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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATGgtaatattcatgtccttatactggttataactaccaataatttgccatatatgttctaagctgttgattcggatgcag

Basic information

species Oryza sativa
transcript LOC_Os12g04990.4
intron # 18
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g04990.3 (Oryza sativa), 5'ss of exon 18
lower sequence: GRMZM2G176546_T01 (Zea mays), 5'ss of exon 10
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATGgtaatattcatgtccttatactggttata--actaccaataatttgccatatatgttctaag-ctgttgattcggatgcag
||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||||| || |||||||| ||||| || |  |||||||||||||||||| |||    | |  ||| ||||  || | || | ||  ||||   |||||||||  || ||| ||||| |||||
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATATATGgtaatatttatgattctgtgttggctatatgaccatcagttatg-gccaagcatgttctaaatctcttgtttcggttgcag

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 5'ss of exon 18
lower sequence: GLYMA10G39540.1 (Glycine max), 5'ss of exon 19
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATGgtaat------attcatgtccttatactggttataactaccaataatttgccatatatgttctaagctgttgattcggatgcag
||||| || || ||||| || ||||| || ||||| ||||| ||||||||||| ||||| || || || ||||| ||| | ||||||| |||| ||||||||||       | ||||  ||  | | | | | |   |    ||  ||||   ||  |     | |||  |  || |  || ||
AAGAATATCTTTAAGTTGGCACAAGGCGAGTACATTGCTCCTGAGAAGATTGAAAATGTATACGCCAAATGCAAATTTGTGGCGCAGTGCTTTGTATATGgtaaggaaataaatcattcccacaaattcggtgtgtgtg---atcgtttgtactagcttgctgatgcttcttttttgtttgtag

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 5'ss of exon 18
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 5'ss of exon 19
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATGgtaatattcatgtccttatactggttataactaccaataatttgccatatatgttctaagctgttgattcggatgcag
||||||||||| ||||| || |||||||| ||||||||||| ||||| ||||||||||| |||||||| ||||| ||| |||| |||| |||| |||||||||| |   |||   || |||   |      | |  ||  ||||||   |   | ||    | ||  |  |     ||
AAGAACATTTTTAAGTTGGCACAAGGAGAGTACATAGCTCCAGAGAAAATTGAGAATGTATATGCTAAATGCAAATTTGTTGCCCAGTGCTTTGTATATGgtaagaaaaatgagattttacaaatctctctttc--atcttttgcctgctgactgct----tatttctctgatgatag

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 5'ss of exon 18
lower sequence: Vv14s0128g00720.t01 (Vitis vinifera), 5'ss of exon 19
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATGgtaatattcatg---tccttatactggttataactaccaataatttgccatatatgttctaagctgttgattcggatgcag
|||||||| |||||| | || || || ||||| ||||| || ||||| ||||||||||| ||||| |||||||| ||| || | || |  ||||| ||||||||     |||   |     | | | ||    |  ||     |  |   | | || |     ||| | | | |  |  ||
AAGAACATCTTCAAGCTGGCACAGGGTGAATATATAGCACCAGAGAAAATTGAGAATGTATATGCCAAGTGCAAATTTGTTTCCCAATGTTTTATCTATGgtaaggcagatggagtttacttgcagattgggccctccccagctaagttctctttgct---gactgcttaattgattttag

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 5'ss of exon 18
lower sequence: PP1S408_23V6.1 (Physcomitrella patens), 5'ss of exon 21
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATGgtaatattcatgtccttatactggttataactaccaataatttgccatatatgttctaagctgttgattcggatgcag--------------------------
||||| || || ||||| ||||||||||| ||||| || || |||||||| |||||||||||   |    |    || ||  | ||||  |  ||| |||||| | ||||| |  ||| |  |     ||||    ||   |||   | ||        ||   || |   ||||                             
AAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAAGATCGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATACATGgta-tgttcat-tttttaaatgga--ggaactcttcatttcttgtggtctaaacaagttgcaactggtgtagatgacttaagatttttttttcatctgaaatga

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 5'ss of exon 18
lower sequence: PP1S33_126V6.1 (Physcomitrella patens), 5'ss of exon 22
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATGgtaatattcatgtccttatactggttataactaccaataatttgccatatatgttctaagctgttgattc--ggatgcag---------------------
||||| || |||||||| ||||| ||||| ||||| || ||||||||||||||||| |||||        |   ||| ||||| |||| ||||||  |||||    |||||    |||     |  ||  || |  ||  | |     || || |    | ||      |  || | | |                     
AAGAATATCTTCAAGTTGGCTCAGGGAGAGTACATTGCGCCCGAGAAGATTGAGAACGTCTACCTGCGAAGTCGGTTCATTGCACAGTGCTTTATTCATGgtg-cgttcattcaattaatggaggcatcccttctcattgtctcagtcatctgcttgtggttgaaacaccatggttactggggttgtgggtgctttaagag

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 5'ss of exon 18
lower sequence: PP1S12_178V6.2 (Physcomitrella patens), 5'ss of exon 21
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATGgta--------------atattcatgtccttatactggttata-actaccaata-atttgccatatatgttcta-agctgttgattcggatgcag------------------------------------------------------------------------
||||||||||||||||||||||||||||||||||| || || || |||||||||||  | |||  |    |   ||||||| ||||||  ||  ||||||||               |   ||   || || || || ||  |   |||   |   | || |  | | ||     | ||| || | || || | |                                                                        
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATTGCACCGGAAAAGATTGAGAACATTTATCTTCGCAGTCGGTTTATTTCGCAGTGTTTCGTATATGgtgcgttcatttaatcgacggtcgcatctttttaatgattgcacgttactttttcgtgtgacggaaacgtgtagcaactggtgttacgtatactggaaaaactaccaactcattgaaatccaatcattcttaccaatcgtataattggttggtggtgaattgcacag

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 5'ss of exon 18
lower sequence: EFJ33980 (Selaginella moellendorffii), 5'ss of exon 20
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATGgtaatattcatgtccttatactggttataactaccaataatttgccatatatgttctaagctgttgattcggatgcag
||||||||||| ||| | || || || ||||||||||| || |||||||||||||||||||||  |||  |||||||  |||| ||||  ||  | || ||| | |   ||    || |  ||  | || | | |  |  |||| || |  | |  |    |||              
AAGAACATTTTTAAGCTTGCACAGGGTGAATACATAGCGCCAGAGAAGATTGAGAATGTCTATCATAAAAGCAAGTTCGTTGCTCAGTGTTTCGTCTACGgtgagaacaat---tttgttttgtgtctagcgagcggt--tttgacacaattctcttcgattgtaacag---------

upper sequence: LOC_Os12g04990.3 (Oryza sativa), 5'ss of exon 18
lower sequence: EFJ37488 (Selaginella moellendorffii), 5'ss of exon 20
AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATGgt---aatattcatgtcct---tatactggttataactaccaataat-----ttgccatatatgtt--ctaagctgttgattcggatgcag-----------------------------------
||||||||||| ||| | || || || ||||||||||| || |||||||||||||||||||||   ||  |||||||  |||| ||||  ||  | || |||   || | |  |||  |   | ||  |  |  | ||  | | |       | ||   |||   |  | ||| | |         ||                                      
AAGAACATTTTTAAGCTTGCACAGGGTGAATACATAGCGCCAGAGAAGATTGAGAATGTCTATCAAAAAAGCAAGTTCGTTGCTCAGTGTTTCGTCTACGgtgagaacaattttgttttgtgtctagcgagtccacctggcgaaaggatcggtcgctgaatagcatggcaaagttttctccctatgtgtgactcggttttgacacaattctcttcgattgtaacag

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|86492874|gb|CI135507.1|CI135507
EST:     TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATG                         GTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGATG
genomic: TGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATGgtaatattca ... tcggatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGATG




















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: 61 (upstream exon), 29 (downstream exon)
Score: 7

AAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCCGAGAAGATTGAGAATGTCTATGCTAAGTGCAAGTTTATTGCGCAGTCCTTTATATATGgtaatattca ... tcggatgcagGTGATAGTTTAAACTCTTCTTTGGTTGCCGTAGTAGCAGTTGAACCAGATGTGTTGAAGGCTTGGGCTGCATCTGAGGGAATCCAGGTAAATATGCTGAC




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