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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATATGCCACGTATATATTGACAAATCAGCTGACATGGATATGGCAAAACATATTGTAATGGATGCAAAAATTGATTACCCAGCAGCCTGCAATGCAATGgtatctatccagtttgctaccgtgtatagtattcaaatagattgcttttacagtttcagttactttttggagtatctttcactgaatattttggacaatt...

Basic information

species Oryza sativa
transcript LOC_Os05g38150.2
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g38150.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G375504_T03 (Zea mays), 5'ss of exon 13
TATATGCCACGTATATATTGACAAATCAGCTGACATGGATATGGCAAAACATATTGTAATGGATGCAAAAATTGATTACCCAGCAGCCTGCAATGCAATGgtatctatccagtttgctaccgtgtatag-tattcaaatagattg-cttttacagtttcagttactttttggagtatctttcactgaatattttggacaatt---
||| || || ||||| ||||||||||||||||||||| ||||||||||||  || || |||||||| |||| |||||||||||||||||||||||| |||||||   || | |||  ||       |||   |  |     ||   | | |   ||||  | | || |||  | ||     | |  |  || ||  || |     
TATTTGTCATGTATACATTGACAAATCAGCTGACATGAATATGGCAAAACGAATAGTGATGGATGCCAAAACTGATTACCCAGCAGCCTGCAATGCTATGgtat--gtctaatttcttattacaactaggcgtgtatgccaatgaacatatttggtttatgatgctgttt--aataatcagc-ccaatcatattacaccaacata

upper sequence: LOC_Os05g38150.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G094309_T01 (Zea mays), 5'ss of exon 6
TATATGCCACGTATATATTGACAAATCAGCTGACATGGATATGGCAAAACATATTGTAATGGATGCAAAAATTGATTACCCAGCAGCCTGCAATGCAATGgtatctatccagtttgctaccgtgtatagtattcaaatagattgcttt-----tacagtttcagttactttttggagtatctttcactgaatattttggacaatt
||| || || ||||| || |||||||||||| ||||| ||||||||||||| || || ||||| || ||||||||||||||||||||||||||||| |||||||   || | |||| |||  | ||||||||| ||   |  |  |||     | ||   | |  |||| |||| |  ||| ||     |            |  
TATCTGTCATGTATACATCGACAAATCAGCTAACATGAATATGGCAAAACAAATAGTGATGGACGCCAAAATTGATTACCCAGCAGCCTGCAATGCTATGgtat--gtctaatttgttacaatttatagtatttaacatgtctcttttcggcttgcatacttaactactctttgca-catccttactcaagagaaccaagtga--

upper sequence: LOC_Os05g38150.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA18G40770.1 (Glycine max), 5'ss of exon 15
TATATGCCACGTATATATTGACAAATCAGCTGACATGGATATGGCAAAACATATTGTAATGGATGCAAAAATTGATTACCCAGCAGCCTGCAATGCAATGgtatct----atccagtttgctaccgtgtatagta----ttcaaatagattgcttttacagtttcagttactttttggagtatctttcactgaatattttggacaatt----------------------------------------
 ||||| || |||||| | |||||| ||||| | || |||||||||||  | ||| | | ||||||||| ||||||||||| |||||||||||||||||||||  |    ||||  |    | ||   | || |     ||||  || ||   | |    |||| ||||  || ||    |  | |||| |   ||  | | |    |                                        
AATATGTCATGTATATGTAGACAAAACAGCTAATATTGATATGGCAAAGAAGATTATTAGGGATGCAAAGATTGATTACCCTGCAGCCTGCAATGCAATGgtaattttacatcccctggaatgcctcctctaatgcatgttcatctacatccatatcttcgtttgagtt--ttcttcatttgccattcattatgtaaatcgaatctatagagtcagcttaatacaatattgtgtgctgatgttcttag

upper sequence: LOC_Os05g38150.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA01G24530.1 (Glycine max), 5'ss of exon 15
TATATGCCACGTATATATTGACAAATCAGCTGACATGGATATGGCAAAACATATTGTAATGGATGCAAAAATTGATTACCCAGCAGCCTGCAATGCAATGgtatctatccagtttgctaccgtgtatagtattc-aaatagattgctttta-cagtttcagttactt-tttggagtatctttcactgaatattttggacaatt----------------------------------------------------
 || || || |||||| ||||||| || ||| | || ||||||||||| || ||||| | ||||||||| |  ||||| || ||||| |||||||| ||||||  || | | ||    | | | |  | |   | ||||| |     || | | || ||     ||  ||| | || |   | | |   ||  |  ||   |                                                     
AATTTGTCATGTATATGTTGACAAGTCTGCTAATATTGATATGGCAAAGCAGATTGTTAGGGATGCAAAGACCGATTATCCTGCAGCTTGCAATGCGATGgtaattagc-atttacacatcctttgcaatgcactaaataaaacatgttaatctgtatcctcctctccttttgggttttactgaattggtaggtgtgatgttattggaatttatggactatgctcatcaaaatatttttgtttttgtattcttag

upper sequence: LOC_Os05g38150.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA03G12240.1 (Glycine max), 5'ss of exon 14
TATATGCCACGTATATATTGACAAATCAGCTGACATGGATATGGCAAAACATATTGTAATGGATGCAAAAATTGATTACCCAGCAGCCTGCAATGCAATGgtatctatccagtttgctaccgtgtatagtatt-caaatagattgctttta-cagtttcagttactt-tttggagtatctttcactgaatattttggacaatt----------------------------------------------------
 || || || |||||| ||||||| || ||| |  | ||||||||||| || ||||| | ||||||||| | |||||| || ||||| |||||||||||||||  || | | ||    | | | |  | |    ||| || |     || | | || ||     ||  |||   || |   | | |   ||| |  ||   |                                                     
AATTTGTCATGTATATGTTGACAAGTCTGCTAATTTTGATATGGCAAAGCAGATTGTTAGGGATGCAAAGACTGATTATCCTGCAGCTTGCAATGCAATGgtaattagc-atttacacatcctttgcaatgcaacaagtaaaacatgttcatctgtatcctcctctccttttaggttttactgaattggtatgtgtgatgttattggaatttatggactgtgctcatcaaaatatttttgttttggtattcttag

upper sequence: LOC_Os05g38150.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA02G41850.1 (Glycine max), 5'ss of exon 11
TATATGCCACGTATATATTGACAAATCAGCTGACATGGATATGGCAAAACATATTGTAATGGATGCAAAAATTGATTACCCAGCAGCCTGCAATGCAATGgta---tctatccagtttgctaccgtgtatagtattcaaatagattgcttttacagtttcagttactttttggagtatctttcactgaatattttggacaatt
  | || || || ||| |||| || || ||| |  |||| |||||||  |  |||||| | ||||||||||| ||||| |||||||||||||| || ||||||   |  ||  | |     ||| |  | |  |||   | ||   ||  |  | | |  |  ||  || |    | ||     |  || |||  |       
AGTTTGTCATGTCTATGTTGATAAGTCTGCTAATGTGGAGATGGCAAGGCGGATTGTACTTGATGCAAAAATAGATTATCCAGCAGCCTGCAACGCCATGgtaaactaaatgtactcaatgaccct--acaagattggtaaagccagcaatgtctgatgtacataacttctctgttttcaaattcc-aacattcag-------

upper sequence: LOC_Os05g38150.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA14G07120.1 (Glycine max), 5'ss of exon 11
TATATGCCACGTATATATTGACAAATCAGCTGACATGGATATGGCAAAACATATTGTAATGGATGCAAAAATTGATTACCCAGCAGCCTGCAATGCAATGgta---tctatccagtttgctaccgtgtatagtattcaaatagattgcttttacagtttcagttactttttggagtatctttcactgaatattttggacaatt
  | ||||| || ||| |||| || || ||| |  |||| ||||| |     |||||| | ||||||||| | ||||| ||||||||||||||||| ||||||   |  ||  | |     ||  | || |  |||   | ||   ||  |  | | |  |  ||  || ||     | ||  | |  |  |||| |      
AGTTTGCCATGTCTATGTTGATAAGTCTGCTAATGTGGAGATGGCGAGGGGGATTGTACTTGATGCAAAATTAGATTATCCAGCAGCCTGCAATGCCATGgtaaactaaatgtactcaatgac--tctacaagattggtaaagccagcaatgtctgatgtacataacttctgt----ttttaaattccaacttttag------

upper sequence: LOC_Os05g38150.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GLYMA07G16510.1 (Glycine max), 5'ss of exon 11
TATATGCCACGTATATATTGACAAATCAGCTGACATGGATATGGCAAAACATATTGTAATGGATGCAAAAATTGATTACCCAGCAGCCTGCAATGCAATGgtatctatccagtttgc-taccgtgtatagtat--tcaaatagat-tgcttttacagtttcagttactttttggagtatctttcactgaatatt--ttggacaatt-------------------------------------------------
 ||||| || |||||| | |||||| ||||| | || |||||||||||  | ||| | | ||||||||| ||||||||||| |||||||||||||||||||||  |   |||||| | ||||  | |  |  |  || |||  || | | ||||||  | ||  |  |  || |||| |  |||| |    |||  ||    || |                                                 
AATATGTCATGTATATGTAGACAAAACAGCTAATATTGATATGGCAAAGAAGATTATTAGGGATGCAAAGATTGATTACCCTGCAGCCTGCAATGCAATGgtaatt--tcagtttacatacccaggaatgcctcctctaatgcatgttcatttaca--tccatatcttcgtttgagttttcttcatttttcattcattatgtaaattgaatctacagactcagctcattacaatattgtgtgctgatgttcttag

upper sequence: LOC_Os05g38150.1 (Oryza sativa), 5'ss of exon 13
lower sequence: Vv13s0019g02360.t01 (Vitis vinifera), 5'ss of exon 14
TATATGCCACGTATATATTGACAAATCAGCTGACATGGATATGGCAAAACATATTGTAATGGATGCAAAAATTGATTACCCAGCAGCCTGCAATGCAATGgtatctatccagtttgctaccgtgtatagtattcaaatagat--tgctttt--acagtttcagttactttttggagtatctttcactgaatattttggacaatt
 || |||||||| ||| | ||||| || ||| | |||||||  ||||| || || ||| ||||||||||| | ||||| || |||||||| ||||||||||||  | ||||   |  |       ||| | ||    |  ||  | |||||  | ||| ||    |  |||  |    | |||||| | || |||  |      
CATCTGCCACGTTTATGTCGACAAGTCTGCTAATATGGATACTGCAAAGCACATCGTATTGGATGCAAAAGTAGATTATCCTGCAGCCTGTAATGCAATGgtaatt-tccataatcttttgactgataatgttaggttgaataatacttttgaatagtgtccaa-atgtttcagccactttttcacagcatttttctgttcc--

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|88839043|gb|CI377967.1|CI377967
EST:     ATATTGTAATGGATGCAAAAATTGATTACCCAGCAGCCTGCAATGCAATG                         GAGACCTTACTAGTTCATAAGGATCTTATGAAGAGTCCAGGCCTTGACGAC
genomic: ATATTGTAATGGATGCAAAAATTGATTACCCAGCAGCCTGCAATGCAATGgtatctatcc ... tgttctgcagGAGACCTTACTAGTTCATAAGGATCTTATGAAGAGTCCAGGCCTTGACGAC




















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: 72 (upstream exon), 69 (downstream exon)
Score: 34

TATATGCCACGTATATATTGACAAATCAGCTGACATGGATATGGCAAAACATATTGTAATGGATGCAAAAATTGATTACCCAGCAGCCTGCAATGCAATGgtatctatcc ... tgttctgcagGAGACCTTACTAGTTCATAAGGATCTTATGAAGAGTCCAGGCCTTGACGACATATTAGTAGCACTAAAAACAGAAG




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