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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGGCGCGCAAGAAGATCCGGGAGTACGACTCCAAGCGCCTCCTCAAGGAGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAGgttcgattctttcttcttcttcttcttgatctcaaagttttagcttttgtttccggtgatccctggctggtttggcgttttttcatttttggcctgattt...

Basic information

species Oryza sativa
transcript LOC_Os11g47330.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g47330.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G107082_T01 (Zea mays), 5'ss of exon 1
CATGGCGCGCAAGAAGATCCGGGAGTACGACTCCAAGCGCCTCCTCAAGGAGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAGgttcgattctttcttcttcttcttcttgatctcaaagttttagcttttgtttccggtgatccctggctggtttggcgttttttcatttttggcctgattt----
||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||| |||||||||   ||||||||||||||||| |  | | | |   |       ||   || ||     ||    | ||   |||| | | |||  | |   |||   | |  |  | ||| |  | ||     
CATGGCGCGCAAGAAGATCCGGGAGTACGACTCCAAGCGCCTCCTCAGGGAGCACCTCAAGCGCCTCGCCGGCATCGACCTCACCATCCTCTCCGCCCAGgt-cagtccgtccgcgtcgcctccctccctcccaccccctttctgtctga--ccggcg-ttcctctccgcactggatctgtcgccgtgttgtctcggttcacgt

upper sequence: LOC_Os11g47330.1 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv14s0060g00550.t01 (Vitis vinifera), 5'ss of exon 1
CATGGCGCGCAAGAAGATCCGGGAGTACGACTCCAAGCGCCTCCTCAAGGAGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAGgtt--cgattctttcttcttcttcttcttgatctcaaagttttagcttttgtttccggtgatccctggctggtttgg-cgttttttcatttttggcctgattt
||||||  | ||||||||| | ||||||||||||||| | || |||||||| ||||||||| | ||||| || ||||| |||||||||  ||| || ||||||  || |   |||||||||  ||  | |||| |    ||||   | |  ||| |  ||||  | |  |  |||   ||   ||  |   ||    | ||  
CATGGCCAGGAAGAAGATCAGAGAGTACGACTCCAAGAGGCTTCTCAAGGATCACCTCAAGAGGCTCGCTGGCATCGATCTCCAGATCTGCTCAGCTCAGgtttccgctctcttcttcttccactcttggatc-cgtgtttttttttgtctttttctatgatgtcagcataatttcatcgaaattctacgattccttttat--

upper sequence: LOC_Os11g47330.1 (Oryza sativa), 5'ss of exon 1
lower sequence: PP1S7_156V6.1 (Physcomitrella patens), 5'ss of exon 2
CATGGCGCGCAAGAAGATCCGGGAGTACGACTCCAAGCGCCTCCTCAAGGAGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAGgttcgattctttcttcttcttcttct----tgatctcaaagttttagcttttgtt-----tccggtgatccctggctggtttggcgttt-tttcatttttggcctgattt----------------------------------
|||||| |||||||| ||||| ||||| |||||||||||| |||| || |||||| | |||   || || || || ||| |    ||    ||||||||||| | ||||||  |  |     |       |||        | | ||   |||||     || | |  | | |  |     |    |   ||| | |||  |  ||                                      
CATGGCTCGCAAGAAAATCCGAGAGTATGACTCCAAGCGCATCCTGAAAGAGCACTTGAAGAAGCTTGCTGGCATTGACATTGCCATAAAATCCGCCCAGgtgctattcttggtagtcaaattgacggagtgagtgatgtatatcagtcgttgttgactctctgctattacatatcaaaacttaaatacgtttgactttcagggtgcacccagtgtaatctatgtgctaccttggtccttgcag

upper sequence: LOC_Os11g47330.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ37257 (Selaginella moellendorffii), 5'ss of exon 1
CATGGCGCGCAAGAAGATCCGGGAGTACGACTCCAAGCGCCTCCTCAAGGAGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAGgttcgattctttcttcttcttcttcttgatctcaaagttttagctt-ttgtttccggtgatccctggctggtttggcgttttttcatttttggcctgattt
||||||  | ||||||||||| ||||| |||||||||||| | |||||| |||||||||||||  | ||  | |||||  |   | |||  ||||| |||||   |||  ||  |  || | || || |  |   |   |||   | | |||| |  |         || | | |                          
CATGGCCAGGAAGAAGATCCGTGAGTATGACTCCAAGCGCTTGCTCAAGCAGCACCTCAAGCGATTGGCGAGCATCGATTTGGCGCTCCATTCCGCGCAGgtagaatttatttcttgtcgtgtttttcaaattgcatcgttactctatcgttttcttttgctttgctcttgatag--------------------------

upper sequence: LOC_Os11g47330.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ27687 (Selaginella moellendorffii), 5'ss of exon 1
CATGGCGCGCAAGAAGATCCGGGAGTACGACTCCAAGCGCCTCCTCAAGGAGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAGgttcgattctttcttcttcttct---tcttgatctcaaagttttagcttttgtttccggtgatccctggctggtttggcgttttttcatttttggcctgattt
 |||||  | ||||||||||| |||||||||||||||||| | |||||| ||||||||||||| || ||  | |||||  |   | |||  ||||| |||||   |||  ||  |  |||      || || | |  || ||   ||||   | ||   || ||  |      |||    ||| ||   | |||         
TATGGCCAGGAAGAAGATCCGTGAGTACGACTCCAAGCGCTTGCTCAAGCAGCACCTCAAGCGACTGGCGAGCATCGATTTGGCGCTCCATTCCGCGCAGgtagaatttatttcttatctgtagtgtcgtgtttttcaaatt---gcttcgttctctattgttcttt------tttattttttctttgctcttgatag-----

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|88355914|gb|CI653324.1|CI653324
EST:     AGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAG                         GTTACACAATCGACGGACTTCACAGAGCTGGTAAACCAGCAGCCATGGCTG
genomic: AGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAGgttcgattct ... ttgtaaaaagGTTACACAATCGACGGACTTCACAGAGCTGGTAAACCAGCAGCCATGGCTG
EST: gi|569081|gb|D39930.1|D39930
EST:     AGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAG                         GTTACACAATCGACGGACTTCACAGAGCTGGTAAACCAGCAGCCATGGCTG
genomic: AGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAGgttcgattct ... ttgtaaaaagGTTACACAATCGACGGACTTCACAGAGCTGGTAAACCAGCAGCCATGGCTG
EST: gi|117247393|gb|CT848567.1|CT848567
EST:     AGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAG                         GTTACACAATCGACGGACTTCACAGAGCTGGTAAACCAGCAGCCATGGCTG
genomic: AGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAGgttcgattct ... ttgtaaaaagGTTACACAATCGACGGACTTCACAGAGCTGGTAAACCAGCAGCCATGGCTG
EST: gi|33670036|gb|CF298275.1|CF298275
EST:     AGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAG                         GTTACACAATCGACGGACTTCACAGAGCTGGTAAACCAGCAGCCATGGCTG
genomic: AGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAGgttcgattct ... ttgtaaaaagGTTACACAATCGACGGACTTCACAGAGCTGGTAAACCAGCAGCCATGGCTG
EST: gi|8856182|gb|AU093500.1|AU093500
EST:     AGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAG                         GTTACACAATCGACGGACTTCACAGAGCTGGTAAACCAGCAGCCATGGCTG
genomic: AGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAGgttcgattct ... ttgtaaaaagGTTACACAATCGACGGACTTCACAGAGCTGGTAAACCAGCAGCCATGGCTG
EST: gi|33671919|gb|CF300158.1|CF300158
EST:     AGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAG                         GTTACACAATCGACGGACTTCACAGAGCTGGTAAACCAGCAGCCATGGCTG
genomic: AGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAGgttcgattct ... ttgtaaaaagGTTACACAATCGACGGACTTCACAGAGCTGGTAAACCAGCAGCCATGGCTG
EST: gi|33657822|gb|CF280436.1|CF280436
EST:     AGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAG                         GTTACACAATCGACGGACTTCACAGAGCTGGTAAACCAGCAGCCATGGCTG
genomic: AGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAGgttcgattct ... ttgtaaaaagGTTACACAATCGACGGACTTCACAGAGCTGGTAAACCAGCAGCCATGGCTG
EST: gi|88387140|gb|CI577926.1|CI577926
EST:     AGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAG                         GTTACACAATCGACGGACTTCACAGAGCTGGTAAACCAGCAGCCATGGCTG
genomic: AGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAGgttcgattct ... ttgtaaaaagGTTACACAATCGACGGACTTCACAGAGCTGGTAAACCAGCAGCCATGGCTG
EST: gi|88826010|gb|CI776575.1|CI776575
EST:     AGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAG                         GTTACACAATCGACGGACTTCACAGAGCTGGTAAACCAGCAGCCATGGCTG
genomic: AGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAGgttcgattct ... ttgtaaaaagGTTACACAATCGACGGACTTCACAGAGCTGGTAAACCAGCAGCCATGGCTG
EST: gi|88314520|gb|CI606588.1|CI606588
EST:     AGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAG                         GTTACACAATCGACGGACTTCACAGAGCTGGTAAACCAGCAGCCATGGCTG
genomic: AGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAGgttcgattct ... ttgtaaaaagGTTACACAATCGACGGACTTCACAGAGCTGGTAAACCAGCAGCCATGGCTG
EST: gi|38481987|gb|CF966050.1|CF966050
EST:     AGCGGCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCGCAG                         GTTACACAATCGACGGACTTCACAGAGCTGGTAAACCAGCAGCCATGGCTG
genomic: AGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAGgttcgattct ... ttgtaaaaagGTTACACAATCGACGGACTTCACAGAGCTGGTAAACCAGCAGCCATGGCTG
EST: gi|88734257|gb|CI757765.1|CI757765
EST:     AGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAG                         GTTACACAATCGACGGACTTCACAGAGCTGGTAAACCAGCAGCCATGGCTG
genomic: AGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAGgttcgattct ... ttgtaaaaagGTTACACAATCGACGGACTTCACAGAGCTGGTAAACCAGCAGCCATGGCTG
EST: gi|88423731|gb|CI617083.1|CI617083
EST:     AGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAG                         GTTACACAATCGACGGACTTCACAGAGCTGGTAAACCAGCAGCCATGGCTG
genomic: AGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAGgttcgattct ... ttgtaaaaagGTTACACAATCGACGGACTTCACAGAGCTGGTAAACCAGCAGCCATGGCTG
EST: gi|88342329|gb|CI645851.1|CI645851
EST:     AGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAG                         GTTACACAATCGACGGACTTCACAGAGCTGGTAAACCAGCAGCCATGGCTG
genomic: AGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAGgttcgattct ... ttgtaaaaagGTTACACAATCGACGGACTTCACAGAGCTGGTAAACCAGCAGCCATGGCTG
EST: gi|88688256|gb|CI731832.1|CI731832
EST:     AGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAG                         GTTACACAATCGACGGACTTCACAGAGCTGGTAAACCAGCAGCCATGGCTG
genomic: AGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAGgttcgattct ... ttgtaaaaagGTTACACAATCGACGGACTTCACAGAGCTGGTAAACCAGCAGCCATGGCTG
EST: gi|88570314|gb|CI661489.1|CI661489
EST:     AGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAG                         GTTACACAATCGACGGACTTCACAGAGCTGGTAAACCAGCAGCCATGGCTG
genomic: AGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAGgttcgattct ... ttgtaaaaagGTTACACAATCGACGGACTTCACAGAGCTGGTAAACCAGCAGCCATGGCTG

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: 21

CATGGCGCGCAAGAAGATCCGGGAGTACGACTCCAAGCGCCTCCTCAAGGAGCACCTCAAGCGCCTCGCCGGTATCGACCTCCAGATCCTCTCCGCCCAGgttcgattct ... ttgtaaaaagGTTACACAATCGACGGACTTCACAGAGCTGGTAAACCAGCAGCCATGGCTGTCAACCATGAAGTTGGTCGTGAAGCCCGACATGCTGTTCGGGAAGCGTG




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