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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtacaactacactgctccgatgatctatttgttaactttttttaacgatcaattaatcagctaaagatttacttagcttgttcggttggaaatgcagATTCTGGACCACGAAGACAACGAGATGATGAGGCCGATGAAGATTGTGCGCTAGTACGTGTCCATAGGAATTATGTATGCACTTCAGTAACATAATTTTG

Basic information

species Oryza sativa
transcript LOC_Os01g03549.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g03549.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G054050_T01 (Zea mays), 3'ss of exon 2
gtaagtacaac-----tacactgctcc-gatgatctatttgttaactttttttaacgatcaattaatcagctaaagatttacttagcttgttcggttggaaatgcagATTCTGGACCACGAAGACAACGAGATGATGAGGCCGATGAAGATTGTGCGCTAGTACGTGTCCATAGGAATTATGTATGCACTTCAGTAACATAATTTTG---
|| |||||  |     |   |  |||| | |  | | | || |   |||  ||  |||||    | || |    |   ||  || |  ||     |   | ||||||||| |||||||||| ||||||||||||||||||||||||||||||||||| |     || ||||  | |   |   ||  | |  |  ||  | |||  |   
gtgagtactgcgcgcatctgcctctccaggtcttttgtctgatggatttggttttcgatctcccattctgtcctaatcttcttttg--tgccgtttcaaacatgcagATTTTGGACCACGAGGACAACGAGATGATGAGGCCGATGAAGATTGTGCGTTGAACGGTTTCCA-GGAAGAAAAACATATATTCTATGAA--TGATTCCGTAT

upper sequence: LOC_Os01g03549.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ29867 (Selaginella moellendorffii), 3'ss of exon 3
-------------------------------------------------gtaagtacaac-tacactgctccgatgatctatttgttaactttttttaacgatcaattaatcagctaaagatttacttagcttgt-tcggttggaaatgcagATTCTGGACCACGAAGACAACGAGATGATGAGGCCGATGAAGATTGTGCGCTAGTACGTGTCCATAGGAATTATGTATGCACTTCAGTAACATAATTTTG
                                                 |  || ||| | |||  |  | | |    || |  ||   |   || |  ||  |       ||  |   |   | || ||||| | ||   |||   |||||||| |||||||||||||||||||||||||||| ||  |||||    |||| |||                                              
gtaagttcttccaagaaccctagaaacgggttctaccgtactcaagtacggtagaacaccgtacgttcgtactacatgctgtccgtacgcacgttct--cgtccgtactgacacttcttgtcgttctaagcttttctcttctggctttgcagATTTTGGACCACGAAGACAACGAGATGATGAGACCATTGAAG---CTGCGATAG----------------------------------------------

upper sequence: LOC_Os01g03549.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ08269 (Selaginella moellendorffii), 3'ss of exon 3
-----------------------------------------gtaagtacaact--acactgctccgatgat-ctatttgttaactttttttaacgatcaattaatcagctaaagatt----tacttagcttgttcggt-tggaaatgcagATTCTGGACCACGAAGACAACGAGATGATGAGGCCGATGAAGATTGTGCGCTAGTACGTGTCCATAGGAATTATGTATGCACTTCAGTAACATAATTTTG
                                           ||||||      ||||  ||  | |  | |||  || |  | |          ||       | |  | |  ||    | || ||||| |  | | |||   |||||||| |||||||||||||||||||||||||||| ||  |||||    |||| |||                                              
gtaagttcttccaagaaccctagaaacgggttctaccgtactcaagtacggtagaacacccctatgttcgtactacatgctgccgtacgcacgttctcgtccgtactgacacatcttgtcgttctaagcttttctgttctggctttgcagATTTTGGACCACGAAGACAACGAGATGATGAGACCATTGAAG---CTGCGATAG----------------------------------------------

