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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggaacagctttgaccaaatctgaaaggattatatttttgcaaaagttaaaaactgatgctaaattattttcttccatcaatgattgcattggaaatgtagGTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAGCATCTCCATCTTTCAGCTCAAGCATAGTGACATATAAAGGGACAGCGAA

Basic information

species Oryza sativa
transcript LOC_Os01g51290.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g51290.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G404207_T01 (Zea mays), 3'ss of exon 3
ggaacagctttgaccaaatctgaaaggattatatttttgcaaaagttaaaaactgatgctaaattattttcttccatcaatgattgcattggaaatgtagGTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAGCATCTCCATCTTTCAGCTCAAGCATAGTGACATATAAAGGGACAGCGAA
  ||    |  |||  |   | | ||  ||||  | |     |   | |     | ||     || ||  | |   ||||||||||||||| ||||| ||||||||| |||||| |  | |||| |||||||| ||||||||||||||| ||||| ||||| |||||||||||  | ||| |||||||||| || || ||
ataatttttaagacttaccattacagttttatcatatcattgatcatgatgctggttgtatcctttttgccctatttcaatgattgcattgcaaatgcagGTCCTGGTTCTGCAATGTTGGGGAACAGGCTAGAAAGCAGACCTATTTCGGCATCACCATCCTTCAGCTCAAGTTTGGTGGCATATAAAGGAACTGCCAA

upper sequence: LOC_Os01g51290.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G330298_T01 (Zea mays), 3'ss of exon 4
--ggaacagctttgaccaaatctgaaaggattatatttttgcaaaagttaaaaactgatgctaaat-tattttcttccatcaatgattgcattggaaatgtagGTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAGCATCTCCATCTTTCAGCTCAAGCATAGTGACATATAAAGGGACAGCGAA
    | || ||||||  || | |  |||  ||| ||||   |||   ||||  | |||||||   | |||   |  || ||||||||||||||||||||| ||||||||  |||||| | ||||||| |||||||| ||||||||||||||| ||||| ||||| |||||||||||  | ||| ||||||||||  | || ||
tcaaaccatctttgagaaatttt--aagacttaaatttggtcaatcattaacca-tgatgctgtttgtatcaccccccttcaatgattgcattggaaatgcagGTCCTGTTTCTGCAATGGTTGGGAACAGGCTAGAAAGCAGACCTATTTCGGCATCACCATCCTTCAGCTCAAGTTTGGTGGCATATAAAGGATCTGCCAA
















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|58609846|gb|CK037879.1|CK037879
EST:     AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAG                         GTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG
genomic: AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAGgtaacaagac ... ggaaatgtagGTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG
EST: gi|58673112|gb|CK061798.1|CK061798
EST:     AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAG                         GTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG
genomic: AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAGgtaacaagac ... ggaaatgtagGTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG
EST: gi|163926291|gb|EG712875.1|EG712875
EST:     AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAG                         GTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG
genomic: AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAGgtaacaagac ... ggaaatgtagGTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG
EST: gi|58657110|gb|CK045790.1|CK045790
EST:     AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAG                         GTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGAACTATTTCA
genomic: AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAGgtaacaagac ... ggaaatgtagGTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCA
EST: gi|58666710|gb|CK055396.1|CK055396
EST:     AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAG                         GTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG
genomic: AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAGgtaacaagac ... ggaaatgtagGTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG
EST: gi|33796671|gb|CF324203.1|CF324203
EST:     AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAG                         GTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG
genomic: AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAGgtaacaagac ... ggaaatgtagGTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG
EST: gi|58603727|gb|CK014255.1|CK014255
EST:     AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAG                         GTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTAATTTCA
genomic: AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAGgtaacaagac ... ggaaatgtagGTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTA-TTTCA
EST: gi|58670422|gb|CK059108.1|CK059108
EST:     AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAG                         GTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG
genomic: AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAGgtaacaagac ... ggaaatgtagGTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG
EST: gi|29671018|gb|CB667293.1|CB667293
EST:     AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAG                         GTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG
genomic: AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAGgtaacaagac ... ggaaatgtagGTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG
EST: gi|29673710|gb|CB669985.1|CB669985
EST:     AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAG                         GTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG
genomic: AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAGgtaacaagac ... ggaaatgtagGTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG
EST: gi|29671060|gb|CB667335.1|CB667335
EST:     AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAG                         GTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG
genomic: AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAGgtaacaagac ... ggaaatgtagGTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG
EST: gi|58662882|gb|CK051568.1|CK051568
EST:     AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAG                         GTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG
genomic: AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAGgtaacaagac ... ggaaatgtagGTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG
EST: gi|58669828|gb|CK058514.1|CK058514
EST:     AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAG                         GTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG
genomic: AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAGgtaacaagac ... ggaaatgtagGTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG
EST: gi|58670563|gb|CK059249.1|CK059249
EST:     AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAG                         GTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG
genomic: AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAGgtaacaagac ... ggaaatgtagGTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG
EST: gi|33676639|gb|CF304878.1|CF304878
EST:     AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAG                         GTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG
genomic: AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAGgtaacaagac ... ggaaatgtagGTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG
EST: gi|29672194|gb|CB668469.1|CB668469
EST:     AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAG                         GTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG
genomic: AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAGgtaacaagac ... ggaaatgtagGTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG
EST: gi|33675957|gb|CF304196.1|CF304196
EST:     AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAG                         GTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG
genomic: AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAGgtaacaagac ... ggaaatgtagGTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG
EST: gi|58673120|gb|CK061806.1|CK061806
EST:     AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAG                         GTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG
genomic: AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAGgtaacaagac ... ggaaatgtagGTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG
EST: gi|163927830|gb|EG709422.1|EG709422
EST:     TATGCCACCGAAGCCTGCAG                         GTCCTGGGTCTGCAGTTGTTTGGAGCAGGCTAGGAAGCAGACCTATTTCAG
genomic: TATGCCACCGAAGCCTGCAGgtaacaagac ... ggaaatgtagGTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG
EST: gi|5803430|gb|AI978400.1|AI978400
EST:     AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAG                         GTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGNCCTATTTCAG
genomic: AAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAGgtaacaagac ... ggaaatgtagGTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAG

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: 67 (upstream exon), 69 (downstream exon)
Score: 18

GCTTTTATTTTATGTTCTGGAGCTGCGTTGGTAATTTGTTTCAAGATTAGAAACCGCAACCATTTAACTGAAGAGTCACCTATGCCACCGAAGCCTGCAGgtaacaagac ... ggaaatgtagGTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAGCATCTCCATCTTTCAGCTCAAGCATAGTGACATATAAAGGGACAGCGAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaaaactgatgctaaattattttcttccatcaatgattgcattggaaatgtagGTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAGCATCTCCATCTTTCAGCTCAAGCATAGTGACATATAAAGGGACAGCGAA
           tgctaaa  putative branch site (score: 18)
              taaattattttctt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggaacagctttgaccaaatctgaaaggattatatttttgcaaaagttaaaaactgatgctaaattattttcttccatcaatgattgcattggaaatgtagGTCCTGGGTCTGCAGTTGTTGGGAGCAGGCTAGGAAGCAGACCTATTTCAGCATCTCCATCTTTCAGCTCAAGCATAGTGACATATAAAGGGACAGCGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - -gaccaaa
- - - - - - - - - - - - - - - - - ttttgca
- - - - - - - - - - - - - - - - - - - - - - - taaaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgattgc