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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttattttcagacttacgcgacactgtttaatttgtaggagctatgtgttttattatctcaccatgccttttttccttctcatgccattatctttatagGTAAACCCCAAAGCAGCAGAATCATTGGCAGATCCTGACGAGTACCCAAACTTGTTTGAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGC

Basic information

species Oryza sativa
transcript LOC_Os02g11840.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g11840.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G141587_T03 (Zea mays), 3'ss of exon 21
-tcttattttcagacttacgc---gacactgtttaatt-tgtaggagctatgtgttttattatctcaccatgccttttttccttctcatgccattatctttatagGTAAACCCCAAAGCAGCAGAATCATTGGCAGATCCTGACGAGTACCCAAACTTGTTTGAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGC
| | || || | || | | ||| | | | | | | | || | | | | | ||| | || || |||| |||| ||||||||| | ||||||||||| || |||| |||||| | |||||||||||||| |||||||||||||| ||||||||||| ||||||||| ||| ||
atgtgatattttgtctcaagtttagacttggcatcgctgtcttcaaattgcacgtctaagt-ttacgaaatgtgcactgatctgttc----catttgctttttagGTAAACTCAAAAGCAGCAGAGTCGCTGGCTGATCCTAATGAGTACCCAAACTTATTTGAAGACTGGCAGATTGCTCTCAACGTAGAAGCTGCTGTTGCCT

upper sequence: LOC_Os02g11840.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G124886_T02 (Zea mays), 3'ss of exon 21
tcttattttcagacttacgcg-acact---gtttaatt-tgtaggagctatgtgttttattatctcac-catgccttttttccttctcatgccattatctttatagGTAAACCCCAAAGCAGCAGAATCATTGGCAGATCCTGACGAGTACCCAAACTTGTTTGAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGC
| ||||| | || | | | | | | ||||| | | | || || | | | | | | ||| || ||| ||| |||| |||| ||||||||||| |||||||| || || |||| |||||| | |||||||||||||| |||||||||||||| |||||||| |||||||||||| ||| || |
tggtatttgtggtctcaagtttagatttgagcataattgtcttcaaactgcaggtctaactttatgaaatgtgcattgttttgttc------catttgctttttagGTAAACCCAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAACTTATTTGAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTC

upper sequence: LOC_Os02g11840.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA13G43680.1 (Glycine max), 3'ss of exon 21
-tcttattttcagacttacgcgacactgtttaatttgtaggagctatgtgttttattatctcaccatgccttttttccttctcatgccattatctt--tatagGTAAACCCCAAAGCAGCAGAATCATTGGCAGATCCTGACGAGTACCCAAACTTGTTTGAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGC
| | ||| | | | | | ||||| | || | | |||| | | || | | | || | ||| || | |||| || || ||||| || ||||||||||| ||||||| || || ||||| ||||||||||| |||||| |||| || ||| ||| |||| | | |
agcatccgttctcattcatttgcc-ttgtttgggtagtcttatc-atgttgacaagtgacttatgg-attaaagagagtacgtatacgtatattttgttgcagGTCAATCCAAAAGCTGCTGAATCATTGGCTAATCCTGAAGAATATCCAAATTTGTTTGAAGATTGGCAAGTTGCACTAGCTGTCGAATCTAAAGCTGTGG

upper sequence: LOC_Os02g11840.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 21
---------------------------------------------------------------------------------------------tcttattttcagac--ttacgcgacactgttt--aatttgtagga-gctatgtgttttatt--atctcaccatgccttttttccttctcatgccattatctttatagGTAAACCCCAAAGCAGCAGAATCATTGGCAGATCCTGACGAGTACCCAAACTTGTTTGAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGC
| | || ||| | || | | |||| ||| || | |||| | || || | | | || || | | | || | || | | |||| || || ||||| || ||||||||||| |||||||| ||||| || || |||||||| || |||||| |||| || ||| ||| |||| | |
gtaatgttatatatatatatatatatatatatataatttagcaacggaatagcctgacatttatgttgtgcacatgatactgtgggtaggaacttctgttctcattccattggcctgccctgtcctggattcttatcatgctacatattgcatgtgaaataaaaatataaattcttatatttatttgttaatatgcacagGTTAATCCAAAAGCCGCCGAATCATTGGCTGATCCTGAGGAGTATCCTAATTTGTTTGATGATTGGCAAGTTGCACTTGCTGTTGAATCTAAAGCTACAG

