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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggttgctaattcgtgctgctgaacgtgtttctattgtcagatattccttgtactaataatggttgtacaatatagATTTTGACTGCCCTTCCTACAATTGAGTTGGACCCTCCCACAATATCTATGACTTTTGGTGTGAATGATTCACCACTGTCTGGCCGCGATGGCACTCAT

Basic information

species Oryza sativa
transcript LOC_Os01g54910.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g54910.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G128688_T02 (Zea mays), 3'ss of exon 7
--------------------------------------------------------------------------------------------gtaggttgctaattcgtgctgctgaacgtgtttctattg-----tcagatattccttgtactaata------atggttgtacaatatagATTTTGACTGCCCTTCCTACAATTGAGTTGGACCCTCCCACAATATCTATGACTTTTGGTGTGAATGATTCACCACTGTCTGGCCGCGATGGCACTCAT
                                                                                              |  |    || || |  |  || | |  |   || |      | |  ||||   | | | || |       ||||||     | ||||| |||| ||| || ||||||||||||||||| |||||||||||||||||||| ||||| ||||||||||||||  || ||||||| ||||||||||||
gtatcactgtatgctttgattggctacttaaccttgtcagttgtcttaaatttaccactacttttggtcttaaaaacatgtgttttagaacaagatttgaacaaatcataatattgcaggcatcaataatacttaattaattatttagtctgcaaacatgtaaagtggttgctatttttagATATTGAGTGCTCTGCCTACAATTGAGTTGGATCCTCCCACAATATCTATGACGTTTGGCGTGAATGATTCACCGTTGGCTGGCCGGGATGGCACTCAT

upper sequence: LOC_Os01g54910.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA06G43820.2 (Glycine max), 3'ss of exon 7
--------------------------gtaggttgctaattcgtgctgctgaacgtgtttctattgtcagatattccttgtactaataatggttgtacaatatagATTTTGACTGCCCTTCCTACAATTGAGTTGGACCCTCCCACAATATCTATGACTTTTGGTGTGAATGATTCACCACTGTCTGGCCGCGATGGCACTCAT
                            |  ||  |   | ||  |  |||     ||||||   |    || |   ||        ||| || ||      ||||| || ||||  | || ||| |||| ||||||||||| ||||| || |||||||||||||| || || || |||||  ||||||| ||||||||||||
ttattaaatttatattcaatttaatttaaacttaatgtcttgtatt-ttgagaacatttctagcat---gtaattgatgactggggtatgtttttatgtcccagATTATGTCTGCTTTGCCCACAGTTGAATTGGACCCTCCTACAATTTCCATGACTTTTGGTGTAAACGACTCCCCACTAGCTGGCCGTGATGGCACTCAT

upper sequence: LOC_Os01g54910.1 (Oryza sativa), 3'ss of exon 7
lower sequence: GLYMA12G14080.1 (Glycine max), 3'ss of exon 7
------------------------gtaggt-tgctaattcgtgctgctgaacgtgtttctattgtcagatattccttgtactaataatggttgtacaatatagATTTTGACTGCCCTTCCTACAATTGAGTTGGACCCTCCCACAATATCTATGACTTTTGGTGTGAATGATTCACCACTGTCTGGCCGCGATGGCACTCAT
                         ||  | | | |||||    |  | |   ||  | || | | | || |  || |    |||   | || ||      || || || ||||  | || ||| |||| ||||||||||| ||||| || |||||||||||||| || || || ||| || |||| || |||||| |||||
aaaagtactcttagataacctaacctaattgtacaaattcaaagttttaattatgcatttactttgatatgtaactggggtaaat---gtttttatgtcccagGTTATGTCTGCTTTGCCCACAGTTGAATTGGACCCTCCTACAATTTCCATGACTTTTGGTGTAAACGACTCCCCATTGGCTGGTCGTGATGGCTCTCAT

upper sequence: LOC_Os01g54910.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ15282 (Selaginella moellendorffii), 3'ss of exon 7
gtaggttgctaattcgtgctgctgaacgtgtttctattgtcagatattccttgtactaataatggttgtacaatatagATTTTGACTGCCCTTCCTACAATTGAGTTGGACCCTCCCACAATATCTATGACTTTTGGTGTGAATGATTCACCACTGTCTGGCCGCGATGGCACTCAT
                    | |     || | || ||    || |  | || || |   | ||   | ||||| ||| |   |   ||  | ||| |  |  |  ||||||| || |||||||||||||||||  |||| ||||||||||| ||  | ||    ||||| |  || 
--------------------gttag--ttgctactttttctcgacaagcttttta-tgccagtgcacgcacaatgtagGTAAAGGAAGCTTTACCTGCGGTGAAAGTGGACCCGCCGACAATATCTATGACTTTCAGTGTTAATGATTCACCGCTTGCGGGGAAGGATGGAAAACAA

upper sequence: LOC_Os01g54910.1 (Oryza sativa), 3'ss of exon 7
lower sequence: EFJ08344 (Selaginella moellendorffii), 3'ss of exon 7
gtaggttgctaattcgtgctgctgaacgtgtttctattgtcagatattccttgtactaataatggttgtacaatatagATTTTGACTGCCCTTCCTACAATTGAGTTGGACCCTCCCACAATATCTATGACTTTTGGTGTGAATGATTCACCACTGTCTGGCCGCGATGGCACTCAT
                    | |     || | || ||    || |  | || || ||  | ||   | |||||  || |   |   ||  | ||| |  |  |  ||||||| || |||||||||||||||||  |||| ||||||||||| ||  | ||    ||||| |  || 
--------------------gttag--ttgctactttttctcgacaagcttttta-taccagtgcacgcacaatgcagGTAAAGGAAGCTTTACCTTCGGTGAAAGTGGACCCGCCGACAATATCTATGACTTTCAGTGTTAATGATTCACCGCTTGCGGGGAAGGATGGAAAACAA

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|2310237|gb|C26392.1|C26392
EST:     TGGCTGGATTGGCTGCTCCAGCAATTGGGCATACTGTGTCAAATTCAGAT                         ATTTTGACTGCCCTTCCTACAATTGAGTTGGACCCTCCCACAATATCTATG
genomic: TGGCTGGATTGGCTGCTCCAGCAATTGGGCATACTGTGTCAAATTCAGATgtaggttgct ... tacaatatagATTTTGACTGCCCTTCCTACAATTGAGTTGGACCCTCCCACAATATCTATG




















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: 52 (upstream exon), 51 (downstream exon)
Score: 22

AACAAGTATGGTAATAGTAGAGGCTGCAGGAGCTGGCGACATAATTTCAATGGCTGGATTGGCTGCTCCAGCAATTGGGCATACTGTGTCAAATTCAGATgtaggttgct ... tacaatatagATTTTGACTGCCCTTCCTACAATTGAGTTGGACCCTCCCACAATATCTATGACTTTTGGTGTGAATGATTCACCACTGTCTGGCCGCGATGGCACTCAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaacgtgtttctattgtcagatattccttgtactaataatggttgtacaatatagATTTTGACTGCCCTTCCTACAATTGAGTTGGACCCTCCCACAATATCTATGACTTTTGGTGTGAATGATTCACCACTGTCTGGCCGCGATGGCACTCAT
                              tactaat  putative branch site (score: 22)
                              tactaataat  TA-rich tract