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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCGgtaagttattgggtacaagaaaagttacctgaacaaagcattgtgttttacataagtagtaaaaaagatttccaatcaatactcaagaagaacttttctggtttcttaatatcttctcgttatgcag

Basic information

species Oryza sativa
transcript LOC_Os04g41470.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G006428_T02 (Zea mays), 5'ss of exon 10
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCGgtaagttattgggtacaagaaaagttacctgaacaaagcattgtgttttacataagtagtaaaaaagatttccaatcaatactcaagaagaacttttctggtttcttaatatcttctcgttatgcag
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||| |||||||||||||||||||||||| ||||  |     | || | |||||||     | ||   | | |||||    | |    |||||  ||||  || |     ||| |   |  ||| |                        
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagt-attgaatgtggcagaaatgacctgaa----actttaaatct-acatagcatggagttcagattgacaattgatgcatgccaagcatcctgttggctgga---------------------

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM5G876621_T01 (Zea mays), 5'ss of exon 10
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCGgtaagttattgggtacaagaaaagttacctgaacaaagcattgtgttttacataagtagtaaaaaagatttccaatcaatactcaagaagaacttttctggtttcttaatatcttctcgttatgcag
||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||| ||||||||||| |||||||||||||||||||||||| ||||  |       |||| |||||||      | | |   |||     |   | |   ||| |  ||||  || |     |     | |  |||                          
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCCCTTGAGAGATACACACATTATTATGAACGATGGGCAGCCAATCAGTCGgtaagt-attgaatgtggttgaagtgacctgaaacttcaaatctacattagcatggagttcattcagagtgacaattgatgcatgccagctgttctgttgg--------------------------

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 10
lower sequence: AT1G65430.1 (Arabidopsis thaliana), 5'ss of exon 10
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCGgtaagttattgggtacaagaaaagttacctgaacaaagcattgtgttttacataagtagtaaaaaagatttccaatcaatactcaagaagaacttttctggtttcttaatatcttctcgttatgcag
||||||||  ||||||   |  |||| |||||||||||||| |||||||||||||| ||||| |||||  | |||||| ||||||| |||||| || | |   ||           |  |     ||      |||||||  ||  |  |         ||  |    | | | |||||  | |||||  |      |||   |  || |       
TATGATGAGACTGAAAAACGCCGAGAGATGGCAAAGAACTCTCTTGAGAGATATACCCACTACTATGAGAGATGGGCAACCAATCAATCGgtatgtaaatttttat--------ccatttag---aattcacatgttttatttagctcct--------cttgaaggggaaatttaagaaagaattttc-agccgtcaaattcatattcct-------

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 10
lower sequence: PP1S9_199V6.1 (Physcomitrella patens), 5'ss of exon 11
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCGgtaagtt---attgggtacaagaaaagt-------tacctgaacaaagcattgtgttttacataa-gtagtaaaaaagattt--ccaatcaat--actcaagaagaacttttctggtttcttaatatc-ttctcgttatgcag----------
||||||||| | ||  ||||||| |||||||| |||||||| |||||  | || |||||||||||||| || |||||  | ||  | || || |||    ||| |  |      |  |       ||| | |   |   | | | |||  |||||   | || | | |  ||  | |     |  | | ||   ||  ||||      | | ||| |   ||   |  | | |          
TATGATGAAGCAGAGCGGAGAAGGGAAATGGCGAAGAACTCCCTTGAACGTTACACACACTATTATGAGCGTTGGGCTACAAACGAATCTgtgagtactaatttgagatggtgcacttcttccactacgttagttatataatctttttcccataacacactagagatgcattgactacctggttaatttaatgtgatgtttttcatcatttcaatcttactcaaatccttctgatgtgtgcag

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 10
lower sequence: PP1S114_2V6.1 (Physcomitrella patens), 5'ss of exon 10
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCGgtaagttattgggtacaagaaaagtt----acctgaacaaagcattgt---gttttacataag--------tagtaaaaaagatttccaatcaat----actcaagaa---gaact----------tttctggtttcttaatatcttctc-gttatgcag
||||||||| | ||  ||||||| |||||||| ||||||||||||||  | |||||||| || |||||||| |||||  | ||  | || ||||||  |   | |   | | | ||    | |||||  | |  ||     |||   |||  |        || |    | ||| |  | ||  |    | | ||  |   || ||          ||||| |  | || | |||| ||  ||| | |||
TATGATGAAGCAGAGCGGAGAAGGGAAATGGCTAAGAACTCGCTTGAACGCTATACACATTACTATGAACGTTGGGCTACAAACGAATCTgtaagtggtgcagaatctgcacattttcccatctgaattaggttttcctcagttcgccatgggattgcacctattgtttaggatcttaactctctctcaatttaaagacgtgatctgcgtttgtgttttcttgacttttgaaatctcctttgtttttcag

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 10
lower sequence: EFJ15174 (Selaginella moellendorffii), 5'ss of exon 10
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCGgtaagttattgggtacaagaaaagttacctgaacaaagcattgtgttttacataagtagtaaaaaagatttccaatcaatactcaagaagaacttttctggtttcttaatatcttctcgttatgcag
|| |||||| |||| ||||| ||||||||||| ||||||||| | |||||||||||||| || || || || |||||  | ||  | || ||    | |    |   ||      || ||||  |   | || |   || | |   | ||| |                                                                
TACGATGAAGCTGAGAGGAGGAGAGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCAgttgagtttccaatttgag------tatctga-taggcctttctaactt-cgttcatggtacag---------------------------------------------------------------

upper sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 10
lower sequence: EFJ08409 (Selaginella moellendorffii), 5'ss of exon 10
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCGgtaagttattgggtacaagaaaagttacctgaacaaagcattgtgttttacataagtagtaaaaaagatttccaatcaatactcaagaagaacttttctggtttcttaatatcttctcgttatgcag
|| |||||| |||| ||||| || |||||||| ||||||||| | |||||||||||||| || || || || |||||  | ||  | || ||    | |    |   ||      || ||||  |   | || |   || |     | ||| |                                                                
TACGATGAAGCTGAGAGGAGGAGGGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCAgttgagtttccaatttgag------tatctga-taggcctttctaactt-cgctcatggtacag---------------------------------------------------------------

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|29614534|gb|CB619547.1|CB619547
EST:     CGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCG                         TCGAGGCAAAAGGCATTAGGAGATCTGCTGAGTTTGCAAAACGACAAG
genomic: CGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCGgtaagttatt ... cgttatgcagTCGAGGCAAAAGGCATTAGGAGATCTGCTGAGTTTGCAAAACGACAAG
EST: gi|66920746|gb|CX107594.1|CX107594
EST:     CGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCG                         TCGAGGCAAAAGGCATTAGGAGATCTGCTGAGTTTGCAAAACGACAAG
genomic: CGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCGgtaagttatt ... cgttatgcagTCGAGGCAAAAGGCATTAGGAGATCTGCTGAGTTTGCAAAACGACAAG

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: 74 (upstream exon), 48 (downstream exon)
Score: 50

TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCGgtaagttatt ... cgttatgcagTCGAGGCAAAAGGCATTAGGAGATCTGCTGAGTTTGCAAAACGACAAG




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