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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtctattgtgctcttatgtgcatcattattttcaacttctccaagttatagcatcttatgcagtttattggtgaaatacttttacatgcttgaagttgatcctaccatgtttagagcactgagcccatgttggcaatccttttgcttttcagCCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAATAGGCAGTTGCGTGAAAAATCAATCAAGACAAAG

Basic information

species Oryza sativa
transcript LOC_Os02g07120.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G168629_T03 (Zea mays), 3'ss of exon 11
------------------------gcaagtctattg----tgctcttatgtgcatcattattttcaacttctcca--agttatagcatcttatgcagtttattggtgaaatactttt----acatgcttgaagttgatcctaccatgtttagagcactgagcccatgttggcaatcc-ttttgcttttcagCCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAATAGGCAGTTGCGTGAAAAATCAATCAAGACAAAG
                        | ||  ||  ||    |  | | | |||      |  | |||   |   ||  || |||       |||   |||| ||| ||  ||  ||      | ||   || | ||     |  || |||  |    |||  ||||||    || ||  ||||||||| ||||||| | ||||||||||| ||||| || || || |||||||| || ||||| |||||||| ||||||||||||||||||||||||
gtgaggttcatcgaactgcagttagaaaaactggtgccattattataacgtggtaatctggtctcatactgggcactagatatgaatgtgtatcttgttt-ttgctgctatgtttagcagaaaatatctgcatttag--attgcacgttctgtttcctgtccccatgc-atcattctgttttgctttgcagCCCTCGCTGGTTGCTGAAGCAAGAGGTCCCAAAAGTTGTCAAGTCTATCAACAGGCAGTTACGTGAAAAATCAATCAAGACAAAG

upper sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G053644_T02 (Zea mays), 3'ss of exon 9
--------------------------------------gcaagtctattgtgctcttatgtgcatcattattttcaacttctccaagt-tatagcat-cttatgcagttta--ttggtgaaatacttttacatgcttgaagttgatcctaccatgtttagagcactgagcccatgttggcaatcc-ttttgcttttcagCCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAATAGGCAGTTGCGTGAAAAATCAATCAAGACAAAG
                                         | | ||  ||| |  | || |  ||||  |   ||     |   | | |||| | |  || ||  | |    || |   || | || | |||       |    | ||  |    |  |    |||  ||||||    || ||  ||||||||||||||||| | ||||||||||| ||||| || || || |||||||| || ||||| |||||||| ||||||||||||||||||||||||
gtgaggttcatcgaactgcagttagaaaaactggtgccattattataacgtggtaatctg-gtctcatactgggcactagatatgaatgtatatcttgtttttgttgctatgcttagcagaaaaattctgcatttagattgcatgttctgtctcagt--gtctcctgtccccatgc-atcattctgttttgcttttcagCCCTCGCTGGTTGCTGAAGCAAGAGGT-CCAAAAGTTGTCAAGTCTATCAACAGGCAGTTACGTGAAAAATCAATCAAGACAAAG

upper sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G053644_T01 (Zea mays), 3'ss of exon 7
gcaagtctattgtgctcttatgtgcatcattattttcaacttctccaagttatagcatcttatgcagtttattggtgaaatacttttacatgcttgaagttgatcctaccatgtttagagcactgagcccatgttggcaatcc-ttttgcttttcagCCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAATAGGCAGTTGCGTGAAAAATCAATCAAGACAAAG
                                                      |  | |  |||  |   || |   || | || | |||       |    | ||  |    |  |    |||  ||||||    || ||  ||||||||||||||||| | ||||||||||| ||||| || || || |||||||| || ||||| |||||||| ||||||||||||||||||||||||
-----------------------------------------------------tgtttttgttgctatgc-ttagcagaaaaattctgcatttagattgcatgttctgtctcagt--gtctcctgtccccatgc-atcattctgttttgcttttcagCCCTCGCTGGTTGCTGAAGCAAGAGGT-CCAAAAGTTGTCAAGTCTATCAACAGGCAGTTACGTGAAAAATCAATCAAGACAAAG

upper sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA17G00570.1 (Glycine max), 3'ss of exon 11
gcaagtctattgtgctcttatgtgcatcattattttcaacttctccaagttatagcatcttatgcagtttattggtgaaatacttttacatgcttgaagttgatcctaccatgtttagagcactgagcccatgttggcaatccttttgcttttcagCCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAATAGGCAGTTGCGTGAAAAATCAATCAAGACAAAG
                                                   || ||      | ||| || |     |  ||     |  |  ||  | |  | |  |  |||     |  | |||  |  | || ||| |    | ||  | ||| ||| |||||||| |||| ||||||||  | ||| |||||||||| || ||||||||||||||||| ||||| || |||||||||
--------------------------------------------------aatggctatcacttcagcttttcctatagttaagccgaggt-tttacaat--aactcaaaatgcagcaattattga--ctgtcttagcactgacat-gcaatgcagTCCTCGATGGTTGTTGAAGCAAGAAGTGTCAAAGATTGTCAAATCTATAAATAGGCAGTTGCGTGAGAAATCTATTAAGACAAAG

upper sequence: LOC_Os02g07120.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA07G40230.2 (Glycine max), 3'ss of exon 12
gcaagtctattgtgctcttatgtgcatcattattttcaacttctccaagttatagcatcttatgcagtttattggtgaaatacttttacatgcttgaagttgatcctaccatgtttagagcactgagcccatgttggcaatccttttgcttttcagCCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAATAGGCAGTTGCGTGAAAAATCAATCAAGACAAAG
                                                    | ||      | ||| || |     |  ||     |  |  ||  | |    | ||  |||     |  | |||  |    || ||| |    | ||  | ||| ||| |||||||| |||| ||||||||  | ||| |||||||||| || ||||||||||||||||| ||||| ||||||||||||
----------------------------------------------------tggctatcacttcagcttttcctatagttaagcccaggt-tttacaataacacataaaatgcagcaattattga--ctgccttagcactgacat-gcaatgcagTCCTCGATGGTTGTTGAAGCAAGAAGTGTCGAAGATTGTCAAATCTATAAATAGGCAGTTGCGTGAGAAATCTATCAAGACAAAG

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|88353222|gb|CI654488.1|CI654488
EST:     CGCCAAACTGGTAACATGACAAAAGGATAAGGTGACATTGATGAGTCTAG                         CCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAA
genomic: CGCCAAACTGGTAACATGACAAAAGGACAAGGTGACATTGATGAGTCTAGgcaagtctat ... tgcttttcagCCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAA
EST: gi|58669402|gb|CK058088.1|CK058088
EST:     CGCCAAACTGGTAACATGACAAAAGGACAAGGTGACATTGATGAGTCTAG                         CCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAA
genomic: CGCCAAACTGGTAACATGACAAAAGGACAAGGTGACATTGATGAGTCTAGgcaagtctat ... tgcttttcagCCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAA
EST: gi|88307071|gb|CI640503.1|CI640503
EST:     CGCCAAACTGGTAACATGACAAAAGGATAAGGTGACATTGATGAGTCTAG                         CCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAA
genomic: CGCCAAACTGGTAACATGACAAAAGGACAAGGTGACATTGATGAGTCTAGgcaagtctat ... tgcttttcagCCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAA
EST: gi|3106834|gb|D42559.1|D42559
EST:     CGCCAAACTGGTAACATGACAAAAGGACAAGGTGACATTGATGAGTCTAG                         CCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAA
genomic: CGCCAAACTGGTAACATGACAAAAGGACAAGGTGACATTGATGAGTCTAGgcaagtctat ... tgcttttcagCCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAA
EST: gi|325494226|gb|JG458750.1|JG458750
EST:     CGCCAAACTGGTAACATGACAAAAGGACAAGGTGACATTGATGAGTCTAG                         CCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAA
genomic: CGCCAAACTGGTAACATGACAAAAGGACAAGGTGACATTGATGAGTCTAGgcaagtctat ... tgcttttcagCCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAA
EST: gi|88288695|gb|CI663484.1|CI663484
EST:     CGCCAAACTGGTAACATGACAAAAGGATAAGGTGACATTGATGAGTCTAG                         CCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAA
genomic: CGCCAAACTGGTAACATGACAAAAGGACAAGGTGACATTGATGAGTCTAGgcaagtctat ... tgcttttcagCCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAA
EST: gi|88333594|gb|CI656666.1|CI656666
EST:     CGCCAAACTGGTAACATGACAAAAGGATAAGGTGACATTGATGAGTCTAG                         CCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAA
genomic: CGCCAAACTGGTAACATGACAAAAGGACAAGGTGACATTGATGAGTCTAGgcaagtctat ... tgcttttcagCCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAA

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: 67 (upstream exon), 60 (downstream exon)
Score: 25

ATGGACATCTTTAACACATTTATTGAGTTGTTACGCCAAACTGGTAACATGACAAAAGGACAAGGTGACATTGATGAGTCTAGgcaagtctat ... tgcttttcagCCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAATAGGCAGTTGCGTGAAAAATCAATCAAGACAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatcctaccatgtttagagcactgagcccatgttggcaatccttttgcttttcagCCCTAGATGGTTGCTGAAACAAGAAGTACCTAAGGTTGTCAAATCCATCAATAGGCAGTTGCGTGAAAAATCAATCAAGACAAAG
 agttgat  putative branch site (score: 25)
                                       tccttttgcttttc  putative PPT
         atgttta  TA-rich tract