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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgataccctcatcgccttattgtttcagatgttcttcagtgagtgatacctattatagtatatctgatgtgtgcgtgttttttcagGGGAGAGCTGACATTTGATCCAGAGGAGGCACTTGCTTTCTTGGCCAAGTACTGTAAATGGGCCGTGGTGACCCTAGCTTCTAAGGGATGCATAGCGAAG

Basic information

species Oryza sativa
transcript LOC_Os01g01620.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g01620.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G171400_T01 (Zea mays), 3'ss of exon 6
--------------------------------------------------------------------------------gtgataccctcatcgccttattgtttcagatgttcttcagtgagtgatacctattatag-----tatatctgatgtgt-gcgtgttttttcagGGGAGAGCTGACATTTGATCCAGAGGAGGCACTTGCTTTCTTGGCCAAGTACTGTAAATGGGCCGTGGTGACCCTAGCTTCTAAGGGATGCATAGCGAAG
                                                                                  |||      |||   | |    ||  || ||     ||||      |||||   ||      |  |  | || ||| || | | | |  ||||||   |||  ||  |||||||||||||| ||||| ||||||| ||||||||| ||||||||||||||||| || ||||| ||||||||||| || |||
gtgagtctttctaagatcgtatgctgatgcatctaagtaggaaagcaatgaaagaaaatggtgaaccggctaaattcgattggatgaaaatatccgttcacatcttttgaagtgtcatagtgcaaccaacctaaggtatgtgcctggacttcatctgttgcttttatctgtagGGGAAGCCTGGAATCAGATCCAGAGGAGGCGCTTGCATTCTTGGGCAAGTACTGCAAATGGGCCGTGGTGACACTTGCTTCAAAGGGATGCATGGCAAAG

upper sequence: LOC_Os01g01620.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G051842_T01 (Zea mays), 3'ss of exon 4
---------------------------------------------------------------gtgataccctcatcgccttattgtttcagatgttcttcagtga----gtgatacctat-tatagtatat--ctgatgtgtgcgtgtttttt-------cagGGGAGAGCTGACATTTGATCCAGAGGAGGCACTTGCTTTCTTGGCCAAGTACTGTAAATGGGCCGTGGTGACCCTAGCTTCTAAGGGATGCATAGCGAAG
                                                                | | |     |      |||    ||| || || |  |||||    |||  ||| || ||  |||| |  |||  ||   | ||||  ||       ||||||||  |||  ||  |||||||||||||| ||||| ||||||| |||||| || |||||||| ||||| || || ||||| ||||||||||| || |||
gtgagtctttccaaaatcgtatattaacgcatctaagtcagaaaggaatgaaagaatgacgaattcaaatggataaaaaaatatatgctcacatcttttgaagtgacatagtgcaaccaatctaaggtatgtgcctggagttcacctgttgcttttatctgcagGGGAGGTCTGGAATCAGATCCAGAGGAGGCGCTTGCGTTCTTGGGCAAGTATTGCAAATGGGCTGTGGTCACACTTGCTTCAAAGGGATGCATGGCAAAG
















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|29667273|gb|CB663548.1|CB663548
EST:     AACATTGACCTTTGCTTTGCCAATGAGGATGAAGCTAGAGAGCTTCTAGG                         GGGAGAGCTGACATTTGATCCAGAGGAGGCACTTGCTTTCTTGGCCAAGTA
genomic: AACATTGACCTTTGCTTTGCCAATGAGGATGAAGCTAGAGAGCTTCTAGGgtgataccct ... gttttttcagGGGAGAGCTGACATTTGATCCAGAGGAGGCACTTGCTTTCTTGGCCAAGTA
EST: gi|33681531|gb|CF309770.1|CF309770
EST:     AACATTGACCTTTGCTTTGCCAATGAGGATGAAGCTAGAGAGCTTCTAGG                         GGGGAGAGCTGACATTTGATC
genomic: AACATTGACCTTTGCTTTGCCAATGAGGATGAAGCTAGAGAGCTTCTAGGgtgataccct ... gttttttcagGGG-AGAGCTGACATTTGATC
EST: gi|29668431|gb|CB664706.1|CB664706
EST:     AACATTGACCTTTGCTTTGCCAATGAGGATGAAGCTAGAGAGCTTCTAGG                         GGGAGAGCTGACATTTGATCCAGAGGAGGCACTTGCTTTCTTGGCCAAGTA
genomic: AACATTGACCTTTGCTTTGCCAATGAGGATGAAGCTAGAGAGCTTCTAGGgtgataccct ... gttttttcagGGGAGAGCTGACATTTGATCCAGAGGAGGCACTTGCTTTCTTGGCCAAGTA
EST: gi|12623048|gb|AU173261.1|AU173261
EST:     AACATTGACCTTTGCTTTGCCAATGAGGATGAAGCTAGAGAGCTTCTAGG                         GGGAGAGCTGACATTTGATCCAGAGGAGGCACTTGCTTTNTTGGCCAAGTA
genomic: AACATTGACCTTTGCTTTGCCAATGAGGATGAAGCTAGAGAGCTTCTAGGgtgataccct ... gttttttcagGGGAGAGCTGACATTTGATCCAGAGGAGGCACTTGCTTTCTTGGCCAAGTA
EST: gi|88956833|gb|CI009055.1|CI009055
EST:     AACATTGACCTTTGCTTTGCCAATGAGGATGAAGCTAGAGAGCTTCTAGG                         GGGAGAGCTGACATTTGATCCAGAGGAGGCACTTGCTTTCTTGGCCAAGTA
genomic: AACATTGACCTTTGCTTTGCCAATGAGGATGAAGCTAGAGAGCTTCTAGGgtgataccct ... gttttttcagGGGAGAGCTGACATTTGATCCAGAGGAGGCACTTGCTTTCTTGGCCAAGTA

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), 71 (downstream exon)
Score: 30

ATGGTTCGTGACTATAGGACACAACTCATTGACCTTTTGGAAACTGGCAACATTGACCTTTGCTTTGCCAATGAGGATGAAGCTAGAGAGCTTCTAGGgtgataccct ... gttttttcagGGGAGAGCTGACATTTGATCCAGAGGAGGCACTTGCTTTCTTGGCCAAGTACTGTAAATGGGCCGTGGTGACCCTAGCTTCTAAGGGATGCATAGCGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttcagtgagtgatacctattatagtatatctgatgtgtgcgtgttttttcagGGGAGAGCTGACATTTGATCCAGAGGAGGCACTTGCTTTCTTGGCCAAGTACTGTAAATGGGCCGTGGTGACCCTAGCTTCTAAGGGATGCATAGCGAAG
                              atctgat  putative branch site (score: 30)
                                            tgttttttc  putative PPT
                   tattatagtatatct  TA-rich tract