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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCAACAATATTTGAGGTAGTGACAGGAGCCGCTAAGAAGCAGGCGAAAGAAAAGACTCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGTGgtaaattaatgagcatgcacttctgttttatcgtgacttgaatctctgctgagtacaatttctttctgcag

Basic information

species Oryza sativa
transcript LOC_Os01g66420.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g66420.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G080917_T02 (Zea mays), 5'ss of exon 4
GCCAACAATATTTGAGGTAGTGACAGGAGCCGCTAAGAAGCAG---GCGAAAGAAAAGACTCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGTGgtaaattaatgagcatgcacttctgttttatcgtgacttgaatctctgctgagtacaat----ttctttctgcag---
|| ||||||||||| ||||| ||||| | ||||||||| || || || ||||| || |||||||| ||||||||||||||||||||||| |||||||||||| || ||| ||| |||| |||| |||||| ||| || | ||||||
---CACGATATTTGAGGTGGTGACGGGAGCAGTCAAGAAGCAGCAGGCAAAGGAGAAGACACCTAACAGTAGCAGCAAGAGCAACAAGCCTAGTTCAAAAGTGgtaaat-gccagccac---tttccgttgccatctgacctgaactattgctgataacaccgacattatgcctgcagcag

upper sequence: LOC_Os01g66420.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G172001_T02 (Zea mays), 5'ss of exon 4
GCCAACAATATTTGAGGTAGTGACAGGAGCCGCTAAGAAGCAGGCGAAAGAAAAGACTCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGTGgtaaattaatgagcatgcacttctgttttatcgtgacttgaatctctgctgagtacaatttctttctgcag---
||| || ||||||||||||||||||||||| || |||||||||||||| || ||||| || || ||||| ||||||||||||| ||||||||| |||||||||||| || ||| | ||||| | ||||| |||||| ||| || | |||||||
GCCCACGATATTTGAGGTAGTGACAGGAGCAGCCAAGAAGCAGGCGAAGGAGAAGACACCTAATAGTAGCAGCAAGAGCAACAGGCCTAGTTCAAAAGTGgtaaatgtctgt-cat---ttcctgttgccatccagcctgaattcttgctgataaca--ttgtgtctgcagcag

upper sequence: LOC_Os01g66420.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G080917_T03 (Zea mays), 5'ss of exon 4
GCCAACAATATTTGAGGTAGTGACAGGAGCCGCTAAGAAGCAG---GCGAAAGAAAAGACTCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGTGgtaaattaatgagcatgcacttctgttttatcgtgacttgaatctctgctgagtacaat----ttctttctgcag---
||| || ||||||||||| ||||| ||||| | ||||||||| || || || ||||| || |||||||| ||||||||||||||||||||||| |||||||||||| || ||| ||| |||| |||| |||||| ||| || | ||||||
GCCCACGATATTTGAGGTGGTGACGGGAGCAGTCAAGAAGCAGCAGGCAAAGGAGAAGACACCTAACAGTAGCAGCAAGAGCAACAAGCCTAGTTCAAAAgtggtaaat-gccagccac---tttccgttgccatctgacctgaactattgctgataacaccgacattatgcctgcagcag

upper sequence: LOC_Os01g66420.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G172001_T04 (Zea mays), 5'ss of exon 4
GCCAACAATATTTGAGGTAGTGACAGGAGCCGCTAAGAAGCAGGCGAAAGAAAAGACTCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGTGgtaaattaatgagcatgcacttctgttttatcgtgacttgaatctctgctgagtacaatttctttctgcag
||| || ||||||||||||||||||||||| || |||||||||||||| || ||||| || || ||||| ||||||||||||| ||||||||| |||||||||||| || ||| | ||||| | ||||| |||||| ||| || | |||||||
GCCCACGATATTTGAGGTAGTGACAGGAGCAGCCAAGAAGCAGGCGAAGGAGAAGACACCTAATAGTAGCAGCAAGAGCAACAGGCCTAGTTCAAAAGTGgtaaatgtctgt-cat---ttcctgttgccatccagcctgaattcttgctgataaca--ttgtgtctgcag

upper sequence: LOC_Os01g66420.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G080917_T01 (Zea mays), 5'ss of exon 4
GCCAACAATATTTGAGGTAGTGACAGGAGCCGCTAAGAAGCAG---GCGAAAGAAAAGACTCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGTGgtaaattaatgagcatgcacttctgttttatcgtgacttgaatctctgctgagtacaat----ttctttctgcag
|| ||||||||||| ||||| ||||| | ||||||||| || || || ||||| || |||||||| ||||||||||||||||||||||| |||||||||||| || ||| ||| |||| |||| |||||| ||| || | ||||||
---CACGATATTTGAGGTGGTGACGGGAGCAGTCAAGAAGCAGCAGGCAAAGGAGAAGACACCTAACAGTAGCAGCAAGAGCAACAAGCCTAGTTCAAAAGTGgtaaat-gccagccac---tttccgttgccatctgacctgaactattgctgataacaccgacattatgcctgcag

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|58595326|gb|CF993634.1|CF993634
EST:     AAAAGACTCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGTG                         CAGTCAAAAGCTGAGTCTCGTTCGAAATCTAAGCTGTCAGCCCCCAAGGAT
genomic: AAAAGACTCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGTGgtaaattaat ... ctttctgcagCAGTCAAAAGCTGAGTCTCGTTCGAAATCTAAGCTGTCAGCCCCCAAGGAT
EST: gi|7134950|gb|AU082754.1|AU082754
EST:     AAAAGACTCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGTG                         CAGTCAAAAGCTGAGTCTCGTTCGAAATCTAAGCTGTCAGCCCCCAAGGAT
genomic: AAAAGACTCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGTGgtaaattaat ... ctttctgcagCAGTCAAAAGCTGAGTCTCGTTCGAAATCTAAGCTGTCAGCCCCCAAGGAT
EST: gi|89187194|gb|CI047261.1|CI047261
EST:     TCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGT-                         --GTCAAAAGCTGAGTCTCGTTCGAAATCTAAGCTGTCAGCCCCCAAGGAT
genomic: TCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGTGgtaaattaat ... ctttctgcagCAGTCAAAAGCTGAGTCTCGTTCGAAATCTAAGCTGTCAGCCCCCAAGGAT
EST: gi|38478593|gb|CF962726.1|CF962726
EST:     AAAAGACTCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGGGCGAAAGTG                         CAGTCAAAAGCTGAGTCTCGTTCGAAATCTAAGCTGTCAGCCCCCAAGGAT
genomic: AAAAGACTCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGTGgtaaattaat ... ctttctgcagCAGTCAAAAGCTGAGTCTCGTTCGAAATCTAAGCTGTCAGCCCCCAAGGAT
EST: gi|218504195|gb|FG956553.1|FG956553
EST:     AAAAGACTCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGTG                         ---TCAAAAGCTGAGTCTCGTTCGAAATCTAAGCTGTCAGCCCCCAAGGAT
genomic: AAAAGACTCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGTGgtaaattaat ... ctttctgcagCAGTCAAAAGCTGAGTCTCGTTCGAAATCTAAGCTGTCAGCCCCCAAGGAT
EST: gi|15854667|gb|BI807479.1|BI807479
EST:     GTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGTG                         CAGTCAAAA-CTGAGTCTCGTTCGAAATCTAA-CTGTCAGCCCCCACAGGA
genomic: GTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGTGgtaaattaat ... ctttctgcagCAGTCAAAAGCTGAGTCTCGTTCGAAATCTAAGCTGTCAGCCCCCA-AGGA
EST: gi|2311211|gb|C27366.1|C27366
EST:     AAAAGACTCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGTG                         CAGTCAAAAGCTGAGTCTCGTTCGAAATCTAAGCTGTCAGCCCCCAAGGAT
genomic: AAAAGACTCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGTGgtaaattaat ... ctttctgcagCAGTCAAAAGCTGAGTCTCGTTCGAAATCTAAGCTGTCAGCCCCCAAGGAT
EST: gi|86433437|gb|CI093780.1|CI093780
EST:     AAAAGACTCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGT-                         --GTCAAAAGCTGAGTCTCGTTCGAAATCTAAGCTGTCAGCCCCCAAGGAT
genomic: AAAAGACTCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGTGgtaaattaat ... ctttctgcagCAGTCAAAAGCTGAGTCTCGTTCGAAATCTAAGCTGTCAGCCCCCAAGGAT

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: 33 (upstream exon), 58 (downstream exon)
Score: 16

GCCAACAATATTTGAGGTAGTGACAGGAGCCGCTAAGAAGCAGGCGAAAGAAAAGACTCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGTGgtaaattaat ... ctttctgcagCAGTCAAAAGCTGAGTCTCGTTCGAAATCTAAGCTGTCAGCCCCCAAGGATGAAGAGGGAAGTGGTGATGATGAGGGAGAGGAAGAGGAGGATGACCATG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCAACAATATTTGAGGTAGTGACAGGAGCCGCTAAGAAGCAGGCGAAAGAAAAGACTCCCAACAGTAGTAGCAAGAGCAACAAGCCTAGTTCGAAAGTGgtaaattaatgagcatgcacttctgttttatcgtgacttgaatctctgctgagtacaatttctttctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA