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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_Os02g58020.2
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|218495876|gb|FG947058.1|FG947058
EST:     GAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCATCAGCTTCAG                         TGACGCATCTTTTGGTTATCCTGGAGGCCCCACCTTATTTAAAAACTTGAA
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

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), 72 (downstream exon)
Score: 61

CTATAAATTCGAATTTCCAACACCAGATGACCGCCCTGGACCACCAATCATCAGCTTCAGgtttcatttc ... gtttgtgcagTGACGCATCTTTTGGTTATCCTGGAGGCCCCACCTTATTTAAAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagatctagcagttagtacattctgaggtatttatgttacgatctgtttgtgcagTGACGCATCTTTTGGTTATCCTGGAGGCCCCACCTTATTTAAAAACTTGAATTTTGGTATTGACCTGGACAGCCGCATAGCAA
                                          tctgttt  CT-rich tract
                            tatttatgtta  TA-rich tract