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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACAAGAGGTTTGCTGGGTTCAAGAAGGACGAGAAGCAGCTTGATTCTGATATTCACCGCAAGTACATCTACGGTGGGCACGTGGCTGACTACATGAGGgtgagctggcactattagatcaattgttcgtgctgtgggttgtattaggaattatgtagctgccttgatgtttataacgttgactaaagcattatataaagtttggattatttgttactgtttagctcagtctgctttattttgattgtcatcaggataaattttcttcttatgtacttgttgcag

Basic information

species Oryza sativa
transcript LOC_Os01g67126.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g67126.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G163081_T02 (Zea mays), 5'ss of exon 7
-----------------------------------TGACAAGAGGTTTGCTGGGTTCAAGAAGGACGAGAAGCAGCTTGATTCTGATATTCACCGCAAGTACATCTACGGTGGGCACGTGGCTGACTACATGAGGgtgagctggcactattagatcaattgttcgtgctgtgggttgtattaggaattatgtagctgccttgatgtttataacgttgactaaagcattatataaagtttggattatttgttactgtttagctcagtctgctttattttgattgtcatcaggataaattttcttcttatgtacttgttgcag
                                    || |||||||||||||| |||||||||||||| |||||| | ||| ||||||  ||||||| ||||||||| ||||| || || ||||||||||||| |||||| ||    |  |     |    ||                                                                                                                                                              
GGAGCATTGGATGGAGGCCTGGATATTCCTCACAGCGAGAAGAGGTTTGCTGGATTCAAGAAGgacgacaagcagttggatgctgatacccaccgcaggtacatctatggtggccatgttgctgactacatgaaggtgagttgtgcttgctgctgaacacatt--------------------------------------------------------------------------------------------------------------------------------------------------------------

upper sequence: LOC_Os01g67126.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM5G815894_T03 (Zea mays), 5'ss of exon 7
TGACAAGAGGTTTGCTGGGTTCAAGAAGGACGAGAAGCAGCTTGATTCTGATATTCACCGCAAGTACATCTACGGTGGGCACGTGGCTGACTACATGAGGgtgagctggcactattagatcaattgttcgtgctgtgggttgtattaggaattatgtagctgccttgatgtttataacgttgactaaagcattatataaagtttggattatttgttactgtttagctcagtctgctttattttgattgtcatcaggataaattttcttcttatgtacttgttgcag
 || |||||||||||||| ||||||||||| || |||||||| ||| ||||||| || |||||||||||||| ||||| || || ||||||||||||||||| || ||    |  |  || |     || |  |     |  | || |   || |  | ||    |||| | ||     |||| |      |||| |  |  ||    |    |                                                                        
CGAGAAGAGGTTTGCTGGTTTCAAGAAGGATGACAAGCAGCTGGATGCTGATATCCATCGCAAGTACATCTATGGTGGCCATGTTGCTGACTACATGAGGgttagttgtgcttgctgcat-atcacatcatatttcatttcctttttgtttttgta-aactaatctgatttatactcaattgatttcgttgttattttgatctttatctcccag------------------------------------------------------------------------

upper sequence: LOC_Os01g67126.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G163081_T03 (Zea mays), 5'ss of exon 7
-----------------------------------TGACAAGAGGTTTGCTGGGTTCAAGAAGGACGAGAAGCAGCTTGATTCTGATATTCACCGCAAGTACATCTACGGTGGGCACGTGGCTGACTACATGAGGgtgagctgg---cactattagatcaattgtt-cgtgctgtgggttgtattaggaattatgtagctgccttgatgtttataacgttgactaaagcattatataaagtttggattatttgttactgtttagctcagtctgctttattttgattgtcatcaggataaattttcttcttatgtacttgttgcag
                                    || |||||||||||||| |||||||||||||| |||||| | ||| ||||||  ||||||| ||||||||| ||||| || || ||||||||||||| |||||| ||      ||  |  |   ||| || | |    |  |||   |   || |  |||                                                                                                                                 
GGAGCATTGGATGGAGGCCTGGATATTCCTCACAGCGAGAAGAGGTTTGCTGGATTCAAGAAGGACGACAAGCAGTTGGATGCTGATACCCACCGCAGgtacatctatggtggccatgttgctgactacatgaaggtgagttgtgcttgctgctgaacacattatttcatttcctttgttccctcgtgattactgtga-------------------------------------------------------------------------------------------------------------------------------

upper sequence: LOC_Os01g67126.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G163081_T04 (Zea mays), 5'ss of exon 7
TGACAAGAGGTTTGCTGGGTTCAAGAAGGACGAGAAGCAGCTTGATTCTGATATTCACCGCAAGTACATCTACGGTGGGCACGTGGCTGACTACATGAGGgtgagctggcactattagatcaattgttcgtgctgtgggttgtattaggaattatgtagctgccttgatgtttataacgttgactaaagcattatataaagtttggattatttgttactgtttagctcagtctgctttattttgattgtcatcaggataaattttcttcttatgtacttgttgcag
 || |||||||||||||| |||||||||||||| |||||| | ||| ||||||  ||||||| ||||||||| ||||| || || ||||||||||||| |||||| ||    |  | | | ||    |  |    |    | | ||         ||   | |  |||| | || | |   |   |||   |    || ||  ||    |||    | || ||   |   ||| ||    |||| |      |||                               
CGAGAAGAGGTTTGCTGGATTCAAGAAGGACGACAAGCAGTTGGATGCTGATACCCACCGCAGGTACATCTATGGTGGCCATGTTGCTGACTACATGAAGgtgagttgtgcttgct-gctgaacacattatttcatttcctttgttc----cctcgtgattactgtgatatctacatca--gggcaaatattggactagaggctgaccgattctcaattgatttaattgttcttctgctctttgttatgtcccag-------------------------------

upper sequence: LOC_Os01g67126.1 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G090738_T01 (Zea mays), 5'ss of exon 7
TGACAAGAGGTTTGCTGGGTTCAAGAAGGACGAGAAGCAGCTTGATTCTGATATTCACCGCAAGTACATCTACGGTGGGCACGTGGCTGACTACATGAGGgtgagctggcactattagat--caattgttcgtgctgtgggttgtattaggaattatgtagctgccttgatgtttataacgttgactaaagcattatataaagtttggattatttgttactgtttagctcagtctgctttattttgattgtcatcaggataaattttcttcttatgtacttgttgcag
 || |||||||||||||| ||||||||||| || |||||||| ||| ||||||| ||||||||||||||||| |||   || || ||||| || |||| ||| |||||    | ||   |  ||  |  | ||  |        | | | || ||   || |    |  | ||||||  | |  | ||    | | |   |                                                                                       
CGATAAGAGGTTTGCTGGCTTCAAGAAGGATGATAAGCAGCTGGATGCTGATATCCACCGCAAGTACATCTATGGTCTCCATGTTGCTGAGTATATGAAGgtaagctgtgcatgttgcttgccagattatagtttttccccccttgtaatgatttggatatcaatttgtaagtttatttcat-aaatatgtaactgtccca---------------------------------------------------------------------------------------

upper sequence: LOC_Os01g67126.1 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv00s0174g00190.t01 (Vitis vinifera), 5'ss of exon 7
TGACAAGAGGTTTGCTGGGTTCAAGAAGGACGAGAAGCAGCTTGATTCTGATATTCACCGCAAGTACATCTACGGTGGGCACGTGGCTGACTACATGAGGgtgagctggcactattagatcaattgttcgtgctgtggg-ttgt-attaggaattatgtagctgccttgatgtttataacgttgactaaagcattatataaagtttggattatttgttactgtttagctcagtctgctttattttgattgtcatcaggataaattttcttcttatgtacttgttgcag
|||||||||||||||||| ||||  | ||| |  ||||| |||||| ||||| ||||||||||||| ||||  ||||| || || ||||  || |||| |||||| |   |   |  | |    |||| | |  |     |||| |||  ||||  || |        | |  ||     |       || |  | |||    |    || |||| ||||  | | |   | | |||                                                   
TGACAAGAGGTTTGCTGGATTCAGCAGGGATGGTAAGCAACTTGATGCTGATGTTCACCGCAAGTATATCTTTGGTGGCCATGTTGCTGCATATATGACGgtgagatctaa--gtctgcttggatgttaggggggaaaaattgtgattctgaatcctgcattattagcggtacttgattagagactccaatccctctatctcatgcacataatttcttacattgttgagaactatgcag-------------------------------------------------

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|2797187|gb|AA750481.1|AA750481
EST:     ATATTCACCGCAAGTACATCTACGGTGGGCACGTGGCTGACTACATGAGG                         TCTATGGCTGAGGAGGAACCTGAGAAATTCCAAGCCCACTTTAGTGAGTAC
genomic: ATATTCACCGCAAGTACATCTACGGTGGGCACGTGGCTGACTACATGAGGgtgagctggc ... cttgttgcagTCTATGGCTGAGGAGGAACCTGAGAAATTCCAAGCCCACTTTAGTGAGTAC
EST: gi|27577094|gb|CA999788.1|CA999788
EST:     CGCAAGTACATCTACGGTGGGCACGTGGCTGACTACATGAGG                         TCTATGGCTGAGGAGGAACCTGAGAAATTCCAAGCCCACTTTAGTGAGTAC
genomic: CGCAAGTACATCTACGGTGGGCACGTGGCTGACTACATGAGGgtgagctggc ... cttgttgcagTCTATGGCTGAGGAGGAACCTGAGAAATTCCAAGCCCACTTTAGTGAGTAC
EST: gi|88766068|gb|CI775158.1|CI775158
EST:     ATATTCACCGCAAGTACATCTACGGTGGGCACGTGGCTGACTACATGAGG                         TCTATGGCTGAGGAGGAACCTGAGAAATTCCAAGCCCACTTTAGTGAGTAC
genomic: ATATTCACCGCAAGTACATCTACGGTGGGCACGTGGCTGACTACATGAGGgtgagctggc ... cttgttgcagTCTATGGCTGAGGAGGAACCTGAGAAATTCCAAGCCCACTTTAGTGAGTAC
EST: gi|218499062|gb|FG952648.1|FG952648
EST:     ATATTCACCGCAAGTACATCTACGGTGGGCACGTGGCTGACTACATGAGG                         TCTATGGCTGAGGAGGAACCTGAGAAATTCCAAGCCCACTTTAGTGAGTAC
genomic: ATATTCACCGCAAGTACATCTACGGTGGGCACGTGGCTGACTACATGAGGgtgagctggc ... cttgttgcagTCTATGGCTGAGGAGGAACCTGAGAAATTCCAAGCCCACTTTAGTGAGTAC
EST: gi|2443100|gb|C74871.1|C74871
EST:     ATATTCACCGCAAATACATCTACGGTGGGCACGTGGCTGACTACATGAGG                         TCTATNGCTGAGGAGGAACCTGAGAAATTCCAAGCCCACTTTAGTGANTAC
genomic: ATATTCACCGCAAGTACATCTACGGTGGGCACGTGGCTGACTACATGAGGgtgagctggc ... cttgttgcagTCTATGGCTGAGGAGGAACCTGAGAAATTCCAAGCCCACTTTAGTGAGTAC
EST: gi|88741629|gb|CI765137.1|CI765137
EST:     ATATTCACCGCAAGTACATCTACGGTGGGCACGTGGCTGACTACATGAGG                         TCTATGGCTGAGGAGGAACCTGAGAAATTCCAAGCCCACTTTAGTGAGTAC
genomic: ATATTCACCGCAAGTACATCTACGGTGGGCACGTGGCTGACTACATGAGGgtgagctggc ... cttgttgcagTCTATGGCTGAGGAGGAACCTGAGAAATTCCAAGCCCACTTTAGTGAGTAC
EST: gi|218499324|gb|FG966003.1|FG966003
EST:     ATATTCACCGCAAGTACATCTACGGTGGGCACGTGGCTGACTACATGAGG                         TCTATGGCTGAGGAGGAACCTGAGAAATTCCAAGCCCACTTTAGTGAGTAC
genomic: ATATTCACCGCAAGTACATCTACGGTGGGCACGTGGCTGACTACATGAGGgtgagctggc ... cttgttgcagTCTATGGCTGAGGAGGAACCTGAGAAATTCCAAGCCCACTTTAGTGAGTAC
EST: gi|88736334|gb|CI759842.1|CI759842
EST:     ATATTCACCGCAAGTACATCTACGGTGGGCACGTGGCTGACTACATGAGG                         TCTATGGCTGAGGAGGAACCTGAGAAATTCCAAGCCCACTTTAGTGAGTAC
genomic: ATATTCACCGCAAGTACATCTACGGTGGGCACGTGGCTGACTACATGAGGgtgagctggc ... cttgttgcagTCTATGGCTGAGGAGGAACCTGAGAAATTCCAAGCCCACTTTAGTGAGTAC
EST: gi|396941604|gb|HO188261.1|HO188261
EST:     ATATTCACCGCAAGTACATCTACGGTGGGCACGTGGCTGACTACATGAGG                         TCTATGGCTGAGGAGGAACCTGAGAAATTCCAAGCCCACTTTAGTGAGTAC
genomic: ATATTCACCGCAAGTACATCTACGGTGGGCACGTGGCTGACTACATGAGGgtgagctggc ... cttgttgcagTCTATGGCTGAGGAGGAACCTGAGAAATTCCAAGCCCACTTTAGTGAGTAC
EST: gi|4879230|gb|AU063529.1|AU063529
EST:     ATATTCACCGCAAGTACATCTACGGTGGGCACGTGGCTGACTACATGAGG                         TCTATGGCTGAGGAGGAACCTGAGAAATTCCAAGCCCACTTTAGTGAGTAC
genomic: ATATTCACCGCAAGTACATCTACGGTGGGCACGTGGCTGACTACATGAGGgtgagctggc ... cttgttgcagTCTATGGCTGAGGAGGAACCTGAGAAATTCCAAGCCCACTTTAGTGAGTAC
EST: gi|218497228|gb|FG948508.1|FG948508
EST:     ATATTCACCGCAAGTACATCTACGGTGGGCACGTGGCTGACTACATGAGG                         TCTATGGCTGAGGAGGAACCTGAGAAATTCCAAGCCCACTTTAGTGAGTAC
genomic: ATATTCACCGCAAGTACATCTACGGTGGGCACGTGGCTGACTACATGAGGgtgagctggc ... cttgttgcagTCTATGGCTGAGGAGGAACCTGAGAAATTCCAAGCCCACTTTAGTGAGTAC
EST: gi|218486091|gb|FG952686.1|FG952686
EST:     ATATTCACCGCAAGTACATCTACGGTGGGCACGTGGCTGACTACATGAGG                         TCTATGGCTGAGGAGGAACCTGAGAAATTCCAAGCCCACTTTAGTGAGTAC
genomic: ATATTCACCGCAAGTACATCTACGGTGGGCACGTGGCTGACTACATGAGGgtgagctggc ... cttgttgcagTCTATGGCTGAGGAGGAACCTGAGAAATTCCAAGCCCACTTTAGTGAGTAC

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: 75 (upstream exon), 75 (downstream exon)
Score: 384

TGACAAGAGGTTTGCTGGGTTCAAGAAGGACGAGAAGCAGCTTGATTCTGATATTCACCGCAAGTACATCTACGGTGGGCACGTGGCTGACTACATGAGGgtgagctggc ... cttgttgcagTCTATGGCTGAGGAGGAACCTGAGAAATTCCAAGCCCACTTTAGTGAGTACCTCAAGAAGGGAATTGACGCTGATGGCATGGAATCACTGTACAAGAAGG




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