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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atactagaagattcaacatcatatgaaaccatctgagttctttcttctaactaacatttggattcatttatgaggtaacaatgccttctgtgctttatagGGTCTACGCATTGGTTGCGTGCTTCAAATTGGCTCTGGATTGTTTCTTTGCTGTGTGGTTTGTTGTTGGGAATGTGTGGATATTCGGGGGCCGTACTTCT

Basic information

species Oryza sativa
transcript LOC_Os01g08340.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g08340.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G004799_T01 (Zea mays), 3'ss of exon 2
---atactagaag---attcaacatcatatgaaaccatctgagttctttcttctaactaacatttggattcatttatgaggtaacaatgccttctgtgctttatagGGTCTACGCATTGGTTGCGTGCTTCAAATTGGCTCTGGATTGTTTCTTTGCTGTGTGGTTTGTTGTTGGGAATGTGTGGATATTCGGGGGCCGTACTTCT
    || | |||    || | | |     || ||   | |||  | |||     |  | | ||||   |||||  |||| || |  | || ||     || | |||| | |||||| ||||||| ||||| |||||||   |||||||||||||||| || ||||||||||| || ||||||||||| || ||  ||||| |||||
ttagtatttgaaatgcatcctataaatggtgcaaatgtttgaagttttt---taatatgatattttcgttcata-atgaagtgatgacgcatt--aatctatgtagGTTTTACGCAATGGTTGCCTGCTTTAAATTGGTGTTGGATTGTTTCTTTGCCGTCTGGTTTGTTGTGGGAAATGTGTGGATGTTTGGTAGCCGTTCTTCT

upper sequence: LOC_Os01g08340.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA17G30020.1 (Glycine max), 3'ss of exon 2
atactagaagattcaacatcatatgaaaccatctgagttctttcttctaactaacatttggattcatttatgaggtaacaatgccttc------tgtgctttatagGGTCTACGCATTGGTTGCGTGCTTCAAATTGGCTCTGGATTGTTTCTTTGCTGTGTGGTTTGTTGTTGGGAATGTGTGGATATTCGGGGGCCGTACTTCT
    | ||   || ||  |  | |   |  ||   |  | |    |   | |   || || | |   |||||| |   | | ||| |         |||   | ||  |  |  || | || |  | ||||||| |  || | ||||| || |||||||| |||||||||||||| ||||| ||||| || ||||| | | | |||
---tttgatattttaatgtattgtttcatgattataactttcaagt---attggaatatgtaatagcttatgaagctgctaagcccttgttcttcttgcaccacagAATGAAGACACTAGTGGAATACTTCAAAATATCTTTAGATTGCTTTTTTGCTGTATGGTTTGTTGTTGGAAATGTATGGATCTTTGGGGGACATTCATCT

upper sequence: LOC_Os01g08340.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT4G32600.1 (Arabidopsis thaliana), 3'ss of exon 2
--------------------------------------------------------------------------------atactagaagattcaacatc-atatgaaaccat----ctgagttctttcttctaact---aacatttg-gattcatttatgaggtaacaat-------gccttctgtgctttatagGGTCTACGCATTGGTTGCGTGCTTCAAATTGGCTCTGGATTGTTTCTTTGCTGTGTGGTTTGTTGTTGGGAATGTGTGGATATTCGGGGGCCGTACTTCT
                                                                                ||  | ||  ||| |   |  | |||   |  |    || |  | ||||||     |   || || ||  ||  | ||  |     |  ||       |     | ||  ||  ||  |  | |   | || |  | ||||||| ||||||||||||| |||||||| ||||||||||| || || ||||| |||||||| || || | | | |||
gtaaacacacatgttcttagatgatctgtttcaactgaaagtttggattttgaattacgttttctctcaaagcttttcttatttttgagaattgagagtttagatgtctcttttgttctaaactttttctttgtgttgaaaatatctgcaatctaattgagtcagtatgattttggtcgttgattttggcttccagACTTAAAGTTATCGTGGAATACTTCAAAATGGCTCTGGATTGCTTCTTTGCGGTGTGGTTTGTGGTAGGTAATGTATGGATATTTGGAGGGCATTCATCT

