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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATCCTTGGTGGAATCCTGCTGTTGAAGAACAAGCTATCATGCGGATCCATCGAATTGGTCAAACAAAGAGTGTTTCCATCAAAAGATTCATCGTCAAGgtactttgtaggtgccatttgttaaatttagtcttctgataactcgcagaacctgtgccatttgctcaaggacttgagaagatggaaatagcttaactaatacacactgaatctggtcaacataatgcaaaatcttcattgccatactttcttaattatggtttatgatgacacag

Basic information

species Oryza sativa
transcript LOC_Os02g32570.1
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g32570.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G057504_T01 (Zea mays), 5'ss of exon 8
GATCCTTGGTGGAATCCTGCTGTTGAAGAACAAGCTATCATGCGGATCCATCGAATTGGTCAAACAAAGAGTGTTTCCATCAAAAGATTCATCGTCAAGgtactttgtaggtgccatttgttaaatttagtcttctgataactcgcagaacctgtgccatttgctcaaggacttgagaagatggaaatagcttaactaatacacactgaatctggtcaacataatgcaaaatcttcattgccatactttcttaattatggtttatgatgacacag
|| |||||||||||||||||||| |||||||||||| ||||||| |||||||||||||||||||| |||| |||||| |||| |||||||||||| ||||||  ||          ||| ||  ||  | |||  | ||||  |  |            ||||||   || | | |  ||| | | ||| |    |  |  |      | |||| |   |  | |      |  |  ||    |   ||  | || ||    ||||      |||
GACCCTTGGTGGAATCCTGCTGTGGAAGAACAAGCTGTCATGCGCATCCATCGAATTGGTCAAACGAAGACTGTTTCTATCAGAAGATTCATCGTGAAGgtatctt----------ttttttgcatcaaatctcatcataatccagat-----------tttgct-ggggccattatcagaagaatata-cgaggcagacccttcgacattctgatgccccgattctcttgttattttttttttgtattggtcatgatataatatggccgtccag

upper sequence: LOC_Os02g32570.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA17G05390.1 (Glycine max), 5'ss of exon 19
GATCCTTGGTGGAATCCTGCTGTTGAAGAACAAGCTATCATGCGGATCCATCGAATTGGTCAAACAAAGAGTGTTTCCATCAAAAGATTCATCGTCAAGgtactttgtaggtgccatttgttaaatttagtcttctgataactcgcagaacctgtgccatttgctcaaggacttgagaagatggaaatagcttaactaatacacactgaatctggtcaacataatgcaaaatcttcattgccatactttcttaattatggtttatgatgacacag
|| || |||||||||||||||||||| ||||||||| | ||||| || ||||| ||||| ||||||||||  ||| |||| | | | || || || ||||||  ||  |  | |||  | |  ||  |  |   |  ||| ||| |||   | || | |||     |     || |   |    |  ||  |     | |    |                                                                      
GACCCATGGTGGAATCCTGCTGTTGAGGAACAAGCTGTTATGCGTATTCATCGTATTGGACAAACAAAGAAGGTTGCCATTAGACGGTTTATTGTGAAGgtatatttaatatcccaaatttggaaaatcatgcac--atatctcacagggtc-gtactatta---tatatttttaatcgggcccagttaattgcttcactgggta----------------------------------------------------------------------

upper sequence: LOC_Os02g32570.2 (Oryza sativa), 5'ss of exon 12
lower sequence: GLYMA12G30540.1 (Glycine max), 5'ss of exon 20
GATCCTTGGTGGAATCCTGCTGTTGAAGAACAAGCTATCATGCGGATCCATCGAATTGGTCAAACAAAGAGTGTTTCCATCAAAAGATTCATCGTCAAGgtactttgtaggtgccatttgttaaatttagtcttctgataactcgcagaacctgtgccatttgctcaaggacttgagaagatggaaatagcttaactaatacacactgaatctggtcaacataatgcaaaatcttcattgccatactttcttaattatggtttatgatgacacag
|| || |||||||||||||||||||| ||||||||| | ||||| || ||||| ||||| ||||||||||  ||| |||| | | | || || || ||||||  ||         || |   |||||| |       || |  | || | | |      ||   | |   | ||   |    |  ||| |||| |||     |||   ||||||                                                             
GACCCATGGTGGAATCCTGCTGTTGAGGAACAAGCTGTTATGCGTATTCATCGTATTGGACAAACAAAGAAGGTTGCCATTAGACGGTTTATTGTGAAGgtatatt-------taatatcccaaatttggaa----aatcatgcacatatcttacatggttgctttatatatttttaa----gttaattgcttcactgg-gtacaagaaatctgc------------------------------------------------------------

upper sequence: LOC_Os02g32570.2 (Oryza sativa), 5'ss of exon 12
lower sequence: Vv06s0061g01190.t01 (Vitis vinifera), 5'ss of exon 19
GATCCTTGGTGGAATCCTGCTGTTGAAGAACAAGCTATCATGCGGATCCATCGAATTGGTCAAACAAAGAGTGTTTCCATCAAAAGATTCATCGTCAAGgta--------ctttgtaggtgcca--tttgttaaatttag-tcttctgat--aactcgcagaacctgtgccatttgctcaaggacttgagaagatggaaatagcttaactaatacacactgaatctggtcaacataatgcaaaatcttcattgccatactttcttaattatggtttatgatgacacag
||||| ||||||||||| ||||| || ||||||||| | |||||||| ||||| ||||| |||||||| || ||    |||||  | ||||| || ||||||        ||   | | |  ||      | | ||  || | |||||    ||| | |  ||  | | || | || |||   ||| |  |   | | |||                                                                                       
GATCCATGGTGGAATCCAGCTGTAGAGGAACAAGCTGTTATGCGGATTCATCGTATTGGACAAACAAAAAGGGTAATGATCAAGCGGTTCATTGTGAAGgtaacatcattctccttggcttgcagaccattcagatggagcttttctgccccaacccccctaa--tatcccctctggtcattcactagtaagagtagtaat---------------------------------------------------------------------------------------

upper sequence: LOC_Os02g32570.2 (Oryza sativa), 5'ss of exon 12
lower sequence: PP1S41_174V6.1 (Physcomitrella patens), 5'ss of exon 19
GATCCTTGGTGGAATCCTGCTGTTGAAGAACAAGCTATCATGCGGATCCATCGAATTGGTCAAACAAAGAGTGTTTCCATCAAAAGATTCATCGTCAAGgtactttgtaggtg--ccatttgttaa---atttagtct--tctgataactcgcagaacctgtgccatttg------ctcaaggacttgagaagatggaaatagctt--aactaatac-acac-tgaatctggtcaa-cataatgcaaaatcttcattgccatactttcttaattatggtttatgatgacacag--
||||| |||||||| || ||||| ||||| || || || |||||||| ||||| ||||||||||| ||   |||     | ||  | || || || ||||||| |   | ||    || || | ||   ||||  | |  | ||||   |      |   |||| | | |      || ||      || || ||     ||  ||  || | || | ||    ||||   ||    | || | || | |    |    | |   |||| |  |    | |    |||   |   
GATCCATGGTGGAACCCGGCTGTCGAAGAGCAGGCAATTATGCGGATACATCGCATTGGTCAAACCAAAGATGTCCAAGTTAAGCGGTTTATTGTAAAGgtacgtgaaatgtaattcaattttgaattgatttgatttgatttgatttatttttctaatcgtgcgaatggttaagcctgaaacgtgcgataatattatgctaattttcaaatgatgctacgtgcgaatacagtagttcttactacatagtagataactgcttgtgttctcagattctctatggtttgatgtacag

upper sequence: LOC_Os02g32570.2 (Oryza sativa), 5'ss of exon 12
lower sequence: EFJ24758 (Selaginella moellendorffii), 5'ss of exon 7
GATCCTTGGTGGAATCCTGCTGTTGAAGAACAAGCTATCATGCGGATCCATCGAATTGGTCAAACAAAGAGTGTTTCCATCAAAAGATTCATCGTCAAGgtactttgtaggtgccatttgttaaatttagtcttctgata-actcgcagaacctgtgccatttgctcaaggacttgagaagatggaaatagcttaactaatacacactgaatctggtcaacataatgcaaaatcttcattgccatactttcttaattatggtttatgatgacacag
|||||||||||||||||||| || ||||||||||| || ||| | ||||| || || || || ||  | |  || || |||||  ||||||||||||| |||  ||     | ||   ||  |   ||    |||| |   | |  || |                                                                                                                              
GATCCTTGGTGGAATCCTGCCGTGGAAGAACAAGCCATAATGAGAATCCACCGTATCGGCCAGACTCAAAACGTATCGATCAAGCGATTCATCGTCAAAgtaagtttccatttcctcctgaaacgcttgaaattcttagggagtttcacag-----------------------------------------------------------------------------------------------------------------------------

upper sequence: LOC_Os02g32570.2 (Oryza sativa), 5'ss of exon 12
lower sequence: EFJ15495 (Selaginella moellendorffii), 5'ss of exon 8
GATCCTTGGTGGAATCCTGCTGTTGAAGAACAAGCTATCATGCGGATCCATCGAATTGGTCAAACAAAGAGTGTTTCCATCAAAAGATTCATCGTCAAGgtactttgtaggtgccatttgttaaatttagtcttctgata-actcgcagaacctgtgccatttgctcaaggacttgagaagatggaaatagcttaactaatacacactgaatctggtcaacataatgcaaaatcttcattgccatactttcttaattatggtttatgatgacacag
|||||||||||||||||||| || ||||||||||| || ||| | ||||| || || || || ||  | |  || || || ||  ||||||||||||| |||  ||     | ||   ||  |   ||    |||||| | | |  || |                                                                                                                              
GATCCTTGGTGGAATCCTGCCGTGGAAGAACAAGCCATAATGAGAATCCACCGTATCGGCCAGACTCAAAACGTATCGATTAAGCGATTCATCGTCAAAgtaagtttccatttcctcctgaaacgcttgaaattctgagagagtttcacag-----------------------------------------------------------------------------------------------------------------------------

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|88197570|gb|CI197420.1|CI197420
EST:     ATCGAATTGGTCAAACAAAGAGTGTTTCCATCAAAAGATTCATCGTCAAG                         GGCACTGTCGAGGAACGAATGGAGGCTGTGCAGGCTCGTAAGCAGCGAATG
genomic: ATCGAATTGGTCAAACAAAGAGTGTTTCCATCAAAAGATTCATCGTCAAGgtactttgta ... gatgacacagGGCACTGTCGAGGAACGAATGGAGGCTGTGCAGGCTCGTAAGCAGCGAATG
EST: gi|89178965|gb|CI043470.1|CI043470
EST:     ATCGAATTGGTCAAACAAAGAGTGTTTCCATCAAAAGATTCATCGTCAAG                         GGCACTGTCGAGGAACGAATGGAGGCTGTGCAGGCTCGTAAGCAGCGAATG
genomic: ATCGAATTGGTCAAACAAAGAGTGTTTCCATCAAAAGATTCATCGTCAAGgtactttgta ... gatgacacagGGCACTGTCGAGGAACGAATGGAGGCTGTGCAGGCTCGTAAGCAGCGAATG
EST: gi|88837636|gb|CI078996.1|CI078996
EST:     ATCGAATTGGTCAAACAAAGAGTGTTTCCATCAAAAGATTTATCGTCAAG                         GGCACTGTCGAGGAACGAATGGAGGCTGTGCAGGCTCGTAAGCAGCGAATG
genomic: ATCGAATTGGTCAAACAAAGAGTGTTTCCATCAAAAGATTCATCGTCAAGgtactttgta ... gatgacacagGGCACTGTCGAGGAACGAATGGAGGCTGTGCAGGCTCGTAAGCAGCGAATG
EST: gi|86479033|gb|CI121666.1|CI121666
EST:     ATCGAATTGGTCAAACGAAGAGTGTTTCCATCAAAAGATTCATCGTCAAG                         GGCACTGTCGAGGAACGAATGGAGGCTGTGCAGGCTCGTAAGCAGCGAATG
genomic: ATCGAATTGGTCAAACAAAGAGTGTTTCCATCAAAAGATTCATCGTCAAGgtactttgta ... gatgacacagGGCACTGTCGAGGAACGAATGGAGGCTGTGCAGGCTCGTAAGCAGCGAATG
EST: gi|89180507|gb|CI044786.1|CI044786
EST:     ATCGAATTGGTCAAACAAAGAGTGTTTCCATCAAAAGATTCATCGTCAAG                         GGCACTGTCGAGGAACGAATGGAGGCTGTGCAGGCTCGTAAGCAGCGAATG
genomic: ATCGAATTGGTCAAACAAAGAGTGTTTCCATCAAAAGATTCATCGTCAAGgtactttgta ... gatgacacagGGCACTGTCGAGGAACGAATGGAGGCTGTGCAGGCTCGTAAGCAGCGAATG

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: 66 (upstream exon), 44 (downstream exon)
Score: 8

GATCCTTGGTGGAATCCTGCTGTTGAAGAACAAGCTATCATGCGGATCCATCGAATTGGTCAAACAAAGAGTGTTTCCATCAAAAGATTCATCGTCAAGgtactttgta ... gatgacacagGGCACTGTCGAGGAACGAATGGAGGCTGTGCAGGCTCGTAAGCAGCGAATGATTTCTGGAGCTTTGACAGATCAGGAAGTACGCAGCGCACGTATAGAAG




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