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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAAAGTTAACCCTACCCAGTGTGAGGCCTTGACCATGGTTTGTGCTCAGgtgtgaatgtgtgataatacccaattttacttgacttaatttgtccaatactcttatgcacttatattgtactgtttgtacaaacagttctctactttgt...

Basic information

species Oryza sativa
transcript LOC_Os03g21950.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g21950.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G010823_T01 (Zea mays), 5'ss of exon 12
GGAAAAGTTAACCCTACCCAGTGTGAGGCCTTGACCATGGTTTGTGCTCAGgtgtgaatgt--gtgataatacccaattttacttgacttaatttgtccaatactcttatgcacttatattgtactgtttgtacaaacagttctctactttgt
|| |||||||| || ||||||||||||||  |||| ||||||||||| |||||   ||  |   || |   |   |||| || |   | || |   |   |       ||   | | |||| |  ||||| |    |  ||  ||| |     
GGGAAAGTTAATCCAACCCAGTGTGAGGCTCTGACAATGGTTTGTGCACAGgtacaaaatttaatgtttgaagaaaattctaatctccatattccttgtgaggactacatattcatctattatgttgtttatggttaaggtgatctgcacc--

upper sequence: LOC_Os03g21950.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA10G02040.1 (Glycine max), 5'ss of exon 12
GGAAAAGTTAACCCTACCCAGTGTGAGGCCTTGACCATGGTTTGTGCTCAGgtg----tgaatgtgtgataatacccaattttacttgact----taatttgtccaatactcttatgcacttatattgtactgtttgtacaaacagt----tctctactttgt----------------------------------------------
|| || ||||||||||||||||||||||| ||||| ||||| ||||| |||||     | |||       | |     |   ||||| | |    | | || |  ||||||  |  |||   |  || ||    |||||  || |      | |  | ||| |                                              
GGGAAGGTTAACCCTACCCAGTGTGAGGCTTTGACAATGGTGTGTGCCCAGgtagacatcaattcacctcattttattaaaatactttaatgttatgacttatggaatactgattggcaaacagtttctatgacttgtaataaaatcacaatttgaattttatggtgactggaaatttctgaattggtgtcatgattcatttatttcag

upper sequence: LOC_Os03g21950.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA02G01930.1 (Glycine max), 5'ss of exon 12
GGAAAAGTTAACCCTACCCAGTGTGAGGCCTTGACCATGGTTTGTGCTCAGgtg---------tgaatgtgtgataatacccaattttacttgacttaatttgtccaatactcttatgcacttatattgtactgtttgtacaaacagttctctactttgt-
|| || |||||||| |||||||||||||| ||||| ||||| ||||| |||||          | | | | | | |||||  | || |        || || | | || | | |     ||    | | |  |  |||     |   ||| | | |||   
GGGAAGGTTAACCCGACCCAGTGTGAGGCTTTGACGATGGTGTGTGCACAGgtagacatcacttcattttattaaaatacttagttatgaccattgtagttag-caaacagtttccgtgacaggcaatttcttaattggtgtcatgattcacgaatttcag

upper sequence: LOC_Os03g21950.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA02G01920.1 (Glycine max), 5'ss of exon 12
GGAAAAGTTAACCCTACCCAGTGTGAGGCCTTGACCATGGTTTGTGCTCAGgtgtgaatgtgtgataatacccaattttacttgacttaatttgtccaatactcttatgcacttatattgtactgtttg-tacaaacagtt-ctctactttgt------------------------------------------------------------------
|| || ||||||||||||||||||||||| ||||| ||||| ||||| |||||          || |  |    | || | || | | || |  |  |||    ||||| ||||||    ||||| |||  | | |||||| || |   ||||                                                                  
GGGAAGGTTAACCCTACCCAGTGTGAGGCTTTGACAATGGTGTGTGCCCAGgta---------gacatcaattcacttcattttattaaaatactttaatg---ttatg-acttatgaaatactgattggcaaacacagtttctatgacttgtaataaaatcacacatattgaattttatggtgactgggaatttctgaattggtgtcatgaatttcag