upper sequence: LOC_Os02g11840.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA15G01680.1 (Glycine max), 3'ss of exon 21
tcttattttcagacttacgcgacact-gtttaatttgtaggagctatgt-gttttattatctcaccatgccttttttccttctcatgccattatctt--tatagGTAAACCCCAAAGCAGCAGAATCATTGGCAGATCCTGACGAGTACCCAAACTTGTTTGAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGC
| || | | || | ||| |||| ||| | | | | || | | | || | | ||| || | |||| || || ||||| || ||||||||||| |||||||| || || ||||| ||||||||||| ||||| |||| || ||| ||| |||| | | |
----ggtaggagcatcagttctcattcatttgccttgtttgagtagtcttatcatgttgacgagtggctcatggattaaagagagtacatatattttattgcagGTTAATCCAAAAGCTGCTGAATCATTGGCTGATCCTGAAGAATATCCAAATTTGTTTGAAGATTGGCAGGTTGCACTAGCTGTCGAATCTAAAGCTGTGG

upper sequence: LOC_Os02g11840.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AT1G52360.1 (Arabidopsis thaliana), 3'ss of exon 21
tcttattttcagacttacgcgacactgtttaatttgtaggagctatgtgttttattatctcaccatgccttttttccttctcatgccattatctttatagGTAAACCCCAAAGCAGCAGAATCATTGGCAGATCCTGACGAGTACCCAAACTTGTTTGAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGC
| | | || |||| || ||| | ||||| | | | || || ||| || | ||| || | | |||| || | |||||||||||||| ||||| |||||||| |||||| |||| | |||||||| |||||| ||||||| ||| |||||||| | |
-----------gttcctttcaaatctttttaggttttagt-gtaatgtggtcaaggaga-caagttgtgggtttaagttaccttgcacttgaat--acagGTTAATTCAAAAGCAGCAGAATCTTTGGCTGATCCTGAGGAGTACTCAAATCTTTTTGAAGATTGGCAAGTTGCTCTTTCTGTGGAAGCTAAAGCTGTAG

upper sequence: LOC_Os02g11840.1 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 21
--tcttattttcagacttacgcgacactgtttaatttgtaggagctatgtgttttattatctcaccatgccttttttccttctcatgccattatctttatagGTAAACCCCAAAGCAGCAGAATCATTGGCAGATCCTGACGAGTACCCAAACTTGTTTGAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGC
| | || || | | | | || || || | | | | | || || | | ||| ||| | ||| |||| | | ||||| ||||||||||||||||||||||| |||||||| || |||||||| |||||||| ||||||| | | ||| |||| | |
catgtcataaatgaaccaagaaaagagataaggagaaaggaaaggagtgaaaattttgaacccttcttgactgcataatgcatgatgtcatga--tttgcagGTGAGCAAAAAAGCTGCAGAATCATTGGCAGATCCTGAAGAGTACCCTAATTTGTTTGAGGACTGGCAGGTTGCTCTTGACATTGAATCTAAAATTTCAG

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: 75 (upstream exon), 74 (downstream exon)
Score: 86

TAATCGTATACCAGAAGCAGCATTGATGTCGAGATCTTATCTTCCGAGCAAAGTCCCTGAGATTGTAACATTATGGAAAAAGGATCTCCAAAAGgtaccatctg ... atctttatagGTAAACCCCAAAGCAGCAGAATCATTGGCAGATCCTGACGAGTACCCAAACTTGTTTGAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgttttattatctcaccatgccttttttccttctcatgccattatctttatagGTAAACCCCAAAGCAGCAGAATCATTGGCAGATCCTGACGAGTACCCAAACTTGTTTGAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGC
           atctcac  putative branch site (score: 86)
 ccttttttccttctca  putative PPT
 attatctttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttattttcagacttacgcgacactgtttaatttgtaggagctatgtgttttattatctcaccatgccttttttccttctcatgccattatctttatagGTAAACCCCAAAGCAGCAGAATCATTGGCAGATCCTGACGAGTACCCAAACTTGTTTGAAGACTGGCAAATTGCTCTCAATGTAGAAGCTAATGTCGCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC