcaa------aaaaaaaaatctttc--------------agGCATTTGATCAGCAGCAACAAGATTTAATTGATGCAGCATCAAAAGCTTTATCATATAGACAAGATATTATTGAGGAAAACATCCGTCTGGCATATGCAG
||  ||  ||  ||||   ||| | ||| |||  || ||||      || || | | |   |  | |||| | | ||      |      ||| | ||              |||||||||| || || ||||||||  |  ||||||| |||||||||||| | || || |||||||| || ||||||||||| || || ||  |||||||  
gttagcttttctttttatctattacaaaatatgtgtaactttatcttgtgacgaattatagttacttattctgttaaccacttagggggtaatttatctttcttgttgtgacagGCATTTGACCAACAACAACAAGACCTTGTTGATGCTGCATCAAAAGCTCTTTCTTACAGACAAGAGATCATTGAGGAAAATATACGCCTAACATATGCCT

upper sequence: LOC_Os01g01800.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT5G23490.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaggccatttctttttatca-taaactattagtcacttggagtaactagtgagtatatcatattatctcaaaaa--aaaaaatcttt-----------cagGCATTTGATCAGCAGCAACAAGATTTAATTGATGCAGCATCAAAAGCTTTATCATATAGACAAGATATTATTGAGGAAAACATCCGTCTGGCATATGCAG
||||||| || |||||| | | | | || ||     | |   |||   | ||  | ||   || |   |   ||    ||| ||  ||           |||||||||||||| |||||||||||| |  |||||||  ||||||||||| | || || |||||||| || ||||| ||||| || || ||  |||||||  
gtaggcctttccttttttttacttatctgttttattcatctcgtattaaatgtatttaatttaattgtttggaagctgaaagattgttgctgttgtaaccagGCATTTGATCAACAGCAACAAGATCTTGTTGATGCTTCATCAAAAGCTCTCTCTTACAGACAAGAGATAATTGAAGAAAATATACGCCTAACATATGCCT

upper sequence: LOC_Os01g01800.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv07s0130g00420.t01 (Vitis vinifera), 3'ss of exon 6
gtaggccatttct----ttttatcataaactattagtcacttggagtaact----agtgagtatatcatattatctcaaaaaaaaaaatctttc----agGCATTTGATCAGCAGCAACAAGATTTAATTGATGCAGCATCAAAAGCTTTATCATATAGACAAGATATTATTGAGGAAAACATCCGTCTGGCATATGCAG
 ||     || ||    |||| | | || | |  |    |||   ||   |    || | ||  ||   |   | |            ||||      |||| |||||||| || ||||||||| |  ||||||| || ||||||||| | ||||| |||||||| ||||||||||||||||| |||||  |||||||| 
ttatatttttcctcaaattttctgagaaccaaacatagcctttatgttttttttgagggggttcatggaaagtttttgtccttcttcttcttcttgctagGCTTTTGATCAACAACAACAAGATCTTGTTGATGCGGCCTCAAAAGCTCTTTCATACAGACAAGACATTATTGAGGAAAACATTCGTCTCTCATATGCAT

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|29674957|gb|CB671232.1|CB671232
EST:     TACTCGATGATAAATATATGTTGGAAAAGCGCATTGCTCAAATGCGGATG                         GCATTTGATCAGCAG
genomic: TACTCGATGATAAATATATGTTGGAAAGGCGCATTGCTCAAATGCGGATGgtaggccatt ... aatctttcagGCATTTGATCAGCAG
EST: gi|32947856|gb|BP184428.1|BP184428
EST:     TACTCGATGATAAATATATGTTGGAAAGGCGCATTGCTCAAATGCGGATG                         GCATTTGATCAGCAGCAACAAGATTTAATTGATGCAGCATCAAAAGCTTTA
genomic: TACTCGATGATAAATATATGTTGGAAAGGCGCATTGCTCAAATGCGGATGgtaggccatt ... aatctttcagGCATTTGATCAGCAGCAACAAGATTTAATTGATGCAGCATCAAAAGCTTTA
EST: gi|58673928|gb|CK062614.1|CK062614
EST:     TACTCGATGATAAATATATGTTGGAAAGGCGCATTGCTCAAATGCGGATG                         GCATTTGATCAGCAGCAACAAGATTTAATTGATGCAGCATCAAAAGCTTTA
genomic: TACTCGATGATAAATATATGTTGGAAAGGCGCATTGCTCAAATGCGGATGgtaggccatt ... aatctttcagGCATTTGATCAGCAGCAACAAGATTTAATTGATGCAGCATCAAAAGCTTTA
EST: gi|29628865|gb|CB633876.1|CB633876
EST:     TACTCGATGATATATATATGTTGGAGAGGCGCATTGCTCAAATGCGGATG                         GCATTTGATCAGC
genomic: TACTCGATGATAAATATATGTTGGAAAGGCGCATTGCTCAAATGCGGATGgtaggccatt ... aatctttcagGCATTTGATCAGC

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: 56 (upstream exon), 54 (downstream exon)
Score: 10

CAAGCACGGATACTCGATGATAAATATATGTTGGAAAGGCGCATTGCTCAAATGCGGATGgtaggccatt ... aatctttcagGCATTTGATCAGCAGCAACAAGATTTAATTGATGCAGCATCAAAAGCTTTATCATATAGACAAGATATTATTGAGGAAAACATCCGTCTGGCATATGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cacttggagtaactagtgagtatatcatattatctcaaaaaaaaaaatctttcagGCATTTGATCAGCAGCAACAAGATTTAATTGATGCAGCATCAAAAGCTTTATCATATAGACAAGATATTATTGAGGAAAACATCCGTCTGGCATATGCAG
      gagtaac  putative branch site (score: 10)
                                               tctttc  putative PPT
                  agtatatcatattatc  TA-rich tract