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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCACTGGTAAGGCAGTCATGCTTGATGAGATAATCAATTATGTACAGTCACTACAACGTCAAGTTGAGgtactattagggtggtggttcagttatttcttggacagttggaatatcactctgtaatctaacacaatctgaacttgcag

Basic information

species Oryza sativa
transcript LOC_Os03g51910.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g51910.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G385543_T01 (Zea mays), 5'ss of exon 5
ATCACTGGTAAGGCAGTCATGCTTGATGAGATAATCAATTATGTACAGTCACTACAACGTCAAGTTGAGgtactattagggtg---gtggttcagttatttc--------ttggaca----gttggaatatcactctgtaatctaacacaatct-gaacttgcag
|||||||| |||||||||||||| |||||||| ||||| ||||| |||||| | ||||| ||||| |||||| | |||| |     || | | | || |||         |  | ||    ||| | |||| |  | ||| ||||| ||| | | || |||||||
ATCACTGGCAAGGCAGTCATGCTCGATGAGATTATCAACTATGTGCAGTCATTGCAACGACAAGTCGAGgtagtgttagtgcatctgtagctgaattgttttggaatatatgtggcatcttgttagtatat-atccagtattctaatacagtttcgagcttgcag

upper sequence: LOC_Os03g51910.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G092091_T02 (Zea mays), 5'ss of exon 3
ATCACTGGTAAGGCAGTCATGCTTGATGAGATAATCAATTATGTACAGTCACTACAACGTCAAGTTGAGgtactattagggtg---gtggttcagttatttcttggacagttggaatatcac-------tctgtaatc------taacacaatct-gaacttgcag
|||||||| |||||||||||||| |||||||| ||||| |||||||||||| | ||||| ||||| |||||| |  ||| |     || ||| | ||  || | | | |  ||  | |||         | | |||||      ||| ||||| | ||||||||||
ATCACTGGCAAGGCAGTCATGCTCGATGAGATTATCAACTATGTACAGTCATTGCAACGACAAGTGGAGgtagtgatagtgcatctgtagttgaattgctt-tggaatatgtgtgacatcttgttagtatatataatccagttctaatacaatttcgaacttgcag

upper sequence: LOC_Os03g51910.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv18s0001g08600.t01 (Vitis vinifera), 5'ss of exon 4
ATCACTGGTAAGGCAGTCATGCTTGATGAGATAATCAATTATGTACAGTCACTACAACGTCAAGTTGAGgtactattagggtggtggttcagttatttctt--ggacagttggaatatcactctgtaatctaacacaatctgaacttgcag----------------------------
|| ||||| |||||||| |||||||||||||| |||||||||||||||||||| ||||  || |||||||||        |   | |||||  | |    |  || || | |   | |    ||||  | |||    || |  | ||                                
ATTACTGGGAAGGCAGTAATGCTTGATGAGATTATCAATTATGTACAGTCACTGCAACAACAGGTTGAGgtat-------gccattgttcaactctaatataggggcattagtggtgttgtgctgttgtttaa---gatttatatttaagaaaaagttagcctcatcaatccttatatg

upper sequence: LOC_Os03g51910.1 (Oryza sativa), 5'ss of exon 5
lower sequence: Vv07s0151g00450.t01 (Vitis vinifera), 5'ss of exon 4
ATCACTGGTAAGGCAGTCATGCTTGATGAGATAATCAATTATGTACAGTCACTACAACGTCAAGTTGAGgtactattagggtggtggttcagttatttcttggacagttggaatatcactctgtaatctaacacaatctgaacttgcag---------------------
|| ||||| || || || |||||||||||||| ||||| ||||| || ||||| ||||| || ||||||||| |       || |   | |   ||   ||  |    |  | ||| | | |  ||||  |   |   |     ||| |                     
ATTACTGGAAAAGCGGTAATGCTTGATGAGATTATCAACTATGTGCAATCACTGCAACGACAGGTTGAGgta-tgcgtttctgatatctgaagaataagtttcatctctttattatgaatataaaatcacatgaagaattcctctgctgacttttaaagatctgaaacta

upper sequence: LOC_Os03g51910.1 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S68_190V6.1 (Physcomitrella patens), 5'ss of exon 3
-------------------------------ATCACTGGTAAGGCAGTCATGCTTGATGAGATAATCAATTATGTACAGTCACTACAACGTCAAGTTGAGgtac-------------tattagggtggtggttcagttatttcttggacagttggaatatcactct-gtaatc-----taacacaatctgaacttgcag------------------------------------
                                |||| || ||||||||||||||||| ||||| ||||| ||||| || || || ||||| |||||||| |||              | | |  |   || |   | |||| | |  |    |     | |  ||| || |||     | |   | | |   || | |                                     
CCTGCAGGACCTCGTACCCGGCTGCCGCAAAGTCACCGGCAAGGCAGTCATGCTTGACGAGATCATCAACTATGTTCAATCCCTCCAACGACAAGTTGAAgtatgtctcttacccattttcaacgcactgctaatgctattccattcatgtcttaggcacccttcttgttatcgctagtgatgaattgtagtctagtattgagttgtatcgtacactttgttatcttttttacag

upper sequence: LOC_Os03g51910.1 (Oryza sativa), 5'ss of exon 5
lower sequence: PP1S69_95V6.1 (Physcomitrella patens), 5'ss of exon 2
-------------------------------ATCACTGGTAAGGCAGTCATGCTTGATGAGATAATCAATTATGTACAGTCACTACAACGTCAAGTTGAGgtactattagggtggtggttcagt---tatttcttggacagttggaatatcactctg---taatctaa-------cacaatctgaacttgcag------------------
                                ||||||| || ||||||||||| ||||| || |||||||| || ||||| || ||||||||||| |||||||        |  |    |  |   ||     | ||  || |  |||    ||||   ||||  |         |  || | ||||| ||                   
CTTGCAGGACCTTGTTCCTGGCTGCCGCAAAGTCACTGGCAAAGCAGTCATGCTCGATGAAATCATCAATTACGTCCAGTCCCTCCAACGTCAAGTCGAGgtacatccctcattctccgccgttctatacacaattgaaggtggtgatagggatctgctgtaattcatatcaggttatgatgttaacttccacattttttttgtgttgcag

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|29626811|gb|CB631822.1|CB631822
EST:     TGCTTGATGAGATAATCAATTATGTACAGTCACTACAACGTCAAGTTGAG                         TTTTTGTCGATGAAACTCGCAACTGTCAACCCTGAGCTTAGCTTTGATATT
genomic: TGCTTGATGAGATAATCAATTATGTACAGTCACTACAACGTCAAGTTGAGgtactattag ... gaacttgcagTTTTTGTCGATGAAACTCGCAACTGTCAACCCTGAGCTTAGCTTTGATATT
EST: gi|25806060|gb|CA762021.1|CA762021
EST:     GTCACTCCACCGTCAAGTTGAG                         TTTTTGTCGATGAAACTCGCAACTGTCAACCCTGAGCTTAGCTTTGATATT
genomic: GTCACTACAACGTCAAGTTGAGgtactattag ... gaacttgcagTTTTTGTCGATGAAACTCGCAACTGTCAACCCTGAGCTTAGCTTTGATATT
EST: gi|32947925|gb|BP184497.1|BP184497
EST:     TGCTTGATGAGATAATCAATTATGTACAGTCACTACAACGTCAAGTTGAG                         TTTTTGTCGATGAAACTCGCAACTGTCAACCCTGAGCTTAGCTTTGATATT
genomic: TGCTTGATGAGATAATCAATTATGTACAGTCACTACAACGTCAAGTTGAGgtactattag ... gaacttgcagTTTTTGTCGATGAAACTCGCAACTGTCAACCCTGAGCTTAGCTTTGATATT

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: 43 (upstream exon), 66 (downstream exon)
Score: 5

ATCACTGGTAAGGCAGTCATGCTTGATGAGATAATCAATTATGTACAGTCACTACAACGTCAAGTTGAGgtactattag ... gaacttgcagTTTTTGTCGATGAAACTCGCAACTGTCAACCCTGAGCTTAGCTTTGATATTGAGCAGATTCTATCGAAACAA




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