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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGTGGAGTAGAATGGGACAAATTATATGAAATAGAAGCAGCATATCAACCTCAAGTCACTGATGAGTTAGATACTCAGAATTTTGAGAAGTTTGAAGAGgttaggggtcgtttcttttggcctaaaggaattcagtttcaataagttggtataaatgttattcctatggtgtgttttgcag

Basic information

species Oryza sativa
transcript LOC_Os10g33640.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g33640.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G088245_T01 (Zea mays), 5'ss of exon 9
TAGTGGAGTAGAATGGGACAAATTATATGAAATAGAAGCAGCATATCAACCTCAAGTCACTGATGAGTTAGATACTCAGAATTTTGAGAAGTTTGAAGAGgttaggggt---cgtttcttttggcctaaaggaattcagtttcaataagttggt-ataaatgttattcctatggtgtgttt-tgcag--------------------
 |||||| |||||||||  ||  ||||||| |||||||| || || |  ||||| ||||| || ||||| || || ||||| |||||||||||||| ||||| |    |    | | || | |     || |||    | || |||   |   | |   |    || | |||  | ||| |  |  |                    
CAGTGGACTAGAATGGGGAAAGCTATATGAGATAGAAGCCGCGTACCTGCCTCAGGTCACAGACGAGTTGGACACCCAGAACTTTGAGAAGTTTGAGGAGgtaataaatgcatggtgctgtcgtttacaaagaaacgtgctttaatttctcactcactcaccggatacttattatctgtgtgcgtggtgttttaatttgtttggcag

upper sequence: LOC_Os10g33640.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA19G34920.1 (Glycine max), 5'ss of exon 9
TAGTGGAGTAGAATGGGACAAATTATATGAAATAGAAGCAGCATATCAACCTCAAGTCACTGATGAGTTAGATACTCAGAATTTTGAGAAGTTTGAAGAGgttaggggtcgtttc--ttttggcctaaaggaattcagtttcaataagttggtataaatgttattcctatggt-gtgttttgcag--------------
|| ||| || |||||||| ||||| ||| |||| ||||| || | |   ||| | |||| |||||||||||||||||| |||||||| ||||||||||||||   | ||| ||    || | || ||    | ||   |    ||    || |||| |  |||||    |  |    ||||                  
TAATGGTGTGGAATGGGATAAATTGTATCAAATGGAAGCTGCCTTTATTCCTGAGGTCAATGATGAGTTAGATACTCAAAATTTTGAAAAGTTTGAAGAGgtatagtgtctttcaaattattgcttattttattttgttagttatccaatgttatacacattattaaattattcaaattttatcttttcacctttgcag

upper sequence: LOC_Os10g33640.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA10G04410.1 (Glycine max), 5'ss of exon 10
TAGTGGAGTAGAATGGGACAAATTATATGAAATAGAAGCAGCATATCAACCTCAAGTCACTGATGAGTTAGATACTCAGAATTTTGAGAAGTTTGAAGAGgt---taggggtcgtttcttttggcctaaaggaattcagtttcaataagttggtataaatgt-tattcctatggtgtgttttgcag------
 |  || || |||||| | || || ||| |||| ||||| |||| |   ||| | |||| ||||||||||||||||||||||||||| |||||||| |||||    | |   | | | || | |  |   | |  |   | ||    | ||    |     | | |||  ||  ||| |||||||       
CAAAGGTGTTGAATGGAATAAGTTGTATCAAATGGAAGCTGCATTTATTCCTGAGGTCAATGATGAGTTAGATACTCAGAATTTTGAAAAGTTTGATGAGgtattcaagtcccttatattcttgttttgtgtagcttgttgtcggccactttccttgttcatattttctcattttgtcttttgcatttgtag

upper sequence: LOC_Os10g33640.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA10G32480.1 (Glycine max), 5'ss of exon 9
TAGTGGAGTAGAATGGGACAAATTATATGAAATAGAAGCAGCATATCAACCTCAAGTCACTGATGAGTTAGATACTCAGAATTTTGAGAAGTTTGAAGAGgttaggggt---cgtttcttttggcctaaaggaattcagtttcaataagttggtataaatgttattcctatggtgtgttttgcag-----------
||  ||  | |||||||||||||| ||  ||||  |||| || | |   ||| | || | |||||| ||||||||||| |||||||||||||||||||||||      |    |||| ||||     | |    |  | |||   |  | || || |||      || |   |  |  ||| |             
TAAAGGTATTGAATGGGACAAATTGTACCAAATGAAAGCTGCTTTTATTCCTGAGGTTAATGATGAATTAGATACTCAAAATTTTGAGAAGTTTGAAGAGgtatattatatatgtttattttcatggatataggtgtaatttttgtctgctgttacaaaccagtatcatgctgcttaatttactaataatgtgtag

upper sequence: LOC_Os10g33640.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA02G00580.1 (Glycine max), 5'ss of exon 10
TAGTGGAGTAGAATGGGACAAATTATATGAAATAGAAGCAGCATATCAACCTCAAGTCACTGATGAGTTAGATACTCAGAATTTTGAGAAGTTTGAAGAGgt----taggggtcgtttctttt---ggcctaaaggaatt---cagtttc----aataagttggtataa--atgttattcctatggtgtgttttgcag
 |  || || |||||||||||||| ||  ||||  | || || |    |||| | |||| |||||| ||||||||||| ||||||||||||||||| |||||    ||    || ||   ||    |   || | ||  |   || |||     | | |  | || | |  || || |   |      || | || ||
CAAAGGTGTTGAATGGGACAAATTGTACCAAATGCAGGCTGCTTTCATACCTGAGGTCAATGATGAATTAGATACTCAAAATTTTGAGAAGTTTGAGGAGgtatattatatatctttatgttcatggatatagaagagctaatcattttttcatagtgaactagtgtcatgatattttgttttactaatgatgtgtag

upper sequence: LOC_Os10g33640.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA10G00830.1 (Glycine max), 5'ss of exon 9
TAGTGGAGTAGAATGGGACAAATTATATGAAATAGAAGCAGCATATCAACCTCAAGTCACTGATGAGTTAGATACTCAGAATTTTGAGAAGTTTGAAGAGgttaggggtcgtttcttttggcctaaaggaattca-gtttcaataagttggtataaatg--ttattcctatggtgtgttttgcag-----------------------------------------
 |  || || |||||||||||||||||  ||||  |||| || |    |||| | |||| |||||| ||||||||||| ||||||||||||||||||||||| |       | |||||| |   |  |  ||  | |    ||| | ||  |     ||    | |   ||| | | ||||                                             
CAAAGGTGTTGAATGGGACAAATTATACCAAATGAAAGCTGCTTTCATACCTGAGGTCAATGATGAATTAGATACTCAAAATTTTGAGAAGTTTGAAGAGgt-atattatatatctttttgttcatggatatagaagagctaatcattttatcattgtgaaccagtgtcatgatattttttttgatattgaatgtcatgatattttgttttactaatgatgtgtag

upper sequence: LOC_Os10g33640.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA03G32160.1 (Glycine max), 5'ss of exon 9
TAGTGGAGTAGAATGGGACAAATTATATGAAATAGAAGCAGCATATCAACCTCAAGTCACTGATGAGTTAGATACTCAGAATTTTGAGAAGTTTGAAGAGgt-taggggtcgtttcttttggcctaaaggaattcagtttcaataagttggtataaatgttattcctatggt-gtgttttgcag-----------------------
 |  || || |||||||| ||||| ||| |||| ||||| || | |   ||| | |||| |||||||||||||||||| |||||||| |||||||||||||| || | ||| ||    ||           ||||| |||   ||  ||  |  || ||||||||  ||| | |  || | ||                        
CAACGGTGTTGAATGGGATAAATTGTATCAAATGGAAGCTGCCTTTATTCCTGAGGTCAATGATGAGTTAGATACTCAAAATTTTGAAAAGTTTGAAGAGgtataagtgtctttcaaattatttctc----attcaattttttta--tttatccaa-tgttattcacatgattgaattattcaaattttatcttttcacctttgtag

upper sequence: LOC_Os10g33640.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA20G35110.2 (Glycine max), 5'ss of exon 10
TAGTGGAGTAGAATGGGACAAATTATATGAAATAGAAGCAGCATATCAACCTCAAGTCACTGATGAGTTAGATACTCAGAATTTTGAGAAGTTTGAAGAGgttaggggt---cgtttcttttggcctaaaggaattcagtttcaataagttggtataaatgttattcctatggtgtgttttgcag-----------
||  ||  | |||||||||||||| ||  ||||  |||| || | |   ||| | || | |||||| ||||||||||| |||||||||||||||||||||||      |     ||| ||||     | |   ||   ||||   |  | || ||  ||      || |   |  |  ||| |             
TAAAGGTATTGAATGGGACAAATTGTACCAAATTAAAGCTGCTTTTATTCCTGAGGTTAATGATGAATTAGATACTCAAAATTTTGAGAAGTTTGAAGAGgtatattatatatttttattttcatggatatagatgtggtttttgtctgctgttactaaccagtatcatgctgcttaatttactaatgatgtgtag