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|86523916|gb|CI164122.1|CI164122
EST:     GCTTCCCCTTCGACGTCGCCGCCGGCCCCGGCTACGTCTACCACTGCCAC                         ATTCTGGACCACGAAGACAACGAGATGATGAGGCCGATGAAGATTGTGCGC
genomic: GCTTCCCCTTCGACGTCGCCGCCGGCCCCGGCTACGTCTACCACTGCCACgtaagtacaa ... ggaaatgcagATTCTGGACCACGAAGACAACGAGATGATGAGGCCGATGAAGATTGTGCGC
EST: gi|88556006|gb|CI486309.1|CI486309
EST:     TTCGACGTCCCCGCCGGCCCCGGCTACGTCTACCACTGCCAC                         ATTCTGGACCACGAAGACAACGAGATGATGAGGCCGATGAAGATTGTGCGC
genomic: TTCGACGTCGCCGCCGGCCCCGGCTACGTCTACCACTGCCACgtaagtacaa ... ggaaatgcagATTCTGGACCACGAAGACAACGAGATGATGAGGCCGATGAAGATTGTGCGC
EST: gi|88662472|gb|CI469794.1|CI469794
EST:     CCCTTTGACGTCCCCGCCGGCCCCGGGTACGTCTACCAGTGCCAC                         ATTGTGGACCACGAAGACAACGAGATGATGAGGCCGATGAAGATTGTGCGG
genomic: CCCTTCGACGTCGCCGCCGGCCCCGGCTACGTCTACCACTGCCACgtaagtacaa ... ggaaatgcagATTCTGGACCACGAAGACAACGAGATGATGAGGCCGATGAAGATTGTGCGC
EST: gi|89198648|gb|CI016733.1|CI016733
EST:     GCTTCCCCTTCGACGTCGCCGCCGGCCCCGGATACGTCTACCACTGCCAC                         ATTCTGGACCACGAAGACCACGAGATGATGAGGCCGATGAAGATTGTGCGC
genomic: GCTTCCCCTTCGACGTCGCCGCCGGCCCCGGCTACGTCTACCACTGCCACgtaagtacaa ... ggaaatgcagATTCTGGACCACGAAGACAACGAGATGATGAGGCCGATGAAGATTGTGCGC
EST: gi|86493731|gb|CI136364.1|CI136364
EST:     GCTTCCCCTTCGACGTCGCCGCCGGCCCCGGCTACGTCTACCACTGCCAC                         ATTCTGGACCACGAAGACAACGAGATGATGAGGCCGATGAAGATTGTGCGC
genomic: GCTTCCCCTTCGACGTCGCCGCCGGCCCCGGCTACGTCTACCACTGCCACgtaagtacaa ... ggaaatgcagATTCTGGACCACGAAGACAACGAGATGATGAGGCCGATGAAGATTGTGCGC
EST: gi|86527788|gb|CI167994.1|CI167994
EST:     GCTTCCCCTTCGACGTCGCCGCCGGCCCCGGCTACGTCTACCACTGCCAC                         ATTCTGGACCACGAAGACAACGAGATGATGAGGCCGATGAAGATTGTGCGC
genomic: GCTTCCCCTTCGACGTCGCCGCCGGCCCCGGCTACGTCTACCACTGCCACgtaagtacaa ... ggaaatgcagATTCTGGACCACGAAGACAACGAGATGATGAGGCCGATGAAGATTGTGCGC
EST: gi|86827154|gb|CI270855.1|CI270855
EST:     GCTTCCCCTTGGACGTCGCCACCGGCCCCGGCTACGTCTACCACTGCCAC                         ATTCTGGACCACGAAGACAACGAGATGATGAGGCCGATGAAGATTGTGCGC
genomic: GCTTCCCCTTCGACGTCGCCGCCGGCCCCGGCTACGTCTACCACTGCCACgtaagtacaa ... ggaaatgcagATTCTGGACCACGAAGACAACGAGATGATGAGGCCGATGAAGATTGTGCGC
EST: gi|88530060|gb|CI457395.1|CI457395
EST:     GCTTCCCCTTCGACGTCGCCGCCGGCCCCGGCTACGTCTACCACTGCCAC                         ATTCTGGACCACGAAGACAACGAGATGATGAGGCCGATGAAGATTGTGCGC
genomic: GCTTCCCCTTCGACGTCGCCGCCGGCCCCGGCTACGTCTACCACTGCCACgtaagtacaa ... ggaaatgcagATTCTGGACCACGAAGACAACGAGATGATGAGGCCGATGAAGATTGTGCGC

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: 36 (upstream exon), 48 (downstream exon)
Score: 3

GACGAGGCTGCTGGTGCGGTTCCGGCCGCTGTCGCCGCCGGACAGCCGCCGCTTCCCCTTCGACGTCGCCGCCGGCCCCGGCTACGTCTACCACTGCCACgtaagtacaa ... ggaaatgcagATTCTGGACCACGAAGACAACGAGATGATGAGGCCGATGAAGATTGTGCGCTAGTACGTGTCCATAGGAATTATGTATGCACTTCAGTAACATAATTTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taacgatcaattaatcagctaaagatttacttagcttgttcggttggaaatgcagATTCTGGACCACGAAGACAACGAGATGATGAGGCCGATGAAGATTGTGCGCTAGTACGTGTCCATAGGAATTATGTATGCACTTCAGTAACATAATTTTG
                   taaagatttactta  TA-rich tract