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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagtgtgatcttgatgctcctttcatggaattgttgtgatcttgtgggatgcattggcttgatgctgaattttatctgtatctggattgcagGAACTGTGCTTGGGCTGCACGAGGACAGCAGATACAAGTCGGAGTCGAAGAAGGTGCATCTTAAACAAGTAGATCTTATCGGATTTGGTTCTGGTCCAGA

Basic information

species Oryza sativa
transcript LOC_Os02g55140.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g55140.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G388453_T01 (Zea mays), 3'ss of exon 5
gtagt--gtgatcttg---atgctcctttcatggaattgttgtgatc-ttgtgggatgcattggcttgatgctgaattttatctgtatctggattgcagGAACTGTGCTTGGGCTGCACGAGGACAGCAGATACAAGTCGGAGTCGAAGAAGGTGCATCTTAAACAAGTAGATCTTATCGGATTTGGTTCTGGTCCAGA
||| |   |  || ||   | ||||||||        || ||| ||  || ||   |||| ||| | ||||||||| ||| |     |||| ||  ||||||| ||||| ||| || | |||||||||||||||||||| || ||||| |||||||| || ||||| || ||| |||| ||| | ||||||||| |  |
gtactcgattctcctgcacacgctcctttttcttctctgatgtcatggttatgaagtgcagtggatggatgctgaaatttctgccggtctgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAGTCTGAATCGAAAAAGGTGCACCTGAAACATGTTGATATTATTGGAGTGGGTTCTGGTGCGAA

upper sequence: LOC_Os02g55140.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G028114_T01 (Zea mays), 3'ss of exon 6
-gtagt--gtgatcttg---atgctcctttcatggaattgttgtgatc-ttgtgggatgcattggcttgatgctgaattttatctgtatctggattgcagGAACTGTGCTTGGGCTGCACGAGGACAGCAGATACAAGTCGGAGTCGAAGAAGGTGCATCTTAAACAAGTAGATCTTATCGGATTTGGTTCTGGTCCAGA
 ||| |   |  || ||   | ||||||||        || ||| ||  || |||  |||| ||| | |||||| || ||| | |   |||| ||  |||||||  |||| ||| || | |||||||||||||||||||| || ||||| |||||||| || ||||| || ||| |||| ||| | |||||||       
ggtacttgattctcctgcacacgctcctttttcttctctgatgtcatggttatggagtgcagtggatggatgctaaaatttctgtcggtctgaatcacagGAACCATGCTGGGGTTGTATGAGGACAGCAGATACAAGTCTGAATCGAAAAAGGTGCACCTGAAACAGGTTGATATTATTGGACTGGGTTCTG-------

upper sequence: LOC_Os02g55140.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G126913_T02 (Zea mays), 3'ss of exon 2
-gtagt--gtgatcttg---atgctcctttcatggaattgttgtgatc-ttgtgggatgcattggcttgatgctgaattttatctgtatctggattgcagGAACTGTGCTTGGGCTGCACGAGGACAGCAGATACAAGTCGGAGTCGAAGAAGGTGCATCTTAAACAAGTAGATCTTATCGGATTTGGTTCTGGTCCAGA
 ||| |   |  || ||   | ||||||||        || ||| ||  || |||  |||| ||| | ||||||||| ||| |     |||| ||  ||||||| ||||| ||| || | ||||||| |||||||||||| || ||||| |||||||| || ||||| || ||| |||| ||| | ||||||||| | ||
ggtactcgattctcctgcacacgctcctttttcttctctgatgtcatggttatggagtgcagtggatggatgctgaaatttctgccggtctgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAACAGATACAAGTCTGAATCGAAAAAGGTGCACCTGAAACAGGTTGATATTATTGGACTAGGTTCTGGTGCGGA

upper sequence: LOC_Os02g55140.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G178958_T01 (Zea mays), 3'ss of exon 2
gtagt--gtgatcttg---atgctcctttcatggaattgttgtgatc-ttgtgggatgcattggcttgatgctgaattttatctgtatctggattgcagGAACTGTGCTTGGGCTGCACGAGGACAGCAGATACAAGTCGGAGTCGAAGAAGGTGCATCTTAAACAAGTAGATCTTATCGGATTTGGTTCTGGTCCAGA
||| |   |  |||||   | ||||||||        || ||| ||  || |||  |||| ||| | ||||||||| ||| |     |||| ||  ||||||| ||||| ||| || | ||||||||||||||||| || || ||||| |||||||| || ||||| || ||| |||| ||| | ||||||||| ||||
gtacttgattctcttgcacacgctcctttttcttctctgatgtcatggttatggagtgcagtggatggatgctgaaatttctgccggtctgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAATCTGAATCGAAAAAGGTGCACCTGAAACAGGTTGATATTATTGGACTGGGTTCTGGTGCAGA

