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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAAGGAGTCATTGGGAAAAGAGTTGATGAGATGGAATCTGGCTTTCTAATGGCACTTGATTACATGATACAGCTTGCTGAGAAGGATAGTGACAATGAGgtactggaaaaactaatttcacattttgccaaaattgatgtcaactcattcataattttcaaaggatgaatatgttaactgctctcctagctttgttgat...

Basic information

species Oryza sativa
transcript LOC_Os11g23790.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g23790.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G079452_T02 (Zea mays), 5'ss of exon 2
TCAAGGAGTCATTGGGAAAAGAGTTGATGAGATGGAATCTGGCTTTCTAATGGCACTTGATTACATGATACAGCTTGCTGAGAAGGATAGTGACAATGAGgtactggaaaaac------taatttcacattttgccaaaattgatgtcaactcattcataattttcaaaggatgaatatgttaactgctctcctagctttgttgat
|||||||| |||||||| || || ||||||||||| || || ||||| ||||||||||||||||||||||| ||||| ||||||| | || |||||||||| | | | ||| | ||| | || | || || || ||| || || | | | | | | | |||| |||| | |
ACAAGGAGTTATTGGGAAGAGGGTGGATGAGATGGAGTCAGGTTTTCTTATGGCACTTGATTACATGATACAACTTGCACAGAAGGACACAGATGATGAGgtacttggtagtcattgcctaactccaccaagtacctgtttgcataacagcttatttattcttcactaggcgt-----taccactcatttgcctatctttactaa-

upper sequence: LOC_Os11g23790.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA03G22370.1 (Glycine max), 5'ss of exon 2
TCAAGGAGTCATTGGGAAAAGAGTTGATGAGATGGAATCTGGCTTTCTAATGGCACTTGATTACATGATACAGCTTGCTGAGAAGGATAGTGACAATGAGgtac-----tggaaaaactaatttcacattttgccaaaattga--tgtcaactcattcataattttcaaaggatgaatatgttaactgctctcctagctttgttgat
|||||||| ||||| || |||||||||||||||||||| | || | ||||| ||||| |||||||| || ||||||||||| || || || ||||| | || | | | | | | ||| | | | | || | | | ||| | | || | | ||| | || |||
ACAAGGAGTTATTGGAAAGAGAGTTGATGAGATGGAATCCGATTTCATGATGGCCCTTGACTACATGATCCAACTTGCTGAGAATGACCAGGATGATAAGgtatgattttcaaacatatgagattataacttgtttagttaaagttagaaatcaacatgttctgttccatcaagaaagttttgttttgcaattatatctt-------

upper sequence: LOC_Os11g23790.2 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA16G09430.1 (Glycine max), 5'ss of exon 2
TCAAGGAGTCATTGGGAAAAGAGTTGATGAGATGGAATCTGGCTTTCTAATGGCACTTGATTACATGATACAGCTTGCTGAGAAGGATAGTGACAATGAGgtactggaaaaactaatttcacattttgccaaaattgatgtcaactcattcataattttcaaaggatgaatatgttaactgctctcctagctttgttgat-----------
|||||||| ||||| || ||||||||||||||||| |||| || | ||||| ||||| |||||||| |||||||| ||||| || || || ||||| | |||| ||| | ||| || | || || || ||| | ||| | || || | || ||| | || ||||| ||
GCAAGGAGTTATTGGAAAGAGAGTTGATGAGATGGAGTCTGATTTCATGATGGCCCTTGACTACATGATCCAGCTTGCCGAGAATGACCAGGATGATAAGgtatgattataacttgttt---agttt---aagttagaaatctacatgttc----tgttccatcgagaaagtttttgtttgcaattatatttttgt-gacaaatctacatt

upper sequence: LOC_Os11g23790.2 (Oryza sativa), 5'ss of exon 2
lower sequence: AT5G48470.1 (Arabidopsis thaliana), 5'ss of exon 2
TCAAGGAGTCATTGGGAAAAGAGTTGATGAGATGGAATCTGGCTTTCTAATGGCACTTGATTACATGATACAGCTTGCTGAGAAGGATAGTGACAATGAGgtactggaaaaactaatttcacattttgcca--aaattgatgtcaactcattcataattttca---aaggatgaatatgtt-aactgctctcctagctttg-ttgat
|||||||| || |||||||| |||||||| |||||||| || ||| | ||||| |||||||||||||| || ||||| || || || ||| | ||||| ||| |||| |||||| || ||| | || ||| || || | || | || | ||| | ||||| ||| |
ACAAGGAGTTATAGGGAAAAGGGTTGATGAAATGGAATCAGGGTTTATGATGGCTCTTGATTACATGATCCAACTTGCAGACAAAGACCAAGACGAGAAGgta-------aaccaattctgcattttccctctgaatgtacacaaaaatatttctagaattgacttgagttttgctacatagaacgaccaggatagctagaattgct

upper sequence: LOC_Os11g23790.2 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv00s0333g00020.t01 (Vitis vinifera), 5'ss of exon 2
TCAAGGAGTCATTGGGAAAAGAGTTGATGAGATGGAATCTGGCTTTCTAATGGCACTTGATTACATGATACAGCTTGCTGAGAAGGATAGTGACAATGAGgtactggaaaaactaatttcacattttgccaaaattgatgtcaactcattcataattttcaaaggatgaatatgttaactgctctcctagctttgttgat------
||||||||||||||||| ||||||||| | ||||| || || ||| | |||||||| |||||||||||||| |||||||| ||||| || || ||||| | | || || |||||| | ||| || | | | | ||| || | | || | || | ||||||
ACAAGGAGTCATTGGGAAGAGAGTTGATCAAATGGAGTCGGGGTTTATGATGGCACTAGATTACATGATACAACTTGCTGAAAAGGACCAGGATGATAAGgtattt---atttcaagttttcattttt---attttggtgcttgcataattactctttgttaattcccatttgctttatattcctttcatttttgttatcaaaact

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|88575612|gb|CI669757.1|CI669757
EST:     TGGCACTTGATTACATGATACAGCTTGCTGAGAAGGATAGTGACAATGAG                         CGTAAATCTCTCCTTGAGGTAGTCAAGCAGACAGTGCTGGATCATCTCACN
genomic: TGGCACTTGATTACATGATACAGCTTGCTGAGAAGGATAGTGACAATGAGgtactggaaa ... taactggcagCGTAAATCTCTCCTTGAGGTAGTCAAGCAGACAGTGCTGGATCATCTCACA
EST: gi|29615880|gb|CB620892.1|CB620892
EST:     TGGCACTTGATTACATGATACAGCTTGCTGAGAAGGATAGTGACAATGAG                         CGTAAATCTCTCCTTGAGGTAGTCAAGCAGACAGTGCTGGATCATCTCACN
genomic: TGGCACTTGATTACATGATACAGCTTGCTGAGAAGGATAGTGACAATGAGgtactggaaa ... taactggcagCGTAAATCTCTCCTTGAGGTAGTCAAGCAGACAGTGCTGGATCATCTCACA
EST: gi|29673555|gb|CB669830.1|CB669830
EST:     TGGCACTTGATTACATGATACAGCTTGCTGAGAAGGATAGTGACAATGAG                         CGTAAATCTCTCCTTGAGGTAGTCAAGCAGACAGTGCTGGATCATCTCACN
genomic: TGGCACTTGATTACATGATACAGCTTGCTGAGAAGGATAGTGACAATGAGgtactggaaa ... taactggcagCGTAAATCTCTCCTTGAGGTAGTCAAGCAGACAGTGCTGGATCATCTCACA
EST: gi|33658439|gb|CF281052.1|CF281052
EST:     TGGCACTTGATTACATGATACAGCTTGCTGAGAAGGATAGTGACCATGAG                         CGTAAATCTCTCC
genomic: TGGCACTTGATTACATGATACAGCTTGCTGAGAAGGATAGTGACAATGAGgtactggaaa ... taactggcagCGTAAATCTCTCC

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), 60 (downstream exon)
Score: 29

TCAAGGAGTCATTGGGAAAAGAGTTGATGAGATGGAATCTGGCTTTCTAATGGCACTTGATTACATGATACAGCTTGCTGAGAAGGATAGTGACAATGAGgtactggaaa ... taactggcagCGTAAATCTCTCCTTGAGGTAGTCAAGCAGACAGTGCTGGATCATCTCACAAAAAAATGCCCTCCACAT




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