Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTCTCCGGGGCAGCTCAAAGGTTGGCAGGCAAGTGGTGGAGACCCTTGTGGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAATgtgagcctcatcatgaagcaaagtagtttactacttactcgaccaccttctttcttacttcttacaatattttctttgtgtttgatgttgtag

Basic information

species Oryza sativa
transcript LOC_Os03g08550.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g08550.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G330907_T01 (Zea mays), 5'ss of exon 2
ATTCTCCGGGGCAGCTCAAAGGTTGGCAGGCAAGTGGTGGAGACCCTTGTGGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAATgtgagcctcatcatgaagcaaagtagtttactacttact-cgaccaccttctttcttacttcttacaat-at-tttctttgtgtttgatgttgtag
||||||| |||||||||| || ||||||||| | ||| || || ||||||||||| ||||||||||| || || ||||||||||||   || |||  |||||||||||  | ||| || | ||| |   || || | || | ||  | |  ||||||||| | |   || || ||||| | |||||| || |||||
ATTCTCCTGGGCAGCTCAGAGCTTGGCAGGCGAATGGCGGTGATCCTTGTGGCCAGTCATGGCAGGGCATTACTTGCTCAGGATCAGGGGTCACTAAAATgtgagccttgtgatgcagtatagttgca-accacctgctaccacagcttcttttcttactccctctcatcatatttctctttgtttgttgctgtag

upper sequence: LOC_Os03g08550.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G153393_T01 (Zea mays), 5'ss of exon 2
ATTCTCCGGGGCAGCTCAAAGGTTGGCAGGCAAGTGGTGGAGACCCTTGTGGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAATgtgagcctcatcatgaagcaaagt---agtttactacttactcgaccaccttc-tttcttact---tcttacaatattttctttgtgtttgatgttgtag
||||||| |||||||||| |||||||||||| | ||| || || ||||||||||| |||||| |||| || || ||||||||||||   || |||  |||||||||||  | ||| || | |||   ||      || | ||    || ||||  ||||||||   ||| || |||||| | || |||||| || |||||
ATTCTCCTGGGCAGCTCACAGGTTGGCAGGCGAATGGGGGTGATCCTTGTGGCCAGTCATGGAAGGGCATTACTTGCTCAGGATCAGGGGTCACTAAAATgtgagccttttgatgcagtatagttgcagccaggcacctgctaacacagcttcacttcttactccctctcactatatttccctt-tgtttgttgctgtag
















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|88362223|gb|CI608614.1|CI608614
EST:     GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAAT                         CAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
genomic: GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAATgtgagcctca ... gatgttgtagCAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
EST: gi|88696564|gb|CI740139.1|CI740139
EST:     GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAAT                         CAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
genomic: GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAATgtgagcctca ... gatgttgtagCAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
EST: gi|88299950|gb|CI580011.1|CI580011
EST:     GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAAT                         CAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
genomic: GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAATgtgagcctca ... gatgttgtagCAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
EST: gi|7219971|gb|AU065234.2|AU065234
EST:     GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAAT                         CAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATA
genomic: GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAATgtgagcctca ... gatgttgtagCAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATA
EST: gi|44665230|gb|CR278664.1|CR278664
EST:     GGGTATCACGTGCTCAGGATCATCAGTTACTGCAAT                         CAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
genomic: GGGTATCACGTGCTCAGGATCATCAGTTACTGCAATgtgagcctca ... gatgttgtagCAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
EST: gi|88421797|gb|CI621441.1|CI621441
EST:     GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAAT                         CAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
genomic: GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAATgtgagcctca ... gatgttgtagCAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
EST: gi|88299567|gb|CI574680.1|CI574680
EST:     GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAAT                         CAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
genomic: GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAATgtgagcctca ... gatgttgtagCAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
EST: gi|88391200|gb|CI595454.1|CI595454
EST:     GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCACTTACTGCAAT                         CAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
genomic: GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAATgtgagcctca ... gatgttgtagCAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
EST: gi|29644649|gb|CB649656.1|CB649656
EST:     GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAAT                         CAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
genomic: GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAATgtgagcctca ... gatgttgtagCAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
EST: gi|29624948|gb|CB629959.1|CB629959
EST:     GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAAT                         CAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
genomic: GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAATgtgagcctca ... gatgttgtagCAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
EST: gi|88402842|gb|CI613290.1|CI613290
EST:     GGCCAATCATGG-AGGGTATCACGTGCTCAGGATCATCAGTTACTGCAAT                         CAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTA-AATATGAATAC
genomic: GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAATgtgagcctca ... gatgttgtagCAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
EST: gi|66914683|gb|CX101531.1|CX101531
EST:     GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAAT                         CAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
genomic: GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAATgtgagcctca ... gatgttgtagCAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
EST: gi|88764540|gb|CI773658.1|CI773658
EST:     GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAAT                         CAAATTAC-AAGCTTGGGGCTCTCCGGTAATTTGGC
genomic: GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAATgtgagcctca ... gatgttgtagCAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGC
EST: gi|88362471|gb|CI623811.1|CI623811
EST:     GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAAT                         CAAATTACCAAGCTTGGGGCTCTCCGG
genomic: GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAATgtgagcctca ... gatgttgtagCAAATTACCAAGCTTGGGGCTCTCCGG
EST: gi|88397054|gb|CI593266.1|CI593266
EST:     GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGGAAT                         CAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
genomic: GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAATgtgagcctca ... gatgttgtagCAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
EST: gi|88726200|gb|CI749855.1|CI749855
EST:     GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAAT                         CAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTANAATATGAATAC
genomic: GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAATgtgagcctca ... gatgttgtagCAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
EST: gi|88386689|gb|CI682838.1|CI682838
EST:     GTTACTGCAAT                         CAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
genomic: GTTACTGCAATgtgagcctca ... gatgttgtagCAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
EST: gi|88403753|gb|CI611408.1|CI611408
EST:     GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAAT                         CAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCG
genomic: GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAATgtgagcctca ... gatgttgtagCAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCG
EST: gi|88432225|gb|CI565258.1|CI565258
EST:     GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAAT                         CAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
genomic: GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAATgtgagcctca ... gatgttgtagCAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
EST: gi|117225926|gb|CT846035.1|CT846035
EST:     GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAAT                         CAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
genomic: GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAATgtgagcctca ... gatgttgtagCAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
EST: gi|88415616|gb|CI589208.1|CI589208
EST:     GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAAT                         CAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGA
genomic: GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAATgtgagcctca ... gatgttgtagCAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGA
EST: gi|88428716|gb|CI599432.1|CI599432
EST:     GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTAATGGAAT                         CAAATTAC-AAGCTTGGG-CT-TCCGGTA-TTTGGCGTA-AATAT-AATAC
genomic: GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAATgtgagcctca ... gatgttgtagCAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
EST: gi|88354679|gb|CI613957.1|CI613957
EST:     GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAAT                         CAAATTAC-AAGCTTGGGGCTCTCCGGTAAT
genomic: GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAATgtgagcctca ... gatgttgtagCAAATTACCAAGCTTGGGGCTCTCCGGTAAT
EST: gi|29635613|gb|CB640622.1|CB640622
EST:     GGCCAATCATGGCAGGGTATCACGTGCTCAAGATCATCAGTTACTGCAAT                         CAAATTACCAAGCTTGGGGCTC
genomic: GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAATgtgagcctca ... gatgttgtagCAAATTACCAAGCTTGGGGCTC
EST: gi|88301108|gb|CI594634.1|CI594634
EST:     GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAAT                         CAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
genomic: GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAATgtgagcctca ... gatgttgtagCAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
EST: gi|29681108|gb|CB677383.1|CB677383
EST:     GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAAT                         CAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
genomic: GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAATgtgagcctca ... gatgttgtagCAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
EST: gi|88399209|gb|CI618399.1|CI618399
EST:     GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAAT                         CAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
genomic: GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAATgtgagcctca ... gatgttgtagCAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
EST: gi|88358901|gb|CI619405.1|CI619405
EST:     GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAAT                         CAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC
genomic: GGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAATgtgagcctca ... gatgttgtagCAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATAC

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: 64 (upstream exon), 69 (downstream exon)
Score: 25

ATTCTCCGGGGCAGCTCAAAGGTTGGCAGGCAAGTGGTGGAGACCCTTGTGGCCAATCATGGCAGGGTATCACGTGCTCAGGATCATCAGTTACTGCAATgtgagcctca ... gatgttgtagCAAATTACCAAGCTTGGGGCTCTCCGGTAATTTGGCGTACAATATGAATACCATGGGTTCATTGATTGAGAT




<











<


<