upper sequence: LOC_Os01g08340.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT1G80400.1 (Arabidopsis thaliana), 3'ss of exon 2
atactagaagattcaacatcatatgaaaccatctgagttctttcttctaactaacatttggattcatttatgaggtaacaatgccttctgtgctttatagGGTCTACGCATTGGTTGCGTGCTTCAAATTGGCTCTGGATTGTTTCTTTGCTGTGTGGTTTGTTGTTGGGAATGTGTGGATATTCGGGGGCCGTACTTCT
                       | |  | |  |   || |||   || | | | |||||| ||  ||    || |||||||    |   ||  |   ||| || |||   | || |    ||||||  ||||  | |||||||||||||| |||||||||||||| |||||||| |||||||| || || |   | |||
----------------------gtaagtctaattactttgtttggcctcaatta-atttgggttggtt----agttaacaat--tgttaatgactggcagGCTCAACGGGCTAGTGGACCACTTCAAGATGGCGATTGATTGTTTCTTTGCGGTGTGGTTTGTTGTGGGGAATGTATGGATATTTGGAGGTCACTCATCT

upper sequence: LOC_Os01g08340.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv11s0016g04450.t01 (Vitis vinifera), 3'ss of exon 2
atactagaagattcaacatcatatgaaaccatctgagttctttcttctaactaacatt-tggattcattta--tgaggtaacaatgccttctgtgctttatagGGTCTACGCATTGGTTGCGTGCTTCAAATTGGCTCTGGATTGTTTCTTTGCTGTGTGGTTTGTTGTTGGGAATGTGTGGATATTCGGGGGCCGTACTTCT
     | |   ||    |   | ||   | ||    | | | | ||  ||     ||| || |   || ||  |    |   |||  ||  | | ||  | ||| ||   | ||| |  |  | ||  ||  |||| |||||||| |||||||||||||||||||| ||||| ||||| ||||| || || || |   | |||
---acatagtgtttgtaaaactgtgtttctatgcatgctttgtattagaatcttaattatgaaaagatgtagtttccctggtaatatctattcttctccacagGCTCAGTGTATTAGCAGACTACTATAAGATGGCCCTGGATTGCTTCTTTGCTGTGTGGTTTGTGGTTGGTAATGTATGGATTTTTGGAGGACACTCCTCT

upper sequence: LOC_Os01g08340.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv09s0002g05120.t01 (Vitis vinifera), 3'ss of exon 2
----atactagaagattcaacatcatatgaaaccatctgagttctttcttctaactaacat-ttggattcatttatgaggtaacaatgccttctgtgctttatagGGTCTACGCATTGGTTGCGTGCTTCAAATTGGCTCTGGATTGTTTCTTTGCTGTGTGGTTTGTTGTTGGGAATGTGTGGATATTCGGGGGCCGTACTTCT
    ||| |  |  |||  | | | | | |  |  | |    ||  |    ||| | | || ||| ||   || |||| ||| |  ||  |||||   |    ||| ||   | | |||| |     || ||  ||||  |||| || |||||||| |||||||||||||| || |||||||||||||| || || |   |||||
tctgatagttaattattttaaa-cttttaacccttttttgtatccattcaataatttatatattgtatcggttaatgatgtagc--tgatttctga--tacccagGTTCAGTGGAATGGTGGACCATTTTAAGATGGCCTTGGACTGCTTCTTTGCAGTGTGGTTTGTTGTGGGCAATGTGTGGATATTTGGAGGTCACTCTTCT

upper sequence: LOC_Os01g08340.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv04s0008g04280.t01 (Vitis vinifera), 3'ss of exon 2
atactagaagattcaaca--tcatatgaaaccatctgagttctttcttctaactaacatttggattcat--ttatgaggtaacaatgccttctgtgctttatagGGTCTACGCATTGGTTGCGTGCTTCAAATTGGCTCTGGATTGTTTCTTTGCTGTGTGGTTTGTTGTTGGGAATGTGTGGATATTCGGGGGCCGTACTTCT
    || ||| || |     ||   ||  |    |    |   ||    |||  || |  |  |  |||  |  | | | |  |     || | | | |   ||  |  | |   |||| |  | ||||||  ||||||||||||| ||||||||||| |||||||| || || || |||||||| || || || |   | || 
----taaaagcttaacttgttctcctgttagttacaagatatcttgagttaaacaaaaactacaaccataatacttaaggagtaggtgtttgtctccctggcagACTAAAGGTTCTGGTGGAATACTTCAAGATGGCTCTGGATTGCTTCTTTGCTGTTTGGTTTGTGGTAGGAAACGTGTGGATCTTTGGAGGGCACTCCTCA

