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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTAGTATATACAGCAAGACCACATGCCCCAAGATCAGAAAAGGTTGTTGGTATAGGATTTCAGCCTGGGTTTGATCCCTACAAGgtaaatcctccctctttgtgcacatcttctgtatttcttgtagttttaattgttagagcagccaattttttagaactttatgggattatttgagctttacagagctccctttttgttatttatgcaattacag

Basic information

species Oryza sativa
transcript LOC_Os11g01872.1
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g01872.1 (Oryza sativa), 5'ss of exon 21
lower sequence: GRMZM2G048067_T03 (Zea mays), 5'ss of exon 16
GCTAGTATATACAGCAAGACCACATGCCCCAAGATCAGAAAAGGTTGTTGGTATAGGATTTCAGCCTGGGTTTGATCCCTACAAGgtaaatcctccctctttgtgcacatcttctgtatttcttgtagttttaattgttagagcagccaattttttagaactttatgggattatttgagctttacagagctcccttt--ttgttatttatgcaattacag---------
| | || ||||| || || ||||| || |||||| ||||||||||||| || ||||| ||||| |||||||||||||| ||||||||||  | ||   | ||      || |||| |||||            ||||||  |||| | || || ||         ||   ||  || |||||||||   ||| ||||  ||| || | ||  | |||  |         
GGTTGTCTATACGGCCAGGCCACACGCACCAAGAACAGAAAAGGTTGTAGGCATAGGGTTTCAACCTGGGTTTGATCCTTACAAGgtaa--catcttgcattac---tatgttctatattttc----------attgttgaagcaactaagttattttctgggcttgcttttgcttaagctttacaattctctctttggttggtact-atttatttatgggtatgacag

upper sequence: LOC_Os11g01872.1 (Oryza sativa), 5'ss of exon 21
lower sequence: GRMZM2G048067_T04 (Zea mays), 5'ss of exon 1
---------------GCTAGTATATACAGCAAGACCACATGCCCCAAGATCAGAAAAGGTTGTTGGTATAGGATTTCAGCCTGGGTTTGATCCCTACAAGgtaaatcctccctctttgtgcacatcttctgtatttcttgtagttttaattgttagagcagccaattttttagaactttatgggattatttgagctttacagagctcccttt--ttgttatttatgcaattacag---------
               | | || ||||| || || ||||| || |||||| ||||||||||||| || ||||| ||||| |||||||||||||| ||||||||||  | ||   | ||      || |||| |||||            ||||||  |||| | || || ||         ||   ||  || |||||||||   ||| ||||  ||| || | ||  | |||  |         
TTTTCTATACTGTAGGGTTGTCTATACGGCCAGGCCACACGCACCAAGAACAGAAAAGGTTGTAGGCATAGGGTTTCAACCTGGGTTTGATCCTTACAAGgtaa--catcttgcattac---tatgttctatattttc----------attgttgaagcaactaagttattttctgggcttgcttttgcttaagctttacaattctctctttggttggtact-atttatttatgggtatgacag

upper sequence: LOC_Os11g01872.1 (Oryza sativa), 5'ss of exon 21
lower sequence: GRMZM2G460090_T01 (Zea mays), 5'ss of exon 13
---GCTAGTATATACAGCAAGACCACATGCCCCAAGATCAGAAAAGGTTGTTGGTATAGGATTTCAGCCTGGGTTTGATCCCTACAAGgtaaatcctccctctttgtgcacatcttctgtatttcttgtagttttaattgttagagcagccaattt--tttagaactttatgggattatttgagctttacagagctccctttt-tgttatttatgcaattacag
   ||  || |||   || || || |||||||||||| ||||||||||||| || ||||| |||||||||||||||||||| ||| ||||||||  | ||  ||  |   |||      |||| ||    || || ||||||  |||  |  || |  | || | || | |||| ||   | | |||||||  |||||||||| | |||||||||  || ||||
TAGGCCTGTCTATGTGGCCAGGCCGCATGCCCCAAGAACAGAAAAGGTTGTGGGCATAGGGTTTCAGCCTGGGTTTGATCCATACGAGgtaaatagttccatttc-tttgcattgc---tattcct----gtcttcattgttgaagctactgatctattctatagctgtttgggctttcctaatctttacaacgctcccttttgtattatttatggtatcacag

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|58681403|gb|CK070090.1|CK070090
EST:     CAGAAAAGGTTGTTGGTATAGGATTTCAGCCTGGGTTTGATCCCTACAAG                         ATTGTAAGTGCATCTCAAGCTGGAGACATTCAGTTCCTTGATGTTAGAAGG
genomic: CAGAAAAGGTTGTTGGTATAGGATTTCAGCCTGGGTTTGATCCCTACAAGgtaaatcctc ... gcaattacagATTGTAAGTGCATCTCAAGCTGGAGACATTCAGTTCCTTGATGTTAGAAGG
EST: gi|58590297|gb|CF988605.1|CF988605
EST:     CAGAAAAGGTTGTTGGTATAGGATTTCAGCCTGGGTGTGATCCCTACAAG                         ATTGTAAGTGCATCTCAAGCTGGAGACATTCAGTTCCTTGATGTTAGAAGG
genomic: CAGAAAAGGTTGTTGGTATAGGATTTCAGCCTGGGTTTGATCCCTACAAGgtaaatcctc ... gcaattacagATTGTAAGTGCATCTCAAGCTGGAGACATTCAGTTCCTTGATGTTAGAAGG
EST: gi|29667221|gb|CB663496.1|CB663496
EST:     CAGAAAAGGTTGTTGGTATAGGATTTCAGCCTGGGTTTGATCCCTACAAG                         ATTGTAAGTGCATCTCAAGCTGGAGACATTCAGTTCCTTGATGTTAGAAGG
genomic: CAGAAAAGGTTGTTGGTATAGGATTTCAGCCTGGGTTTGATCCCTACAAGgtaaatcctc ... gcaattacagATTGTAAGTGCATCTCAAGCTGGAGACATTCAGTTCCTTGATGTTAGAAGG

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), 54 (downstream exon)
Score: 19

GCTAGTATATACAGCAAGACCACATGCCCCAAGATCAGAAAAGGTTGTTGGTATAGGATTTCAGCCTGGGTTTGATCCCTACAAGgtaaatcctc ... gcaattacagATTGTAAGTGCATCTCAAGCTGGAGACATTCAGTTCCTTGATGTTAGAAGGGCATCTGAACCCTACCTCACTATTGAAGCACATAGGGGTTCATTAATGG




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