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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttttgctgcttgtattttatgtttaagaaggcattcatgcagtagtaagatatggatttattttgttcttctttcagCTGTCAATAAGGATGATCTGTTGCAAATGGTAAGATTTGGTGCGGAAATGGTATTCAGTTCCAAGGACAGCACAATTACAGATGAGGATATTGACCGTAT

Basic information

species Oryza sativa
transcript 13113.m00246
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 13
lower sequence: AC235535.1_FGT001 (Zea mays), 3'ss of exon 13
gtatgtttttgctgcttgtattttatgtttaa---gaaggcattcatgcagtagtaagatatggatttattt--------tgttcttctttcagCTGTCAATAAGGATGATCTGTTGCAAATGGTAAGATTTGGTGCGGAAATGGTATTCAGTTCCAAGGACAGCACAATTACAGATGAGGATATTGACCGTAT
||||| || || |  |||  |||  | |||      |     ||  |  | ||||  ||||||||||  | |        | || ||  || |||||||||||||||||| ||  ||||||||||  | |||||||| |||||||| |||||||| |||||||||||||| || |||||||| |||||||||||
gtatggttatgatatttgcctttgctatttgtttcaagcatttttctttactagttggatatggattattctgacaacattcttttttgttaagCTGTCAATAAGGATGACCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT

upper sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G010085_T01 (Zea mays), 3'ss of exon 10
gtatgtttttgctgcttgtattttatgtttaaga-aggcattcatgcagtagtaagatatggatttattt--------tgttcttctttcagCTGTCAATAAGGATGATCTGTTGCAAATGGTAAGATTTGGTGCGGAAATGGTATTCAGTTCCAAGGACAGCACAATTACAGATGAGGATATTGACCGTAT
||||| ||||| |  |||   ||| | |||     | |||||  |  | ||||  ||| ||||||  | |        | |  ||  || |||||||||||||||||||||  ||||||||||  | |||||||| |||||||| |||||||| |||||||||||||| || |||||||| |||||||||||
gtatggttttgatatttgccatttctatttgttttaagcattt-tttactagtttgatctggattgttctgacaacattctcatttattaagCTGTCAATAAGGATGATCTTCTGCAAATGGTGCGGTTTGGTGCTGAAATGGTTTTCAGTTCTAAGGACAGCACAATAACTGATGAGGACATTGACCGTAT

upper sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA17G02640.1 (Glycine max), 3'ss of exon 13
----------gtatgtttttgctgcttgtattttatgtttaagaaggcattcatgcagtagtaagatatgg-atttattttgttcttcttt-cagCTGTCAATAAGGATGATCTGTTGCAAATGGTAAGATTTGGTGCGGAAATGGTATTCAGTTCCAAGGACAGCACAATTACAGATGAGGATATTGACCGTAT
           |   ||||  || | | | | |||| |||        ||| ||| | || ||  | |||| |   | | | ||  | | | ||||||| ||||| |||||  || | |||||||| ||||||||||| |||||||| || |||||||||||||| |||||||||||||||||||||||| | ||
gtaagggtttctggattttatcttcgtttttattat-tttgttgctagatttatggatta-tataacatggtacacaatctatttgtgtatgcagCTGTTAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT

upper sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA07G38050.2 (Glycine max), 3'ss of exon 13
-----------gtatgtttttgctgcttgtattttatgtttaagaaggcattcatgcagtagtaagatatggatttattttgttcttctttcagCTGTCAATAAGGATGATCTGTTGCAAATGGTAAGATTTGGTGCGGAAATGGTATTCAGTTCCAAGGACAGCACAATTACAGATGAGGATATTGACCGTAT
            |  |||||  ||   | | | |||| ||   | | | ||| ||| | || ||  | ||||    || |  || |   | ||||||| ||||| |||||  || | |||||||| ||||||||||| |||||||| || |||||||||||||| |||||||||||||||||||||||| | ||
gtaagggttttctgggttttatctttgtttttattattttgttgcaag-attgatggatta-tataacatggtacaatctatttgtgtatgcagCTGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGTGCTGAAATGGTTTTTAGTTCCAAGGACAGTACAATTACAGATGAGGATATTGACAGAAT

upper sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA15G10370.1 (Glycine max), 3'ss of exon 13
gtatgtttttgctgcttg---tattttatgtttaagaaggcattcatgcag-tagtaagatatggatttattttgttcttctttcagCTGTCAATAAGGATGATCTGTTGCAAATGGTAAGATTTGGTGCGGAAATGGTATTCAGTTCCAAGGACAGCACAATTACAGATGAGGATATTGACCGTAT
||| |  ||   ||  |    | | || | | |  |  |  | |  ||  | | ||   |||||| |  |||   || |   | |||| || ||||| |||||  || | |||||||| |||||||| || |||||||| |||||||||||||| || |||||||||||||| ||||||||  | ||
gtaggaattcaatgaataacttttcttgtttctttgctgaaagttgtgtggattgtctaatatggttccattggcttttatgtgcagCGGTAAATAAAGATGAATTGCTTCAAATGGTTAGATTTGGGGCTGAAATGGTTTTCAGTTCCAAGGATAGTACAATTACAGATGAAGATATTGATAGAAT

upper sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 13
lower sequence: GLYMA13G28720.1 (Glycine max), 3'ss of exon 13
gtatgtttttgctgcttg---tattttatgtttaagaaggcattcatgcag-tagtaagatatggatttattttgttcttctttcagCTGTCAATAAGGATGATCTGTTGCAAATGGTAAGATTTGGTGCGGAAATGGTATTCAGTTCCAAGGACAGCACAATTACAGATGAGGATATTGACCGTAT
|||||  ||   ||  |    | | || | | |  |  |  | |  ||  | | ||   || ||| |  |||   || |   | |||| || ||||| |||||  || | |||||||| |||||||| || |||||||| |||||||||||||| || |||||||||||||||||||||||  | ||
gtatggattcaatgaataatttttcttgtttctttgctgaaagttgtgtggattgtctaatgtggttccattgatttttatgtgcagCGGTAAATAAAGATGAGTTGCTTCAAATGGTTAGATTTGGGGCTGAAATGGTTTTCAGTTCCAAGGATAGTACAATTACAGATGAGGATATTGATAGAAT

upper sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 13
lower sequence: AT3G06400.1 (Arabidopsis thaliana), 3'ss of exon 13
gtatgtttttgctgcttgtattttatgtttaagaaggcattcatgcagtagtaagatatggatttattttgttcttctttcagCTGTCAATAAGGATGATCTGTTGCAAATGGTAAGATTTGGTGCGGAAATGGTATTCAGTTCCAAGGACAGCACAATTACAGATGAGGATATTGACCGTAT
||| ||   |  | |    |||     |||| | |    ||||| |  |   |  ||  | |||||| ||     |    |||||||||||||||||||  || | ||||||||||||| |||||| || ||||| |||||||| || || |||||||| ||||| |||||||||||  | ||
gtaagtgcgttatacagtgattgc---tttatgcattggttcat-ctctgacagaattggtatttatcttaactat---gcagCTGTCAATAAGGATGAGTTGCTTCAAATGGTAAGATATGGTGCTGAGATGGTGTTCAGTTCTAAAGATAGCACAATCACAGACGAGGATATTGATAGAAT

upper sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 13
lower sequence: AT5G18620.1 (Arabidopsis thaliana), 3'ss of exon 13
gtatgtttttgctgcttgtattttatgtttaagaaggcattcatgcagtagtaagatatggatttattttgttcttctttcagCTGTCAATAAGGATGATCTGTTGCAAATGGTAAGATTTGGTGCGGAAATGGTATTCAGTTCCAAGGACAGCACAATTACAGATGAGGATATTGACCGTAT
||| ||  |||     ||    |  |   |     ||  ||  |     |   | |||  ||||| |||| ||    || ||||||| |||||||||||  || | |||||||| |||| |||||| |||||||| || ||||| || || ||||||||||| ||||||||||||||| | ||
gtaagtgcttgtgtactgaggctgttagatgtattggattttctcttacatatatatactgatttcttttctttgctttccagCTGTTAATAAGGATGAGTTGCTTCAAATGGTGAGATATGGTGCTGAAATGGTGTTTAGTTCTAAAGATAGCACAATTACGGATGAGGATATTGACAGAAT