upper sequence: LOC_Os02g55140.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G018558_T02 (Zea mays), 3'ss of exon 2
gtagt--gtgatcttg---atgctcctttcatggaattgttgtgatc-ttgtgggatgcattggcttgatgctgaattttatctgtatctggattgcagGAACTGTGCTTGGGCTGCACGAGGACAGCAGATACAAGTCGGAGTCGAAGAAGGTGCATCTTAAACAAGTAGATCTTATCGGATTTGGTTCTGGTCCAGA
||| |   |  || ||   | ||||||||        || ||| ||  || ||   |||| ||| | ||||||||| ||| |     |||| ||  ||||||| ||||| ||| || | |||||||||||||||||||| || || || |||||||| || ||||| || ||| |||| ||| | ||||||||| |  |
gtactcgattctcctgcacacgctcctttttcttctctgatgtcatggttatgaagtgcagtggatggatgctgaaatttctgccggtctgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAGTCTGAATCAAAAAAGGTGCACCTGAAACATGTTGATATTATTGGAGTGGGTTCTGGTGCGAA

upper sequence: LOC_Os02g55140.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G468367_T01 (Zea mays), 3'ss of exon 2
-----gtagtgtgatcttgatgctcctttcatggaattgttgtgatc-ttgtgggatgcattggcttgatgctgaattttatctgtatctggattgcagGAACTGTGCTTGGGCTGCACGAGGACAGCAGATACAAGTCGGAGTCGAAGAAGGTGCATCTTAAACAAGTAGATCTTATCGGATTTGGTTCTGGTCCAGA
       | | | ||      ||||||||        || ||| ||  || |||  |||| ||| | ||||||||| ||| |     |||| ||  ||||||| ||||| ||| || | |||||||||||||||||||| || ||||| |||||||| || |                                     
gtactcgattctcatgcacgcgctcctttttcttctctgatgtcatagttatggagtgcagTGGATGGATGCTGAAATTTCTGCCGGTCTG-ATCACAGGAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAGTCTGAATCGAAAAAGGTGCACCTGA-------------------------------------

upper sequence: LOC_Os02g55140.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G126913_T01 (Zea mays), 3'ss of exon 2
gtagt--gtgatcttg---atgctcctttcatggaattgttgtgatc-ttgtgggatgcattggcttgatgctgaattttatctgtatctggattgcagGAACTGTGCTTGGGCTGCACGAGGACAGCAGATACAAGTCGGAGTCGAAGAAGGTGCATCTTAAACAAGTAGATCTTATCGGATTTGGTTCTGGTCCAGA
||| |   |  || ||   | ||||||||        || ||| ||  || |||  |||| ||| | ||||||||| ||| |     |||| ||  ||||||| ||||| ||| || | ||||||| |||||||||||| || ||||| |||||||| || ||||| || ||| |||| ||| | ||||||||| | ||
gtactcgattctcctgcacacgctcctttttcttctctgatgtcatggttatggagtgcagtggatggatgctgaaatttctgccggtctgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAACAGATACAAGTCTGAATCGAAAAAGGTGCACCTGAAACAGGTTGATATTATTGGACTAGGTTCTGGTGCGGA

upper sequence: LOC_Os02g55140.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G388453_T02 (Zea mays), 3'ss of exon 5
-gtagt--gtgatcttg---atgctcctttcatggaattgttgtgatc-ttgtgggatgcattggcttgatgctgaattttatctgtatctggattgcagGAACTGTGCTTGGGCTGCACGAGGACAGCAGATACAAGTCGGAGTCGAAGAAGGTGCATCTTAAACAAGTAGATCTTATCGGATTTGGTTCTGGTCCAGA
 ||| |   |  || ||   | ||||||||        || ||| ||  || ||   |||| ||| | ||||||||| ||| |     |||| ||  ||||||| ||||| ||| || | |||||||||||||||||||| || ||||| |||||||| || ||||| || ||| |||| ||| | ||||||||| |  |
ggtactcgattctcctgcacacgctcctttttcttctctgatgtcatggttatgaagtgcagtggatggatgctgaaatttctgccggtctgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAGTCTGAATCGAAAAAGGTGCACCTGAAACATGTTGATATTATTGGAGTGGGTTCTGGTGCGAA

upper sequence: LOC_Os02g55140.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G018558_T01 (Zea mays), 3'ss of exon 2
-gtagt--gtgatcttg---atgctcctttcatggaattgttgtgatc-ttgtgggatgcattggcttgatgctgaattttatctgtatctggattgcagGAACTGTGCTTGGGCTGCACGAGGACAGCAGATACAAGTCGGAGTCGAAGAAGGTGCATCTTAAACAAGTAGATCTTATCGGATTTGGTTCTGGTCCAGA
 ||| |   |  || ||   | ||||||||        || ||| ||  || ||   |||| ||| | ||||||||| ||| |     |||| ||  ||||||| ||||| ||| || | |||||||||||||||||||| || || || |||||||| || ||||| || ||| |||| ||| | ||||||||| |  |
ggtactcgattctcctgcacacgctcctttttcttctctgatgtcatggttatgaagtgcagtggatggatgctgaaatttctgccggtctgaatcacagGAACCGTGCTGGGGTTGTATGAGGACAGCAGATACAAGTCTGAATCAAAAAAGGTGCACCTGAAACATGTTGATATTATTGGAGTGGGTTCTGGTGCGAA

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|29673815|gb|CB670090.1|CB670090
EST:     TGGGATCCAGGAAGATTTTAAGCTGACTGCTGCGGCAGCAATTGCTTCAG                         GAACTGTGCTTGGGCTGCACGAGGACAGCAGATACAAGTCGGAGTCGAAGA
genomic: TGGGATCCAGGAAGATTTTAAGCTGACTGCTGCGGCAGCAATTGCTTCAGgtagtgtgat ... tggattgcagGAACTGTGCTTGGGCTGCACGAGGACAGCAGATACAAGTCGGAGTCGAAGA
EST: gi|8856196|gb|AU093514.1|AU093514
EST:     TGGGATCCAGGAAGATTTTAAGCTGACTGCTGCGGCA-CAATTGCTTCAG                         GAACTGTGCTTGGGCTGCACGAGGACAGCAGATACAAGTCGGAGTCGAAGA
genomic: TGGGATCCAGGAAGATTTTAAGCTGACTGCTGCGGCAGCAATTGCTTCAGgtagtgtgat ... tggattgcagGAACTGTGCTTGGGCTGCACGAGGACAGCAGATACAAGTCGGAGTCGAAGA
EST: gi|87005397|gb|CI285619.1|CI285619
EST:     TGGGATCCAGGAAGATTTTAAGCTGACTGCTGCGGCAGCAATTGCTTCAG                         GAACTGTGCTTGGG
genomic: TGGGATCCAGGAAGATTTTAAGCTGACTGCTGCGGCAGCAATTGCTTCAGgtagtgtgat ... tggattgcagGAACTGTGCTTGGG
EST: gi|29623639|gb|CB628650.1|CB628650
EST:     TGGGATCCAGGAAGATTTTAAGCTGACTGCTGCGGCAGCAATTGCTTCAG                         GAACTGTGCTTGGGCTGCACGAGGACAGCAGATACAAGTCGGAGTCGAAGA
genomic: TGGGATCCAGGAAGATTTTAAGCTGACTGCTGCGGCAGCAATTGCTTCAGgtagtgtgat ... tggattgcagGAACTGTGCTTGGGCTGCACGAGGACAGCAGATACAAGTCGGAGTCGAAGA
EST: gi|29663047|gb|CB659322.1|CB659322
EST:     TGGGATCCAGGAAGATTTTAAGCTGACTGCTGCGGCAGCAATTGCTTCAG                         GAACTGTGCTTGGGCTGCACGAGGACAGCAGATACAAGTCGGAGTCGAAGA
genomic: TGGGATCCAGGAAGATTTTAAGCTGACTGCTGCGGCAGCAATTGCTTCAGgtagtgtgat ... tggattgcagGAACTGTGCTTGGGCTGCACGAGGACAGCAGATACAAGTCGGAGTCGAAGA

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: 75 (upstream exon), 61 (downstream exon)
Score: 112

GCCAAGTCTGCTCAAGCTAGCAGCGCGGCTATTGTTTTTGCTTCAGTGGGTGGGATCCAGGAAGATTTTAAGCTGACTGCTGCGGCAGCAATTGCTTCAGgtagtgtgat ... tggattgcagGAACTGTGCTTGGGCTGCACGAGGACAGCAGATACAAGTCGGAGTCGAAGAAGGTGCATCTTAAACAAGTAGATCTTATCGGATTTGGTTCTGGTCCAGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatcttgtgggatgcattggcttgatgctgaattttatctgtatctggattgcagGAACTGTGCTTGGGCTGCACGAGGACAGCAGATACAAGTCGGAGTCGAAGAAGGTGCATCTTAAACAAGTAGATCTTATCGGATTTGGTTCTGGTCCAGA
                   gcttgat  putative branch site (score: 112)
                              aattttatctgtat  TA-rich tract