upper sequence: LOC_Os01g08340.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ36853 (Selaginella moellendorffii), 3'ss of exon 1
atactagaagattcaacatcatatgaaaccatctgagttctttcttctaactaacatttggattcatttatgaggtaacaat-gccttctgtgctttatagGGTCTACGCATTGGTTGCGTGCTTCAAATTGGCTCTGGATTGTTTCTTTGCTGTGTGGTTTGTTGTTGGGAATGTGTGGATATTCGGGGGCCGTACTTCT---------
                                 |  | |  ||| | |  ||  | |||  || | ||| |    |     | | ||  | |  |    || ||        |||| | |   |||||  | ||  ||||||| ||||| || |||||||| || |||||||| ||||||||||| || || |   | ||          
--------------------------------gtatggtgcttccttttgctgtcttttttatacttttctctattgttcttcgactaatctattcatcagtgttggaagGCTGGTGGAGAAGTTCAAGATTGCGTTGGATTGCTTCTTCGCGGTGTGGTTCGTCGTTGGGAACGTGTGGATATTTGGCGGACACTCCTCGTCCCGCGAA

upper sequence: LOC_Os01g08340.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EFJ27808 (Selaginella moellendorffii), 3'ss of exon 1
----------atactagaagattcaacatcatatgaaaccatctgagttctttcttctaactaacatttggattcatttatgaggtaacaat-gccttctgtgctttatagGGTCTACGCATTGGTTGCGTGCTTCAAATTGGCTCTGGATTGTTTCTTTGCTGTGTGGTTTGTTGTTGGGAATGTGTGGATATTCGGGGGCCGTACTTCT
          |     |  |||||  |     |  |  |    |  | |  ||| | |  ||  | |||  ||   ||| |    |     | | ||  | |  |    || ||        |||| | |   |||||  | ||  ||||||| ||||| || |||||||| || |||||||| ||||||||||| || || |   | || 
gtcgcgaggaagggacgtggattccgcgagtgacaattcggggtatggtgcttccttttgctttcttttttatatttttctctattgttcttcgactaatctattcatcagTGTTGGAAGGCTGGTGGAGAAGTTCAAGATTGCGTTGGATTGCTTCTTCGCGGTGTGGTTCGTCGTTGGGAACGTGTGGATATTTGGCGGACACTCCTCG

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: 17 (upstream exon), 69 (downstream exon)
Score: 3

TATATGAGCCTAATTCTTATGTAGTAGTTTCGTCTGCTCATGGATCAGAAGTTGTGGACAGTGGTAATAATGGTGGAGTAGCAAGGATTGCAAGTCCAAGgtagcattat ... tgctttatagGGTCTACGCATTGGTTGCGTGCTTCAAATTGGCTCTGGATTGTTTCTTTGCTGTGTGGTTTGTTGTTGGGAATGTGTGGATATTCGGGGGCCGTACTTCT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaactaacatttggattcatttatgaggtaacaatgccttctgtgctttatagGGTCTACGCATTGGTTGCGTGCTTCAAATTGGCTCTGGATTGTTTCTTTGCTGTGTGGTTTGTTGTTGGGAATGTGTGGATATTCGGGGGCCGTACTTCT
                                      ccttctgt  CT-rich tract
                attcatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atactagaagattcaacatcatatgaaaccatctgagttctttcttctaactaacatttggattcatttatgaggtaacaatgccttctgtgctttatagGGTCTACGCATTGGTTGCGTGCTTCAAATTGGCTCTGGATTGTTTCTTTGCTGTGTGGTTTGTTGTTGGGAATGTGTGGATATTCGGGGGCCGTACTTCT

- - - - - - - aacatca
- - - - - - - - - - - - -aaaccat
- - - - - - - - - - - - - - - - - - - - - - - - -actaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtaacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttctg