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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagataacacctgttttcatatttacctgtgtgcacatgcacgccttgttctcattgttgcacaaactaatgctgattcctctaatccaattgctagACATGTCCTCCACAAGTATATAAATGAGGATGTTTCATTAGGAAGTTGGTTTATTGGATTAGATGTCGAGCATATCGACGACCGGAGACTTTGTTGTGGT

Basic information

species Oryza sativa
transcript LOC_Os02g06840.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G132866_T01 (Zea mays), 3'ss of exon 9
gtgagataacacctgttttcatatttacctgtgtgcacatgcacgccttgttctc-attgttgcacaaactaatgctgattcctctaatccaattgc--tagACATGTCCTCCACAAGTATATAAATGAGGATGTTTCATTAGGAAGTTGGTTTATTGGATTAGATGTCGAGCATATCGACGACCGGAGACTTTGTTGTGGT
|||||  | ||   |  |      | |  | | |  | ||  ||   | ||| |  |   || ||   ||| | ||||   |   |||||  |  |    || ||| |||| |||||||| ||||| || || ||||| ||||||  |||||| || ||  ||||||| ||||||||||| |||||||| ||||| ||||| 
gtgagtcagcaatagcatgggc-ctgaattttctcgagatttacagttcgttttggagccttacattgactta-gctg---ctaataatctgaccgtaacagGCATATCCTTCACAAGTACATAAACGAAGACGTTTCGTTAGGATCTTGGTTCATCGGGCTAGATGTTGAGCATATCGATGACCGGAGGCTTTGCTGTGGC

upper sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA06G46230.2 (Glycine max), 3'ss of exon 9
----gtgag-ataacacctgttttcatatttacctgtgtgcacatgcacgccttgttctcattgttgcacaaactaatgctgattcctctaatccaattgctagACATGTCCTCCACAAGTATATAAATGAGGATGTTTCATTAGGAAGTTGGTTTATTGGATTAGATGTCGAGCATATCGACGACCGGAGACTTTGTTGTGGT
    ||| |  |||  |   |||  |  || |      |  |    |       ||||| ||  |||  |   || |  |||  |       |     |   ||  |||| || |||||||||   || |||||||| ||| |||||   |||||||||||| | ||||| |||||||| || || || |||||||||||||| 
gagtgtgtgtgtaattcacctttgtaagttaaatcaaatcaatgaac-taaaaggttcttat-attgtgc--tctcaccctgtgtgtatatgtttttctttcagGAATGTTCTTCACAAGTATGCCAACGAGGATGTGTCACTAGGATCCTGGTTTATTGGACTTGATGTGGAGCATATAGATGATCGAAGACTTTGTTGTGGC

upper sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA12G10520.1 (Glycine max), 3'ss of exon 9
-----gtgag-ataacacctgttttcatatttacctgtgtgcacatgcacgccttgttctcattgttgcacaaactaatgctgattcctctaatccaattgctagACATGTCCTCCACAAGTATATAAATGAGGATGTTTCATTAGGAAGTTGGTTTATTGGATTAGATGTCGAGCATATCGACGACCGGAGACTTTGTTGTGGT
     |||||   ||  |   |||  | ||| |      |  |    |       ||||| ||  |||  |   || |  ||| |   | ||       |   ||  |||| || |||||||||   || |||||||| ||| |||||   |||||||||||| | ||||| |||||||| || || || |||||||||||||| 
ctggagtgagtggaattcacctttataaattaaatcaaatcaatgaac-taaaaggttcttat-attgtgc--tctcaccctg-tgtgtatatgttttctttcagGAATGTTCTTCACAAGTATGCCAACGAGGATGTGTCACTAGGATCCTGGTTTATTGGACTTGATGTGGAGCATATAGATGATCGAAGACTTTGTTGTGGC

upper sequence: LOC_Os02g06840.2 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv19s0090g00560.t01 (Vitis vinifera), 3'ss of exon 9
gtgagataacacctgttttcatatttacctgtgtgcacatg-cacgccttgttctcattgttgcacaaactaatgctgattcctctaatccaattgctagACATGTCCTCCACAAGTATATAAATGAGGATGTTTCATTAGGAAGTTGGTTTATTGGATTAGATGTCGAGCATATCGACGACCGGAGACTTTGTTGTGGT
|| || |  ||  ||   |  |    |   |||   |  |  || |||    | |      ||| |  |||  || ||  ||   ||||    |  |||| ||||| || |||||||||   ||||||||||||||||| |||  |||||||||||| || || |  |||||||| || |||||| |||| ||||| |||
gtaagtttccaaatgccgtttttagaaaaagtgactaattatcatgccaaaatttt----ctgccctgact--tggtg-ctctcataatg-gttatctagGCATGTGCTTCACAAGTATGCTAATGAGGATGTTTCATTGGGATCTTGGTTTATTGGTTTGGACGCAGAGCATATTGATGACCGGCGACTGTGTTGCGGT

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|29682551|gb|CB678826.1|CB678826
EST:     CAATTGTATGCTATTTCAAAAGATCTAGCACCCTACATATCTATAAACAG                         ACATGTCCTCCACAAGTATATAAATGAGGATGTTTCATTAGGAAGTTGGTT
genomic: CAATTGTATGCTATTTCAAAAGATCTAGCAACCTACATATCTATAAACAGgtgagataac ... caattgctagACATGTCCTCCACAAGTATATAAATGAGGATGTTTCATTAGGAAGTTGGTT
EST: gi|86868611|gb|CI332988.1|CI332988
EST:     CAATTGTATGCTATTTCAAAAGATCTAGCAACCTACATATCTATAAACAG                         ACATGTCCTCCACAAGTATATAAATGAGGATGTTTCATTAGGAAGTTGGTT
genomic: CAATTGTATGCTATTTCAAAAGATCTAGCAACCTACATATCTATAAACAGgtgagataac ... caattgctagACATGTCCTCCACAAGTATATAAATGAGGATGTTTCATTAGGAAGTTGGTT
EST: gi|88274436|gb|CI394842.1|CI394842
EST:     CAATTGTATGCTATTTCAAAAGATCTAGCAACCTACATATCTATAAACAG                         ACATGTCCTCCACAAGTATATAAATGAGGATGTTTCATTAGGAAGTTGGTT
genomic: CAATTGTATGCTATTTCAAAAGATCTAGCAACCTACATATCTATAAACAGgtgagataac ... caattgctagACATGTCCTCCACAAGTATATAAATGAGGATGTTTCATTAGGAAGTTGGTT
EST: gi|29657303|gb|CB653578.1|CB653578
EST:     CAATTGTATGCTATTTCAAAAGATCTAGCAACCTACATATCTATAAACAG                         ACATGTCCTCCACAAGTATATAAATGAGGATGTTTCATTAGGAAGTTGGTT
genomic: CAATTGTATGCTATTTCAAAAGATCTAGCAACCTACATATCTATAAACAGgtgagataac ... caattgctagACATGTCCTCCACAAGTATATAAATGAGGATGTTTCATTAGGAAGTTGGTT
EST: gi|87006638|gb|CI295021.1|CI295021
EST:     CAATTGTATGCTATTTCAAAAGATCTAGCAACCTACATATCTATAAACAG                         ACATGTCCTCCACAAGTATATAAATGAGGATGTTTCATTAGGAAGTTGGTT
genomic: CAATTGTATGCTATTTCAAAAGATCTAGCAACCTACATATCTATAAACAGgtgagataac ... caattgctagACATGTCCTCCACAAGTATATAAATGAGGATGTTTCATTAGGAAGTTGGTT

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), 73 (downstream exon)
Score: 14

ATTGGAAATTTGGCGAACCAGGAAACAAATATTTTCGGCATGCTACTGGTCAATTGTATGCTATTTCAAAAGATCTAGCAACCTACATATCTATAAACAGgtgagataac ... caattgctagACATGTCCTCCACAAGTATATAAATGAGGATGTTTCATTAGGAAGTTGGTTTATTGGATTAGATGTCGAGCATATCGACGACCGGAGACTTTGTTGTGGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccttgttctcattgttgcacaaactaatgctgattcctctaatccaattgctagACATGTCCTCCACAAGTATATAAATGAGGATGTTTCATTAGGAAGTTGGTTTATTGGATTAGATGTCGAGCATATCGACGACCGGAGACTTTGTTGTGGT
                     aaactaat  TA-rich tract