upper sequence: LOC_Os10g33640.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA13G18670.2 (Glycine max), 5'ss of exon 9
TAGTGGAGTAGAATGGGACAAATTATATGAAATAGAAGCAGCATATCAACCTCAAGTCACTGATGAGTTAGATACTCAGAATTTTGAGAAGTTTGAAGAGgt---taggggtcgtttcttttggcctaaaggaattcagtttcaataagttggtataaatg-ttattcctatggtgtgttttgcag------
 |  || || |||||||| ||  | ||| |||| ||||| |||| |   ||| | |||| ||||||||||||||||||||||||||| |||||||| |||||      |  || | | || | |  |   | |  |   | ||    | |||   |      || |||  ||  | | |||||||       
CAAAGGTGTTGAATGGGATAAGCTCTATCAAATGGAAGCTGCATTTATTCCTGAGGTCAATGATGAGTTAGATACTCAGAATTTTGAAAAGTTTGATGAGgtattcgagtttcttatattcttgttttgtgtagcttgttgtcggccacttgtcgtgttcaatttttctcattttatcttttgcatttgtag

upper sequence: LOC_Os10g33640.1 (Oryza sativa), 5'ss of exon 9
lower sequence: AT2G20470.1 (Arabidopsis thaliana), 5'ss of exon 9
TAGTGGAGTAGAATGGGACAAATTATATGAAATAGAAGCAGCATATCAACCTCAAGTCACTGATGAGTTAGATACTCAGAATTTTGAGAAGTTTGAAGAGgttaggggtc--------------gtttcttttggcctaaaggaattca-gtttcaataagttggtataaatgttattcctatggtgtgttttgcag------------
|      || || ||||| | | |||  || || || ||||| | |   ||  | |||| ||| || ||||| ||||||||||||||||||||||| ||||| |    ||               ||||||||||  |  |   |   |     ||| ||  | | | |    ||| | || ||   | || |  |             
TGAAACTGTTGATTGGGATACAATATTCGATATGGATGCAGCTTTTGTTCCAGAGGTCAATGACGATTTAGACACTCAGAATTTTGAGAAGTTTGACGAGgtaacaaatcttttatcgcatcatatttcttttggatttgatcgacctatacggcaaaaaagttgcagattgattaattctttgtgttattatatatttggaaatgcag

upper sequence: LOC_Os10g33640.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv05s0049g01220.t01 (Vitis vinifera), 5'ss of exon 9
TAGTGGAGTAGAATGGGACAAATTATATGAAATAGAAGCAGCATATCAACCTCAAGTCACTGATGAGTTAGATACTCAGAATTTTGAGAAGTTTGAAGAGgttaggggtcgtttcttttggcctaaagg--------aattcagtttcaataagttggtataaatgttattcctatggtgtgttttgcag---
|   || || || ||||||||||| ||| |||| ||||| |||| |   ||| | |||| ||||||||||||||| || || |||||||||||||||||||| ||| || | ||||  | |  | |  |        | | | | ||  | | |||  | |   || | | ||     |   || ||  |   
TGAAGGTGTTGACTGGGACAAATTGTATCAAATTGAAGCTGCATTTATTCCTGAGGTCAATGATGAGTTAGATACCCAAAACTTTGAGAAGTTTGAAGAGgtgaggagt-gcttctacttgtatgagtgttgtggatactcctgcttggagatgtttttgttgctgatttaccccctattgattatgaggcag

upper sequence: LOC_Os10g33640.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv07s0005g03690.t01 (Vitis vinifera), 5'ss of exon 9
TAGTGGAGTAGAATGGGACAAATTATATGAAATAGAAGCAGCATATCAACCTCAAGTCACTGATGAGTTAGATACTCAGAATTTTGAGAAGTTTGAAGAGgttagg----ggtcgtttcttttg----------gcctaaaggaattc--agtttcaataagttg---gtataaatgttattcctatggtgtgt-tttgcag
|   ||    |||||||| | | |||||   || ||||| |||| |   ||  | ||||  ||||| |||||||||||||||||||| ||||| ||||||||   |    | ||  ||||||||          |||  ||    ||   |||||    | ||||    | ||  | ||   |||||  | ||  |||||||
TGAAGGTACTGAATGGGATAGACTATATCTTATGGAAGCTGCATTTATTCCCGAGGTCAGAGATGAATTAGATACTCAGAATTTTGAAAAGTTCGAAGAGgtattgatatgctctattcttttgctgatcttgtgccacaacttgtttggagttttttcatgttgcttatctactttttgagcctattttatgggtttgcag

