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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGAAGTTGACATGACTGGGCAGTATACCCTCAAGAGTGATGTTTATAGCTTTGGAGTTGTCATGCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAGgtattcctatttttctctgattctgcatccctgaattgtttatgcctacatttgatgattcctaatttcttagtcctgacccctgactgttgtgtcaaactatcgtctcag

Basic information

species Oryza sativa
transcript LOC_Os10g25090.1
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g25090.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G004572_T01 (Zea mays), 5'ss of exon 14
CTGAAGTTGACATGACTGGGCAGTATACCCTCAAGAGTGATGTTTATAGCTTTGGAGTTGTCATGCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAGgtattcctatttttctctgattctgcatccctgaattgtttatgcctacatttgatgattcctaatttcttagtcctgacccctgactgttgtgtcaaactatcgtctcag
|||| || || ||| | || ||||||||||||||||||||||| || |||||||| || ||||||||||| |||||||||||||| |||||||||||||||||| |||||  |     ||| |  || | |||  ||    |  || |   |||   || |     || || ||   |||  |||||| |  | ||| |  ||  || |||
CTGAGGTCGAGATGTCCGGTCAGTATACCCTCAAGAGTGATGTCTACAGCTTTGGGGTCGTCATGCTGGAACTCTTGACAGGCCGTAAACCATTTGACAGgtatgcctatcatcactagatgc--cagcactgcgtt----aaaccca---ttgcccatgcagcggtttttggt---gac--ctgactatgatttcacaacattatcgcag

upper sequence: LOC_Os10g25090.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA03G42360.1 (Glycine max), 5'ss of exon 16
CTGAAGTTGACATGACTGGGCAGTATACCCTCAAGAGTGATGTTTATAGCTTTGGAGTTGTCATGCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAGgta---------ttcctatttttctctgattctgcatccctgaattgt-ttatgcctacatttgatgattcctaatttcttagtcctgacccctgactgttgtgtcaaactatcgtctcag
||||||||| | || |||| ||||||||  | || |||||||| || |||||||||||||||||| |||| ||  | |  || || ||||||||||| ||||          ||  | ||||  |||| |    | |   |||    | || |||  | |||  |    |    || |  || |  || | ||||| ||       ||  |   ||  |||
CTGAAGTTGCCTTGTCTGGTCAGTATACTTTGAAAAGTGATGTCTACAGCTTTGGAGTTGTCATGTTGGAACTTCTCAGCGGACGGAAACCATTTGATAGgtgaattaatggttttttttttggtctgctctcacgtttttgagcaatattctgcagaaattgaaattatgtagatataataatgttgtctcctgattgcga----aacattctgtaacag

upper sequence: LOC_Os10g25090.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA16G01790.1 (Glycine max), 5'ss of exon 14
CTGAAGTTGACATGACTGGGCAGTATACCCTCAAGAGTGATGTTTATAGCTTTGGAGTTGTCATGCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAGgtattcctatttttctctgattctgcatccctgaattgtttatgcctacatttgatgattcctaatttcttagtcctgacccctgactgttgtgtcaaactatcgtctcag
| |||||||   || |||| || ||||| || |||||||||||||||||||| |||||||||||| |||| ||  | |  || || ||||| ||||| |||||    |  | | |  | |    ||||  | |  ||  || | | |  |    |   || | ||  |    |  |  |  | ||| ||||    |   |  ||    |||
CCGAAGTTGGTTTGTCTGGTCATTATACTCTTAAGAGTGATGTTTATAGCTTCGGAGTTGTCATGTTGGAACTTCTTAGTGGACGGAAACCGTTTGATAGgtaagattgatatacctttaagtagcataacagttttacttttacatgtac---acactttcaaacattaatgggcacatgcatgattgttaaaacgttccttc--tacag

upper sequence: LOC_Os10g25090.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GLYMA07G05230.1 (Glycine max), 5'ss of exon 14
CTGAAGTTGACATGACTGGGCAGTATACCCTCAAGAGTGATGTTTATAGCTTTGGAGTTGTCATGCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAGgt--attcctatttttctctgattctgcatccctgaattgtttatgcctacatttgatgattcctaatttcttagtcctgacccctgactgttgtgtcaaactatcgtctcag
| ||||||| | || |||| || ||||| || ||||||||||||||||||||||||||||||||| |||| ||  | |  || || ||||||||||| ||||  |    |  | | |  | |     |||  | |  ||  || | | |  |    |   || | ||  |    |  |  |  ||||| ||||    |   |  ||   ||||
CCGAAGTTGGCTTGTCTGGTCATTATACTCTTAAGAGTGATGTTTATAGCTTTGGAGTTGTCATGTTGGAACTTCTTAGTGGACGGAAACCATTTGATAGgtgaaagattgatatacctttaagtaacataacagttttacttttacatgtac---acactttcaaacataaatgggcacatgcctgattgttaaaacgttccttc--ttcag

upper sequence: LOC_Os10g25090.1 (Oryza sativa), 5'ss of exon 14
lower sequence: Vv09s0002g00150.t01 (Vitis vinifera), 5'ss of exon 14
CTGAAGTTGACATGACTGGGCAGTATACCCTCAAGAGTGATGTTTATAGCTTTGGAGTTGTCATGCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAGgtattcctatttttct-ctgattctgca-tccctgaattgtttatgcctacatttgatgattcctaatt-tcttagtcctgaccc--ctgactgttgtgtcaaactatcgtctcag
|||| |||| |||| | || || ||||| || |||||||||||||| || ||||| || ||||||||||||||  |  | || || ||||||||||| |||||    | ||   || ||     | || |   |  |||   | |    |      | |   |  |||  |   | |    ||    || ||| || ||| ||  | |  |  |||
CTGAGGTTGCCATGTCAGGTCAATATACTCTGAAGAGTGATGTTTACAGTTTTGGTGTAGTCATGCTGGAGCTTCTTTCTGGACGTAAACCATTTGATAGgtaaaaatgttgcactactagccatccaatgattccattaccttttttgaagagaaaaggacctgaatcataccattttctacttagctaactattatgttaacattttctgacag

upper sequence: LOC_Os10g25090.1 (Oryza sativa), 5'ss of exon 14
lower sequence: PP1S279_14V6.1 (Physcomitrella patens), 5'ss of exon 4
CTGAAGTTGACATGACTGGGCAGTATACCCTCAAGAGTGATGTTTATAGCTTTGGAGTTGTCATGCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAGgtattccta--tttttctctgattctgcatccctgaattgtttatgcctacatttgatgattcctaatttcttagtcctgacccctgactgttgtgtcaaactatcgtctcag
          |||| ||||    ||     | ||| |||||||||| |||||||||||||||||| | |||||| | || || ||||| ||  | ||||||     | |   |||| | |||    |  | | | | || ||     || | | |  |  | |    ||  || |   ||    |||     ||  | | ||   | |  |  
---------CCATGTCTGGAACATACGATGTGAAGGGTGATGTTTACAGCTTTGGAGTTGTCATGTTCGAGCTCATTACTGGGCGCAAGCCTCTGGACAGGGGACACGAgccttttgtttgaagaggggttcatcatttcttagaatctgc-tgtatttgtactcgtttcatttga--tgcttgctggtaagtgcatgagacgcgcatagcc-

upper sequence: LOC_Os10g25090.1 (Oryza sativa), 5'ss of exon 14
lower sequence: PP1S64_28V6.2 (Physcomitrella patens), 5'ss of exon 15
CTGAAGTTGACATGACTGGGCAGTATACCCTCAAGAGTGATGTTTATAGCTTTGGAGTTGTCATGCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAGgtattcctatttttctctgattctgcatccctgaattgtttatgcctacatttgatgattcctaatttcttagtcctgacccctgactgttgtgtcaaactatcgtctcag
||||| |   ||   ||||   ||||    | || || || |||||||||||||| ||||| ||||| |||||  ||||||| ||||| || || ||||||||   | |  | | |   ||  ||  |    |  || ||  |  ||    || |  |||   ||   | |    |  |  |    |       || | | ||        
CTGAATTCAGCACATCTGGAATGTATGATGTGAAAAGCGACGTTTATAGCTTTGGTGTTGTGATGCTTGAGCTTATGACAGGACGCAAGCCTTTAGACAGgtaactcgaactctgt---atcttgtgtttgagggtt-ttcttttctgatcttaagaatta--aacaccgtgtctcacattctgttcaacaaaatctagcgataac-----

upper sequence: LOC_Os10g25090.1 (Oryza sativa), 5'ss of exon 14
lower sequence: EFJ07060 (Selaginella moellendorffii), 5'ss of exon 4
CTGAAGTTGACATGACTGGGCAGTATACCCTCAAGAGTGATGTTTATAGCTTTGGAGTTGTCATGCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAGgtat--tcctatttttctctgattctgcatccctgaattgtttatgcctacatttgatgattcctaatttcttagtcctgacccctgactgttgtgtcaaactatcgtctcag
| ||  ||| |||| ||||   ||| ||  ||||||| |||||||| ||||||||||| || |||||||||||  | || ||  | ||| |  | ||||||||   || |    ||||   || |   |    |   |   | |   | | | ||||   ||||                                                 
CGGAGTTTGCCATGTCTGGCGTGTACACTGTCAAGAGCGATGTTTACAGCTTTGGAGTGGTGATGCTGGAGCTTCTAACCGGAAGAAAATCGCTAGACAGgtaaaatcttgaagttcttccatccaagagttttatgtaagtaagctccaaacttgaaacttccag-----------------------------------------------

upper sequence: LOC_Os10g25090.1 (Oryza sativa), 5'ss of exon 14
lower sequence: EFJ18843 (Selaginella moellendorffii), 5'ss of exon 4
CTGAAGTTGACATGACTGGGCAGTATACCCTCAAGAGTGATGTTTATAGCTTTGGAGTTGTCATGCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAGgtattcctatttttctctgattctgcatccctgaattgtttatgcctacatttgatgattcctaatttcttagtcctgacccctgactgttgtgtcaaactatcgtctcag
| ||  ||| |||| ||||   ||| ||  ||||||| |||||||| ||||||||||| || |||||||||||  | || ||  | ||| |  | ||||||||       ||      | |  | |||||  || || | | |   ||   |  |  | |   || |||                                          
CGGAGTTTGCCATGTCTGGCGTGTACACTGTCAAGAGCGATGTTTACAGCTTTGGAGTGGTGATGCTGGAGCTTCTAACCGGAAGAAAATCGCTAGACAGgtaaaa--gcttgaagaagttcttccatccaagagttttatgtaagtaagctcca-aacttgaaacttccag---------------------------------------

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|86842917|gb|CI342166.1|CI342166
EST:     GAGTT-TCATGGT-GAGCTC-TGACAGGCCCCAAACCATTTGACAG                         CGCTAGACTCCGGACAGAGCAGTCACTTGTCC-GTGGGCAACGCCCCAGCT
genomic: GAGTTGTCATGCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAGgtattcctat ... atcgtctcagCGCTAGACTCCGGACAGAGCAGTCACTTGTCCGGTGGGCAACGCCCCAGCT
EST: gi|29662000|gb|CB658275.1|CB658275
EST:     TTTGGAGTTGTCATGCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAG                         CGCTAGACTCCGGACAGAGCAGTCACTTGTCCGGTGGGCAACGCCCCAGCT
genomic: TTTGGAGTTGTCATGCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAGgtattcctat ... atcgtctcagCGCTAGACTCCGGACAGAGCAGTCACTTGTCCGGTGGGCAACGCCCCAGCT
EST: gi|2317518|gb|C22572.1|C22572
EST:     TTTGGAGTTGTCATGCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAG                         CGCTAGACTCCGGACAGAGCAGTCACTTGTCCGGTGGGCAACGCCCCAGCT
genomic: TTTGGAGTTGTCATGCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAGgtattcctat ... atcgtctcagCGCTAGACTCCGGACAGAGCAGTCACTTGTCCGGTGGGCAACGCCCCAGCT
EST: gi|86851183|gb|CI312584.1|CI312584
EST:     TTTGGAGTTGTCATGCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAG                         CGCTAGACTCCGGACAGAGCAGTCACTTGTCCGGTGGGCAACGCCCCAGCT
genomic: TTTGGAGTTGTCATGCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAGgtattcctat ... atcgtctcagCGCTAGACTCCGGACAGAGCAGTCACTTGTCCGGTGGGCAACGCCCCAGCT
EST: gi|86427833|gb|CI072930.1|CI072930
EST:     TGGAGCTCTTGACAGGCCGCAAACCATTTGACAG                         CGCTAGACTCCGGACAGAGCAGTCACTTGTCCGGTGGGCAACGCCCCAGCT
genomic: TGGAGCTCTTGACAGGCCGCAAACCATTTGACAGgtattcctat ... atcgtctcagCGCTAGACTCCGGACAGAGCAGTCACTTGTCCGGTGGGCAACGCCCCAGCT
EST: gi|86253208|gb|CI058133.1|CI058133
EST:     ATGCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAG                         CGCTAGACTCCGGACAGAGCAGTCACTTGTCCGGTGGGCAACGCCCCAGCT
genomic: ATGCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAGgtattcctat ... atcgtctcagCGCTAGACTCCGGACAGAGCAGTCACTTGTCCGGTGGGCAACGCCCCAGCT
EST: gi|88226798|gb|CI224783.1|CI224783
EST:     GCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAG                         CGCTAGACTCCGGACAGAGCAGTCACTTGTCCGGTGGGCAACGCCCCAGCT
genomic: GCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAGgtattcctat ... atcgtctcagCGCTAGACTCCGGACAGAGCAGTCACTTGTCCGGTGGGCAACGCCCCAGCT
EST: gi|88850243|gb|CI091736.1|CI091736
EST:     GAGTTGTCATGCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAG                         CGCTAGACTCCGGACAGAGCAGTCACTTGTCCGGTGGGCAACGCCCCAGCT
genomic: GAGTTGTCATGCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAGgtattcctat ... atcgtctcagCGCTAGACTCCGGACAGAGCAGTCACTTGTCCGGTGGGCAACGCCCCAGCT
EST: gi|87004671|gb|CI300993.1|CI300993
EST:     TTTGGAGTTGTCATGCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAG                         CGCTAGACTCCGGACAGAGCAGTCACTTGTCCGGTGGGCAACGCCCCAGCT
genomic: TTTGGAGTTGTCATGCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAGgtattcctat ... atcgtctcagCGCTAGACTCCGGACAGAGCAGTCACTTGTCCGGTGGGCAACGCCCCAGCT
EST: gi|86497623|gb|CI140256.1|CI140256
EST:     TTTGGAGTTGTCATGCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAG                         CGCTAGACTCCGGACAGAGCAGTCACTTGTCCGGTGGGCAACGCCCCACCT
genomic: TTTGGAGTTGTCATGCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAGgtattcctat ... atcgtctcagCGCTAGACTCCGGACAGAGCAGTCACTTGTCCGGTGGGCAACGCCCCAGCT
EST: gi|2317454|gb|C22508.1|C22508
EST:     TTTGGAGTTGTCATGCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAG                         CGCTAGACTCCGGACAGAGCAGTCACTTGTCCGGTGGGCAACGCCCCAGCT
genomic: TTTGGAGTTGTCATGCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAGgtattcctat ... atcgtctcagCGCTAGACTCCGGACAGAGCAGTCACTTGTCCGGTGGGCAACGCCCCAGCT
EST: gi|88261961|gb|CI365537.1|CI365537
EST:     TGACA-GCCGCAAACCA-TTGACAG                         CGCTA-ACTCCGGACAGAGCAGTCACTTGTCCGGTGGGCAACGCCCCAGGC
genomic: TGACAGGCCGCAAACCATTTGACAGgtattcctat ... atcgtctcagCGCTAGACTCCGGACAGAGCAGTCACTTGTCCGGTGGGCAACGCCCCA-GC
EST: gi|88203910|gb|CI203759.1|CI203759
EST:     CTGGAGCTCTTGACAGGCCGCAAACCATTTGACAG                         CGCTAGACTCCGGACAGAGCAGTCACTTGTCCGGTGGGCAACGCCCCAGCT
genomic: CTGGAGCTCTTGACAGGCCGCAAACCATTTGACAGgtattcctat ... atcgtctcagCGCTAGACTCCGGACAGAGCAGTCACTTGTCCGGTGGGCAACGCCCCAGCT
EST: gi|86412966|gb|CI067371.1|CI067371
EST:     TTTGGAGTTGTCATGCTGGAGCTCTTGACAGGCCGCAAACCATTTGACGG                         CGCTAGACTCCGGACAGAGCAGTCACTTGTCCGGTGGGCAACGCCCCAGCT
genomic: TTTGGAGTTGTCATGCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAGgtattcctat ... atcgtctcagCGCTAGACTCCGGACAGAGCAGTCACTTGTCCGGTGGGCAACGCCCCAGCT
EST: gi|88226800|gb|CI224785.1|CI224785
EST:     CTGGAGCTCTTGACAGGCCGCAAACCATTTGACAG                         CGCTAGACTCCGGACAGAGCAGTCACTTGTCCGGTGGGCAACGCCCCAGCT
genomic: CTGGAGCTCTTGACAGGCCGCAAACCATTTGACAGgtattcctat ... atcgtctcagCGCTAGACTCCGGACAGAGCAGTCACTTGTCCGGTGGGCAACGCCCCAGCT
EST: gi|86870434|gb|CI320530.1|CI320530
EST:     ACCA-TTGACAG                         CGCTAGACTCCGGACAGACCAGTCACTTGTCCGGTGGGCAACGCCCCAGCT
genomic: ACCATTTGACAGgtattcctat ... atcgtctcagCGCTAGACTCCGGACAGAGCAGTCACTTGTCCGGTGGGCAACGCCCCAGCT

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: 49 (upstream exon), 66 (downstream exon)
Score: 10

CTGAAGTTGACATGACTGGGCAGTATACCCTCAAGAGTGATGTTTATAGCTTTGGAGTTGTCATGCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAGgtattcctat ... atcgtctcagCGCTAGACTCCGGACAGAGCAGTCACTTGTCCGGTGGGCAACGCCCCAGCTGCATGACATCGATGCGTTGGACCGGATGGTCGACCCAGCGCTCAAGGGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGAAGTTGACATGACTGGGCAGTATACCCTCAAGAGTGATGTTTATAGCTTTGGAGTTGTCATGCTGGAGCTCTTGACAGGCCGCAAACCATTTGACAGgtattcctatttttctctgattctgcatccctgaattgtttatgcctacatttgatgattcctaatttcttagtcctgacccctgactgttgtgtcaaactatcgtctcag

- - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT