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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttcatttctgatatgttttctttcaatgtttaacgaaatttgttctcttcccatgtgcaaccatggtttcttgttctctggcttgctactatatttgtaattctttctagctttcttattaagatctagcagttagtacattctgaggtatttatgttacgatctgtttgtgcagTGACGCATCTTTTGGTTATCCTGGAGGCCCCACCTTATTTAAAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAA

Basic information

species Oryza sativa
transcript LOC_Os02g58020.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58020.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G013890_T01 (Zea mays), 3'ss of exon 11
gtttcatttctgatatgttttctttcaatgtttaacgaaatttgttctcttccc-atgtgcaaccatggtttcttgttctctggcttgctactatatttgtaattctttctagctttcttat-taagatctagcagttagtacattctgaggtatttatgttacgatctgtttgtgcagTGACGCATCTTTTGGTTATCCTGGAGGCCCCACCTTATTTAAAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAA
                                           ||| | || |  ||    ||   |   ||  ||   ||||  |||     || |||||||||||||| | || |   |   ||  | |||   |       ||||  | |   ||| || |  ||| | | |||||||| || || |||||||| |||||||| || ||||| |||||||| |||||||||||||| ||||||||||||||||||||||
-------------------------------------------gttttatttcagatacctaatgcta--tttatgaaatctgtattgg----atgtttgtaattctttcaacctcttcaaggcaaattttaggcatccacgtgttctctgttgaatatatt-ctttctatctttgcagTGATGCCTCATTTGGTTACCCTGGAGGGCCTACCTTGTTTAAAAATTTGAATTTTGGTATCGACCTGGACAGCCGCATAGCAA

upper sequence: LOC_Os02g58020.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA13G10530.1 (Glycine max), 3'ss of exon 10
gtttcatttctgatatgttttctttcaatgtttaacgaaatttgttctcttcccatgtgcaaccatggtttct-tgttctctggcttgctactatatttgtaattctttctagctttcttattaagatctagcagttagtacattctgaggtatttatgttacgatctgtttgtgcagTGACGCATCTTTTGGTTATCCTGGAGGCCCCACCTTATTTAAAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAA
                          |     ||| |    || ||      |  ||  | ||  || ||| | ||  |    |  | | |  |||    |  |    |  ||| ||     || |   || | || |    | ||  |  | ||       | |||  | |||||||||| ||||| |||||||||||||| |||||||   | ||||| || ||||| ||||| ||||| || ||||| || || ||||
------------------------gtagaacataa-ggcccttctttcagctctgtggactacattgatttatatgaaccaatgaataccaaaataaagtttgtcacatacagcatt-----taggccttatctgtgacctaaatcgaaaatttt-------caatc-atatgtgcagTGATGCATCATTTGGTTATCCTGGGGGCCCCATTCTGTTTAAGAATTTGAACTTTGGGATTGATCTCGACAGTCGTATTGCAA

upper sequence: LOC_Os02g58020.3 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv02s0025g02160.t01 (Vitis vinifera), 3'ss of exon 11
gtttcatttctgatatgttttctttcaatgtttaacgaaatttgttctcttcccatgtgcaaccatggtttcttgttctctggcttgctactatatttgtaattctttctagctttcttattaagatctagcagttagtacattctgaggtatttatgttacg-atctgtttgtgcagTGACGCATCTTTTGGTTATCCTGGAGGCCCCACCTTATTTAAAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAA
                                                                     ||      | |   ||||     |||   | |  | | | |   |   | | ||||  || |  | ||    ||| | | || || ||||| |  |  |||   |||||||| ||||| |||||||||||||| ||||||   |||||||| || ||||||||||| || || || ||||||||||| ||||
---------------------------------------------------------------------tttacaacccccatcttgaagaaata---gaatatttattttattccttaactaag--ctggatgcta----attgtaatgtgttgatgtttcttaaatgtgactgcagTGATGCATCATTTGGTTATCCTGGGGGCCCCTTATTATTTAAGAATTTGAATTTTGGGATAGATCTAGACAGCCGCATTGCAA

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|27576082|gb|CA998776.1|CA998776
EST:     GAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCATCAGCTTCAG                         TGACGCATCTTTTGGTTATCCTGGAGGCCCCACCTTATTTAAAAACTTGAA
genomic: GAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCATCAGCTTCAGgtttcatttc ... gtttgtgcagTGACGCATCTTTTGGTTATCCTGGAGGCCCCACCTTATTTAAAAACTTGAA
EST: gi|29662747|gb|CB659022.1|CB659022
EST:     GAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCATCAGCTTCAG                         TGACGCATCTTTTGGTTATCCTGGAGGCCCCACCTTATTTAAAAACTTGAA
genomic: GAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCATCAGCTTCAGgtttcatttc ... gtttgtgcagTGACGCATCTTTTGGTTATCCTGGAGGCCCCACCTTATTTAAAAACTTGAA
EST: gi|3766930|gb|AU031040.1|AU031040
EST:     GAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCATCAGCTTCAG                         TGACGCATCTTTTGGTTATCCTGGAGGCCCCACCTTATTTAAAAACTTGAA
genomic: GAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCATCAGCTTCAGgtttcatttc ... gtttgtgcagTGACGCATCTTTTGGTTATCCTGGAGGCCCCACCTTATTTAAAAACTTGAA
EST: gi|29676044|gb|CB672319.1|CB672319
EST:     GAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCATCAGCTTCAG                         TGACGCATCTTTTGGTTATCCTGGAGGCCCCACCTTATTTAAAAACTTGAA
genomic: GAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCATCAGCTTCAGgtttcatttc ... gtttgtgcagTGACGCATCTTTTGGTTATCCTGGAGGCCCCACCTTATTTAAAAACTTGAA
EST: gi|27546087|gb|CA764161.2|CA764161
EST:     GAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCATCAGCTTCAG                         TGACGCATCTTTTGGTTATCCTGGAGGCCCCACCTTATTTAAAAACTTGAA
genomic: GAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCATCAGCTTCAGgtttcatttc ... gtttgtgcagTGACGCATCTTTTGGTTATCCTGGAGGCCCCACCTTATTTAAAAACTTGAA
EST: gi|218495876|gb|FG947058.1|FG947058
EST:     GAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCATCAGCTTCAG                         TGACGCATCTTTTGGTTATCCTGGAGGCCCCACCTTATTTAAAAACTTGAA
genomic: GAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCATCAGCTTCAGgtttcatttc ... gtttgtgcagTGACGCATCTTTTGGTTATCCTGGAGGCCCCACCTTATTTAAAAACTTGAA
EST: gi|29664090|gb|CB660365.1|CB660365
EST:     ATCAGCTTCAG                         TGACGCATCTTTTGGTTATCCTGGAGGCCCCACCTTATTTAAAAACTTGAA
genomic: ATCAGCTTCAGgtttcatttc ... gtttgtgcagTGACGCATCTTTTGGTTATCCTGGAGGCCCCACCTTATTTAAAAACTTGAA
EST: gi|29662748|gb|CB659023.1|CB659023
EST:     GAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCATCAGCTTCAG                         TGACGCATCTTTTGGTTATCCTGGAGGCCCCACCTTATNTAAAAACTTGAA
genomic: GAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCATCAGCTTCAGgtttcatttc ... gtttgtgcagTGACGCATCTTTTGGTTATCCTGGAGGCCCCACCTTATTTAAAAACTTGAA
EST: gi|218483226|gb|FG956166.1|FG956166
EST:     GAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCATCAGCTTCAG                         TGACGCATCTTTTGGTTATCCTGGAGGCCCCACCTTATTTAAAAACTTGAA
genomic: GAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCATCAGCTTCAGgtttcatttc ... gtttgtgcagTGACGCATCTTTTGGTTATCCTGGAGGCCCCACCTTATTTAAAAACTTGAA
EST: gi|86909957|gb|CI292894.1|CI292894
EST:     GAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCATCAGCTTCAG                         TGACGCATCTTTTGGTTATCCTGGAGGCCCCACCTTATTTAAAAACTTGAA
genomic: GAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCATCAGCTTCAGgtttcatttc ... gtttgtgcagTGACGCATCTTTTGGTTATCCTGGAGGCCCCACCTTATTTAAAAACTTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagatctagcagttagtacattctgaggtatttatgttacgatctgtttgtgcagTGACGCATCTTTTGGTTATCCTGGAGGCCCCACCTTATTTAAAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAA
                                          tctgttt  CT-rich tract
                            tatttatgtta  TA-rich tract