upper sequence: LOC_Os03g21950.1 (Oryza sativa), 5'ss of exon 12
lower sequence: AT5G50950.2 (Arabidopsis thaliana), 5'ss of exon 12
GGAAAAGTTAACCCTACCCAGTGTGAGGCCTTGACCATGGTTTGTGCTCAGgtgtgaat-gtgtgataatacccaattt-----tacttga-cttaatttgtccaa-tactcttatgcacttatattgtactgtttgta-caaacagttctctactttgt
||||| || || ||||| ||||||||||||||||| |||||||||||||| ||  |     |     |||||  | |||      |  |||  |||| |||   |  || |||| | ||     | | |  || ||| | ||||||    | ||      
GGAAAGGTAAATCCTACACAGTGTGAGGCCTTGACTATGGTTTGTGCTCAAgtaagttccattcaccaatacatattttactaacatatgaatttaaattgctaaggtagtcttgttcatg---actcttttggttgcatcaaacaaaattgtag-----

upper sequence: LOC_Os03g21950.1 (Oryza sativa), 5'ss of exon 12
lower sequence: AT2G47510.1 (Arabidopsis thaliana), 5'ss of exon 13
GGAAAAGTTAACCCTACCCAGTGTGAGGCCTTGACCATGGTTTGTGCTCAGgtgtgaat-gtgtgataatac---ccaattttacttgacttaatttgtccaatactcttatgcacttatattgt-actgtttgtacaaacagttctctactttgt--
|| || || || ||||| ||||||||||||||||| ||||||||||| |||||  |     | |   |||||   |  | |  |    | | ||| |      ||   || |    || |    | ||||||||      ||       || |||   
GGGAAGGTAAATCCTACACAGTGTGAGGCCTTGACTATGGTTTGTGCACAGgtaagtcccatctatcaatacattcttagtacagaccaatgaatctagatgctaaggttgtattattgttccttgactgtttgggttg-caaccaataacattgcag

upper sequence: LOC_Os03g21950.1 (Oryza sativa), 5'ss of exon 12
lower sequence: Vv07s0005g00880.t01 (Vitis vinifera), 5'ss of exon 13
GGAAAAGTTAACCCTACCCAGTGTGAGGCCTTGACCATGGTTTGTGCTCAGgtgtgaatgtgtgataatacccaattttacttgacttaatttgtccaatactcttatgcacttatattgtactgtttgtacaaacagttctctactttgt-----
||||| ||||||||||| |||||||||||  | || ||||| |||||||||||   | | ||||    |   ||||| |  || | | |  |  |   ||   |      | | ||     | |  || |  | |   ||    |||         
GGAAAGGTTAACCCTACTCAGTGTGAGGCTCTCACAATGGTCTGTGCTCAGgta-aagtttgtg----tcttcaattctggttaattaagatgatatgatcaaccagaaaattcatcagcaagtaattatcaagatgtttgaagactgcaataatg

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|66913561|gb|CX100409.1|CX100409
EST:     GAAAAGTTAACCCTACCCAGTGTGAGGCCTTGACCATGGTTTGTGCTCAG                         GTTATGGGTAATCATGTTGGTGTCACAGTAGGTGGTTCGAATGGACATTTT
genomic: GAAAAGTTAACCCTACCCAGTGTGAGGCCTTGACCATGGTTTGTGCTCAGgtgtgaatgt ... gtttttgcagGTTATGGGTAATCATGTTGGTGTCACAGTAGGTGGTTCGAATGGACATTTT




















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: 69 (upstream exon), 64 (downstream exon)
Score: 22

GGAAAAGTTAACCCTACCCAGTGTGAGGCCTTGACCATGGTTTGTGCTCAGgtgtgaatgt ... gtttttgcagGTTATGGGTAATCATGTTGGTGTCACAGTAGGTGGTTCGAATGGACATTTTGAGTTGAATGTCTTTAAGCCAATGATTGCAGCTGGATTACTTAGA




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