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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTCGGCGATGAGCTGCATCACTCTGGATGGAACGCTTGCAGTTCTTGCCATGGTGATCCATCGGCTAGCCGCCGTTTCTTGATTCTGCCTTCGTTGCTgtgagtgttaatgtggctatatttagatggatggatgaatcctcgtatctgttgatgttaaacagcgaactggatttgtaaattgctccaatgtctgttgcag

Basic information

species Oryza sativa
transcript LOC_Os01g68770.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g68770.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G138686_T01 (Zea mays), 5'ss of exon 7
ATGTCGGCGATGAGCTGCATCACTCTGGATGGAACGCTTGCAGTTCTTGCCATGGTGATCCATCGGCTAGCCGCCGTTTCTTGATTCTGCCTTCGTTGCTgtgagtgttaatgtggctatatttagatggatggatgaatcc-----tcgtatctgttga-tgttaaacagcgaactgg--atttgtaa-attgctccaatgtctgtt-gcag
|  |||| ||||||||||||||||| || |||||| | ||||| ||  ||||||| || |||||||| |  ||||| ||| |||| ||||||||||||||||||||  |        || |   |||||    |||||||         || |   | || || | | |   | ||||   || |||      ||| ||||| || || ||||
ACATCGGTGATGAGCTGCATCACTCGGGCTGGAACTCCTGCAGCTCCAGCCATGGCGACCCATCGGCCAAGCGCCGCTTCCTGATCCTGCCTTCGTTGCTgtgagtactgcatcaaataaacggagatgatcagatgaatatatcagctgtcttactcgactgctgacctcaggactgagaatctgtggtgccgcttcaatggctatttgcag

upper sequence: LOC_Os01g68770.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G114484_T01 (Zea mays), 5'ss of exon 2
ATGTCGGCGATGAGCTGCATCACTCTGGATGGAACGCTTGCAGTTCTTGCCATGGTGATCCATCGGCTAGCCGCCGTTTCTTGATTCTGCCTTCGTTGCTgtgagtgttaatgtggctatatttagatggatggatgaatcc-----tcgtatctgttga-tgttaaacagcgaactgg--atttgtaa-attgctccaatgtctgtt-gcag
|  ||||||| |||||||||||||| || |||||| | ||||| || ||||| || || |||||||| |  ||||| ||| |||| ||||||||||||||||||||  |        || |   |||||    |||||||         || |   | || || | | |   | ||||   || |||      ||| ||||| || || ||||
ACATCGGCGACGAGCTGCATCACTCGGGCTGGAACTCCTGCAGCTCCTGCCACGGCGACCCATCGGCCAAGCGCCGCTTCCTGATCCTGCCTTCGTTGCTgtgagtactgcatcaaataaacggagatgatcagatgaatatatcagctgtcttactcgactgctgacctcaggactgagaatctgtggtgccgcttcaatggctatttgcag

upper sequence: LOC_Os01g68770.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G103812_T02 (Zea mays), 5'ss of exon 2
ATGTCGGCGATGAGCTGCATCACTCTGGATGGAACGCTTGCAGTTCTTGCCATGGTGATCCATCGGCTAGCCGCCGTTTCTTGATTCTGCCTTCGTTGCTgtgagtgttaatgtggctatatttagatggatggatgaatcc-----tcgtatctgttga-tgttaaacagcgaactgg--atttgtaa-attgctccaatgtctgtt-gcag
|  ||||||| ||||||||||||||||| |||||| | ||||| || ||||| ||||| |||||||| |  ||||| ||| |||| |||||||| |||||||||||  |        || ||| |||||    |||||||         || |   | || || | |||   | ||||   || |||      ||| ||||| || || ||||
ACATCGGCGACGAGCTGCATCACTCTGGCTGGAACTCCTGCAGCTCCTGCCACGGTGACCCATCGGCCAAGCGCCGCTTCCTGATCCTGCCTTCCTTGCTgtgagtactgcatcaaataaattgagatgatcagatgaatatatcagctgtcttactcgactgctgaactcaggactgagaatctgtggtgccgcttcaatggctatttgcag

upper sequence: LOC_Os01g68770.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G117726_T01 (Zea mays), 5'ss of exon 1
ATGTCGGCGATGAGCTGCATCACTCTGGATGGAACGCTTGCAGTTCTTGCCATGGTGATCCATCGGCTAGCCGCCGTTTCTTGATTCTGCCTTCGTTGCTgtgagtgttaat---gtggctata-tttagatggat-ggatgaatcctcgtatctgttgatgttaaacagcgaactggatttgtaa-attgctccaatgtctgtt-gcag
|  ||||||||||||||||||||||||| |||||| | ||||| || ||||||||||||||||| || |  || |  ||| |||| || ||||| ||| ||||||| |  |    ||||  ||  | |  ||  || | |||||||       ||| |||  | |   |  ||   | || |||    | ||| |||||  | || ||||
ACATCGGCGATGAGCTGCATCACTCTGGCTGGAACTCGTGCAGCTCCTGCCATGGTGATCCATCAGCAAAGCGTCACTTCCTGATCCTTCCTTCATTGTTgtgagtatagaataagtggacatggtctgaatcaattgaatgaatc-----ggctgctgacctcagg-actga---gaatatgtggtgtggcttcaatggttatttgcag

upper sequence: LOC_Os01g68770.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM5G837351_T01 (Zea mays), 5'ss of exon 2
---ATGTCGGCGATGAGCTGCATCACTCTGGATGGAACGCTTGCAGTTCTTGCCATGGTGATCCATCGGCTAGCCGCCGTTTCTTGATTCTGCCTTCGTTGCTgtgagtgttaatgtggctatatttagatggatggatgaatcctcgtatctgttgatgttaaacagcgaactggatttgtaaattgctccaatgtctgttgcag
    ||      |  ||||| || ||  || |  ||  | ||      |   |  |      | |    ||  | |  | | |         |  ||       |  | | | |    |||  ||     ||| ||||   |  |  | | || |||   |      | || |   ||  | |||                     
GCACTGGAATTAACAAGCTGGATTACCTTGCAACGATGGATTTGGACCCCGACTCT-----CCTACATACTCCCAGgtgatccacaggctctcagtcacccacatcggcgatga----gctgcatcactctggctgga---actcgtgcagctcttgccat-----ggtgatcc--atcagcaaagcatc----------------

upper sequence: LOC_Os01g68770.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G058930_T01 (Zea mays), 5'ss of exon 5
ATGTCGGCGATGAGCTGCATCACTCTGGATGGAACGCTTGCAGTTCTTGCCATGGTGATCCATCGGCTAGCCGCCGTTTCTTGATTCTGCCTTCGTTGCTgtgagtgttaat---gtggctata-tttagatggat-ggatgaatcctcgtatctgttgatgttaaacagcgaactggatttgtaa-attgctccaatgtctgtt-gcag
|  ||||||||||||||||||||||||| |||||| | ||||| || ||||||||||||||||| || |  || || ||| |||| || |||||||||||||||||    |    ||||  ||  | |  ||  || | |||||||       ||| |||  | |   |  ||   | || |||    | ||| |||||  | || ||||
ACATCGGCGATGAGCTGCATCACTCTGGCTGGAACTCGTGCAGCTCCTGCCATGGTGATCCATCAGCAAAGCGTCGCTTCCTGATCCTACCTTCGTTGCTgtgagtacagaataagtggacatggtctgaatcaattgaatgaatc-----ggctgctgacctcagg-actga---gaatatgtggtgtggcttcaatggttatttgcag

upper sequence: LOC_Os01g68770.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G171376_T01 (Zea mays), 5'ss of exon 2
ATGTCGGCGATGAGCTGCATCACTCTGGATGGAACGCTTGCAGTTCTTGCCATGGTGATCCATCGGCTAGCCGCCGTTTCTTGATTCTGCCTTCGTTGCTgtgagtgttaatgtggctatatttagatggatggatgaatcc-----tcgtatctgttga-tgttaaacagcgaactgg--atttgtaa-attgctccaatgtctgtt-gcag
|  |||||||  ||||||||||||| || |||||| | ||||| || ||||| || || |||||||| |  ||||| ||| |||| ||||||||||||||||||||  |        || |   |||||    |||||||         || |   | || || | | |   | ||||   || |||      ||| ||||| || || ||||
ACATCGGCGACAAGCTGCATCACTCGGGCTGGAACTCCTGCAGCTCCTGCCACGGCGACCCATCGGCCAAGCGCCGCTTCCTGATCCTGCCTTCGTTGCTgtgagtactgcatcaaataaacggagatgatcagatgaatatatcagctgtcttactcgactgctgacctcaggactgagaatctgtggtgccgcttcaatggctatttgcag

upper sequence: LOC_Os01g68770.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT4G14040.1 (Arabidopsis thaliana), 5'ss of exon 2
ATGTCGGCGATGAGCTGCATCACTCTGGATGGAACGCTTGCAGTTCTTGCCATGGTGATCCATCGGCTAGCCGCCGTTTCTTGATTCTGCCTTCGTTGCTgtgagtgttaatgtggctatatttagatggatggatgaatcctcgtatctgttgatgttaaacagcgaactggatttgtaaattgctccaatgtctgt-tgcag
|| | || |||||||| || ||| |||| |||||| ||||||| ||||||||||||||| | || |||    | |||| | |  |  | ||            ||  |||||||    ||  ||| || ||          |||  || | |||||| | ||  |   |||  |    ||  || ||    ||| ||  || ||
ATATAGGAGATGAGCTTCACCACACTGGTTGGAACTCTTGCAGCTCTTGCCATGGTGATGCTTCTGCTGATAGACGTTACCTTGTCTTACC------------AGGCTTAATgtaag-atccttacattgacc------ctctcacatttcttgatgatgaattg---actaaaa--atatgtttctttcttgtttgaatgaag

upper sequence: LOC_Os01g68770.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT4G14030.1 (Arabidopsis thaliana), 5'ss of exon 2
ATGTCGGCGATGAGCTGCATCACTCTGGATGGAACGCTTGCAGTTCTTGCCATGGTGATCCATCGGCTAGCCGCCGTTTCTTGATTCTGCCTTCGTTGCTgtgagtgttaatgtggctatatttagatggatggatgaatcctcgtatctgttgatgttaaacagcgaactggatttgtaaattgctccaatgtctgttgcag
 ||| || |||||||| ||||| ||||| |||||| |||| |||||||||||||||||| | || | |    | ||||   |  |  | || ||  |  ||| |   ||    |   | | |||   |       |  |||    | |  |||  |||| |    |  | | |||    | |||| |   |||          
TTGTTGGTGATGAGCTTCATCATTCTGGTTGGAACTCTTGTAGTTCTTGCCATGGTGATGCTTCTGTTGATAGACGTTATCTCGTGTTACCGTCTCTTATgtaaagatt--ctttagtctttttgattcttctcttatatctctctgtgagtt--tgtttattgactgaatagat--aaatattgttttgatgaag-------

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|11442705|gb|BF430608.1|BF430608
EST:     CATGGTGATCCATCGGCTAGCCGCCGTTTCTTGATTCTGCCTTCGTTGCT                         GTCTGGCCGTGTGTATGTCGTTGACACGCTGAAGGACCCAAGGGCGCCTGC
genomic: CATGGTGATCCATCGGCTAGCCGCCGTTTCTTGATTCTGCCTTCGTTGCTgtgagtgtta ... tctgttgcagGTCTGGCCGTGTGTATGTCGTTGACACGCTGAAGGACCCAAGGGCGCCTGC
EST: gi|29644288|gb|CB649295.1|CB649295
EST:     CATGGTGATCCATCGGCTAGCCGCCGTTTCTTGATTCTGCCTTCGTTGCT                         GTCTGGCCGTGTGTATGTCGTTGACACGCTGAAGGACCCAAGGGCGCCTGC
genomic: CATGGTGATCCATCGGCTAGCCGCCGTTTCTTGATTCTGCCTTCGTTGCTgtgagtgtta ... tctgttgcagGTCTGGCCGTGTGTATGTCGTTGACACGCTGAAGGACCCAAGGGCGCCTGC
EST: gi|58669621|gb|CK058307.1|CK058307
EST:     CATGGTGATCCATCGGCTAGCCGCCGTTTCTTGATTCTGCCTTCGTTGCT                         GTCTGGCCGTGTGTATGTCGTTGACACGCTGAAGGACCCAAGGGCGCCTGC
genomic: CATGGTGATCCATCGGCTAGCCGCCGTTTCTTGATTCTGCCTTCGTTGCTgtgagtgtta ... tctgttgcagGTCTGGCCGTGTGTATGTCGTTGACACGCTGAAGGACCCAAGGGCGCCTGC
EST: gi|29641234|gb|CB646241.1|CB646241
EST:     CATGGTGATCCATCGGCTAGCCGCCGTTTCTTGATTCTGCCTTCGTTGCT                         GTCTGGCCGTGTGTATGTCGTTGACACGCTGAAGGACCCAAGGGCGCCTGC
genomic: CATGGTGATCCATCGGCTAGCCGCCGTTTCTTGATTCTGCCTTCGTTGCTgtgagtgtta ... tctgttgcagGTCTGGCCGTGTGTATGTCGTTGACACGCTGAAGGACCCAAGGGCGCCTGC
EST: gi|29642049|gb|CB647056.1|CB647056
EST:     CATGGTGATCCATCGGCTAGCCGCCGTTTCTTGATTCTGCCTTCGTTGCT                         GTCTGGCCGTGTGTATGTCGTTGACACGCTGAAGGACCCAAGGGCGCCTGC
genomic: CATGGTGATCCATCGGCTAGCCGCCGTTTCTTGATTCTGCCTTCGTTGCTgtgagtgtta ... tctgttgcagGTCTGGCCGTGTGTATGTCGTTGACACGCTGAAGGACCCAAGGGCGCCTGC
EST: gi|33677794|gb|CF306033.1|CF306033
EST:     CATGGTGATCCATCGGCTAGCCGCCGTTTCTTGATTC-GTCTTCGTTGCT                         GTCTGGCCGTGTGTATGTCGTTGACACGCTGAAGGACCCAAGGGCGCCTGC
genomic: CATGGTGATCCATCGGCTAGCCGCCGTTTCTTGATTCTGCCTTCGTTGCTgtgagtgtta ... tctgttgcagGTCTGGCCGTGTGTATGTCGTTGACACGCTGAAGGACCCAAGGGCGCCTGC
EST: gi|29660708|gb|CB656983.1|CB656983
EST:     CATGGTGATCCATCGGCTAGCCGCCGTTTCTTGATTCTGCCTTCGTTGCT                         GTCTGGCCGTGTGTATGTCGTTGACACGCTGAAGGACCCAAGGGCGCCTGC
genomic: CATGGTGATCCATCGGCTAGCCGCCGTTTCTTGATTCTGCCTTCGTTGCTgtgagtgtta ... tctgttgcagGTCTGGCCGTGTGTATGTCGTTGACACGCTGAAGGACCCAAGGGCGCCTGC
EST: gi|14571328|gb|BI118696.1|BI118696
EST:     CATGGTGATCCATCGGCTAGCCGCCGTTTCTTGATTCTGCCTTCGTTGCT                         GTCTGGCCGTGTGTATGTCGTTGACACGCTGAAGGACCCAAGGGCGCCTGC
genomic: CATGGTGATCCATCGGCTAGCCGCCGTTTCTTGATTCTGCCTTCGTTGCTgtgagtgtta ... tctgttgcagGTCTGGCCGTGTGTATGTCGTTGACACGCTGAAGGACCCAAGGGCGCCTGC

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: 37 (upstream exon), 74 (downstream exon)
Score: 28

ATGTCGGCGATGAGCTGCATCACTCTGGATGGAACGCTTGCAGTTCTTGCCATGGTGATCCATCGGCTAGCCGCCGTTTCTTGATTCTGCCTTCGTTGCTgtgagtgtta ... tctgttgcagGTCTGGCCGTGTGTATGTCGTTGACACGCTGAAGGACCCAAGGGCGCCTGCCTTGCATAAGGTGGTCGAGGCTGAGGACATTGCTGAGAAGACAGGGCTT




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