upper sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 13
lower sequence: Vv05s0020g01780.t01 (Vitis vinifera), 3'ss of exon 13
---------gtatgtttttgctgcttgtattttatgtttaagaaggcattcatgcagtagtaagatatggatttattttgttctt-------ctttcagCTGTCAATAAGGATGATCTGTTGCAAATGGTAAGATTTGGTGCGGAAATGGTATTCAGTTCCAAGGACAGCACAATTACAGATGAGGATATTGACCGTAT
          | ||  ||    |||||  ||  |   | |       ||||||  |     ||    |    || | ||||| ||        || ||||||| || || ||||| ||  |||||||||| || |||||||| |||||||| ||||| |||||||| ||||||||||| ||||| || || ||| | ||
gtgagccatttctgcattacaagcttgctttgcactatgacatgctaattcatagaactagaaccactaacattttgttgtttttgtgggcttttgcagCTGTGAACAAAGATGAGCTACTGCAAATGGTCAGGTTTGGTGCTGAAATGGTTTTCAGCTCCAAGGATAGCACAATTACGGATGAAGACATAGACAGGAT

upper sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 13
lower sequence: EFJ31365 (Selaginella moellendorffii), 3'ss of exon 13
gtatgtttttgctgcttgtattttatgtttaagaaggcat-tcatgcagtagtaagatatggatttattttgttcttctttcagCTGTCAATAAGGATGATCTGTTGCAAATGGTAAGATTTGGTGCGGAAATGGTATTCAGTTCCAAGGACAGCACAATTACAGATGAGGATATTGACCGTAT
                          |||    ||    | | ||   ||   ||  | || | | |||  |||   ||  |||||||||| || ||||| || ||||| |||||||||||||| ||||| |||||||| ||  |||| |||||||| || || || || |||||||| || ||
--------------------------gttcctcaaactctgttatagtgtttgaaactctgtaatcattccgtttcgctg-cagCTGTCAACAAAGATGAGCTCTTGCAGATGGTAAGATTTGGCGCGGAGATGGTATTTAGCGCCAATGACAGCACTATCACGGAGGAAGATATTGATCGCAT

upper sequence: 13113.m00246 (Oryza sativa), 3'ss of exon 13
lower sequence: EFJ06565 (Selaginella moellendorffii), 3'ss of exon 13
gtatgtttttgctgcttgtattttatgtttaagaaggcattcatgcagtagt--aagatatggatttattttgttcttctttcagCTGTCAATAAGGATGATCTGTTGCAAATGGTAAGATTTGGTGCGGAAATGGTATTCAGTTCCAAGGACAGCACAATTACAGATGAGGATATTGACCGTAT
                                   |    |||  |  |  |  ||  | || | | |||  |||   ||  |||||||||| || ||||| || ||||| |||||||||||||| ||||| |||||||| ||  |||| |||||||| || || || || |||||||| || ||
-----------------------------------gttcctcaaactctgtttgaaactctgtaatcattccgtttcgctg-cagCTGTCAACAAAGATGAGCTCTTGCAGATGGTAAGATTTGGCGCGGAGATGGTATTTAGCGCCAATGACAGCACTATCACGGAGGAAGATATTGATCGCAT

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: 66 (upstream exon), 75 (downstream exon)
Score: 59

TATACCATCGAGGAGAAAGTGATTGAGAGGGCATACAAGAAGCTTGCATTGGATGCTTTGGTCATTCAACAAGGCCGACTGGCAGAGCAGAAGAgtatgttttt ... cttctttcagCTGTCAATAAGGATGATCTGTTGCAAATGGTAAGATTTGGTGCGGAAATGGTATTCAGTTCCAAGGACAGCACAATTACAGATGAGGATATTGACCGTAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaagaaggcattcatgcagtagtaagatatggatttattttgttcttctttcagCTGTCAATAAGGATGATCTGTTGCAAATGGTAAGATTTGGTGCGGAAATGGTATTCAGTTCCAAGGACAGCACAATTACAGATGAGGATATTGACCGTAT
                                  tttattttgttcttct  CT-rich tract
                           atatggatttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttttgctgcttgtattttatgtttaagaaggcattcatgcagtagtaagatatggatttattttgttcttctttcagCTGTCAATAAGGATGATCTGTTGCAAATGGTAAGATTTGGTGCGGAAATGGTATTCAGTTCCAAGGACAGCACAATTACAGATGAGGATATTGACCGTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT