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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTTGATCATGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtatgcactattcaccaaatgatcatctatatccttatcattcatctagcaacaatatttatgtaatctgcag

Basic information

species Oryza sativa
transcript LOC_Os11g04980.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g04980.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA20G28200.1 (Glycine max), 5'ss of exon 6
TGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTTGATCATGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtatgcactattca--ccaaatgatcatctatatccttat-cattcatctagcaacaatatttatgta-atctgcag-------------------
 | ||||| ||||||||||| ||||||||||||||| |||| ||||||||||| ||  | ||||| ||||| || || ||||| || ||||| ||||||||||||   | | ||    |  ||   || | | | ||||   ||  | || |     |  || |  |  | | |||                    
AGTATTGGGTTGTATTTTATTAACAGACCTGAGTGGCTCATTGTTGATCATGCTTGCTCTGCATACTCATTTGTATCAGTGCCTCTGTATGATACTCTTGgtatgttgtctacaatttatctggaaatttcttttcttacatatctaccttggccttaccttcagatttaacagcaagaaactgcttgttctgtag

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA15G34650.1 (Glycine max), 5'ss of exon 2
----------------------TGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTTGATCATGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtat--gcactattcaccaaatgatcatct-atatccttatcattcatctagcaacaatatttatgtaatctgcag
                       | ||||| ||||||||||| ||||||||||||||| |||| ||||||||||| ||  | ||||| ||||| |||   ||   | ||| ||  ||       ||    | ||||    |  |  |  ||  |||| |  |   | ||||||   |   ||                
TTATGGAATCCAAAAGGGCTCTAGTATTGGGTTGTATTTTATTAACAGACCTGAGTGGCTCATTGTTGATCATGCTTGCTCTGCATACTCATTTGTGCAAgttatattttgtg-tacctcaaacattaaaattattgctgagctacttgtcagatattccaactgtacatctaatcatggtag---------------

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GLYMA10G39540.1 (Glycine max), 5'ss of exon 6
TGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTTGATCATGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtatgc-----actattcaccaaatgat-----------catctatatc-----cttatcattc-atctagcaacaatat-ttatgtaatctgcag
 | ||||| ||||||||||| ||||||||||||||| |||| ||||||||||| ||  |  |||| ||||| || || ||||| || ||||| |||||||||| ||     |  ||| | ||    ||           ||| | || |     |||| | |   || || || ||| |  ||   |  |||| ||
AGTATTGGGTTGTATTTTATTAACAGACCTGAGTGGCTCATTGTTGATCATGCTTGCTCTTCATACTCATTTGTATCAGTGCCTCTGTATGATACTCTTGgtacgctgtctataatttatcaggaaatttcttttcttacatgtctaccttggccttaccttctgatttaacagcaagaaattgcttgttctgtag

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT5G27600.1 (Arabidopsis thaliana), 5'ss of exon 6
TGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTTGATCATGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtatgcactattcaccaaatgatca-tctatatccttatcattcatctagcaacaatattt----atgtaat-ctgcag---------
||| ||||  | |||||||| |||||||| |||||| |  | || |||||||| ||||||||||||||||| || ||||| ||  | ||||| || |||||||  || | |  |    ||  |   ||| ||   ||    ||   | |||        ||    || | || || | |         
TGCGTTGGACTCTATTTTATTAACAGACCAGAGTGGTTGGTTGTGGATCATGCTTGTGCAGCATATTCATTTGTCTCTGTTCCTTTATATGATACACTTGgtaaccaatctaaatttgattttttctctttagttttcgagttttgcaagccttgtctcttcttaatatgattcttctggttacgcag

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 5'ss of exon 6
TGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTTGATCATGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtatgca-ctattcaccaaatgatcatctat-atccttatcattcatctagcaacaatatttatgtaa-tctgcag------------------------------------
||  ||||  | |||||||| ||||||||||||||| |||| ||||||||||||||  | |||| |||||  || || || ||  | |||||||||||||||  | |  |  | |    || |   | |||    ||| |   |    | || | |  | |  |  || ||| |                                      
TGTGTTGGCCTATATTTTATCAACAGACCTGAGTGGCTCATTGTTGATCATGCCTGCTCTGCATTTTCATATGTATCAGTTCCTTTATATGACACTCTTGgttcgtaattggttattgtataaaactttatcggacttttgcctagcttggccaaaccactgctacaaatctactaaagcttaacaaagccttgataattgttgctctgcag

upper sequence: LOC_Os11g04980.1 (Oryza sativa), 5'ss of exon 6
lower sequence: PP1S408_23V6.1 (Physcomitrella patens), 5'ss of exon 8
TGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTTGATCATGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtatgcactattcaccaaatgatcatctatatccttatcattcatctagcaacaatatttatgt--aatctgcag-------------------------
||  ||||  | ||  | || ||  || | || ||| ||||    || |  || ||||  || ||||| |  |||||||| |||||||||||||||||||||| ||   |  |  |     |  ||| | ||       | |     |    |  ||||| | |  | |  | |                          
TGTGTTGGAATATACATGATCAATCGAGCAGAATGGGTCATCTCAGAACTAGCATGTGTCGCTTATTCCTATGTGTCTGTTCCACTTTATGACACTCTTGgtaagctgcacccttctctgaaatatcaacattgaacagactagctaaatgtctttatttgtctcgatttcgtaactaatcagactcttagttttgagtt

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|29671403|gb|CB667678.1|CB667678
EST:     CGTGTCTGTGCCACTTTATGACACTCTTG                         GTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTT
genomic: CGTGTCTGTGCCACTTTATGACACTCTTGgtatgcacta ... taatctgcagGTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTT
EST: gi|33676001|gb|CF304240.1|CF304240
EST:     TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTG                         GTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTT
genomic: TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtatgcacta ... taatctgcagGTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTT
EST: gi|58696224|gb|CK084911.1|CK084911
EST:     TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTG                         GTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTT
genomic: TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtatgcacta ... taatctgcagGTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTT
EST: gi|58690407|gb|CK079094.1|CK079094
EST:     TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTG                         GTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTT
genomic: TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtatgcacta ... taatctgcagGTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTT
EST: gi|58611948|gb|CK039660.1|CK039660
EST:     TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTG                         GTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTT
genomic: TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtatgcacta ... taatctgcagGTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTT
EST: gi|33675052|gb|CF303291.1|CF303291
EST:     TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTG                         GTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTT
genomic: TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtatgcacta ... taatctgcagGTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTT
EST: gi|58692164|gb|CK080851.1|CK080851
EST:     TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTG                         GTCCAGATGCAGTTCAGTTCATTGTCAACCATGGGACAGTAGAAGCTATTT
genomic: TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtatgcacta ... taatctgcagGTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTT
EST: gi|58663800|gb|CK052486.1|CK052486
EST:     TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTG                         GTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTT
genomic: TGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtatgcacta ... taatctgcagGTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTT

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: 69 (upstream exon), 68 (downstream exon)
Score: 14

TGCATTGGTTTGTATTTTATAAACAGACCTGAGTGGATCATAGTTGATCATGCCTGTGCAGCATATTCATTCGTGTCTGTGCCACTTTATGACACTCTTGgtatgcacta ... taatctgcagGTCCAGATGCAGTTCAGTTCATTGTCAACCATGCGACAGTAGAAGCTATTTTCTGTGTGCCTCAAACACTAAGCACT




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