upper sequence: LOC_Os10g33640.1 (Oryza sativa), 5'ss of exon 9
lower sequence: PP1S87_129V6.1 (Physcomitrella patens), 5'ss of exon 9
TAGTGGAGTAGAATGGGACAAATTATATGAAATAGAAGCAGCATATCAACCTCAAGTCACTGATGAGTTAGATACTCAGAATTTTGAGAAGTTTGAAGAGgttaggggtcgtttct-tttggcctaaaggaattcagtttcaataag-----ttggta---taaatgttattc--ctatggtg-tgttttgcag------
 |  ||| |   |||||| |  ||||||||||| || || || | | ||||  |||| |  |||||||| |||||||||||||||||||| |||||||||||||   ||| || || | | |   |   |  | |  ||  ||| ||     |||| |   | |  ||| ||   || || || |  ||| ||       
CAAAGGATTGCCATGGGAAAGGTTATATGAAATGGAGGCCGCTTTTAAACCGGAAGTGAAAGATGAGTTGGATACTCAGAATTTTGAGAAATTTGAAGAGgttaacagtccttcctatctagaacattcgtttacctttcaaatcagaatctttggcactcttagagttgttaaactctgatgataattttcaaatagtt

upper sequence: LOC_Os10g33640.1 (Oryza sativa), 5'ss of exon 9
lower sequence: PP1S22_429V6.1 (Physcomitrella patens), 5'ss of exon 9
TAGTGGAGTAGAATGGGACAAATTATATGAAATAGAAGCAGCATATCAACCTCAAGTCACTGATGAGTTAGATACTCAGAATTTTGAGAAGTTTGAAGAGgttaggggtcgtttcttttggcctaaaggaattcagtttcaataagttggtataaatgttattcctat-ggtgtgttttgcag------------------
   |||| ||   ||||| ||  | ||||| || || ||||| | | ||||| | || |  |||||| | || |||||||||||||||||||| ||||||||  ||  || ||  |      |  ||   ||  | || |  |  | | |     |||||||     | |||||  | || |                   
CCATGGATTACCTTGGGATAAGCTGTATGAGATGGATGCAGCTTTTAAACCTGAGGTGAAAGATGAGCTGGACACTCAGAATTTTGAGAAGTTCGAAGAGgtctggcatccttcttacaccacccaatctatata-ttactgtcggcttgaggttatgttatgtaggtaggtgtactgtgaatcatggatatctggtactg

upper sequence: LOC_Os10g33640.1 (Oryza sativa), 5'ss of exon 9
lower sequence: PP1S86_100V6.1 (Physcomitrella patens), 5'ss of exon 9
TAGTGGAGTAGAATGGGACAAATTATATGAAATAGAAGCAGCATATCAACCTCAAGTCACTGATGAGTTAGATACTCAGAATTTTGAGAAGTTTGAAGAGgttaggggtcgtttcttttggcctaaaggaattcagtttca-ataagtt-ggtataaatgttatt--cctatggtgtgttttgcag--------------
   |||| |    ||||| ||  | ||||| || || ||||| | | ||||  | || |  |||||| | ||||||||||||||||||||||| |||||||||     || || || |    |  ||   |||   || || ||    | ||  ||  || || |   |||   ||||     |                
CCATGGATTGCCTTGGGATAAGCTGTATGATATGGAGGCAGCTTTTAAACCCGAGGTGAAAGATGAGCTGGATACTCAGAATTTTGAGAAGTTCGAAGAGgtttaccatcattcctgtccaacctaatcgattatcttacacatggcctaggggtatctgatactggtctagattgtgcgcaccgatgtctactcacatc

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: 58 (upstream exon), 48 (downstream exon)
Score: 5

TAGTGGAGTAGAATGGGACAAATTATATGAAATAGAAGCAGCATATCAACCTCAAGTCACTGATGAGTTAGATACTCAGAATTTTGAGAAGTTTGAAGAGgttaggggtc ... tgttttgcagTCTTCAGACAATATTCAATGTTCAGCAAAGGCGGGACCTTGGAGAAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGTGGAGTAGAATGGGACAAATTATATGAAATAGAAGCAGCATATCAACCTCAAGTCACTGATGAGTTAGATACTCAGAATTTTGAGAAGTTTGAAGAGgttaggggtcgtttcttttggcctaaaggaattcagtttcaataagttggtataaatgttattcctatggtgtgttttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA