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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcacagttatgatgtatctctgctgctaatcaagtggcacgattttctgtgtttatcagcaacttttcatttgatcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCGGTTACTGATAAGATCTTCTCTAATACAACGACAATTACTGAATATCTCA

Basic information

species Oryza sativa
transcript LOC_Os03g50480.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G109383_T01 (Zea mays), 3'ss of exon 5
gtatcacagttatgat--gtatctctgctgctaatcaagtggca-cgattttctgtgtttatcagcaacttttcatttgatcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCGGTTACTGATAAGATCTTCTCTAATACAACGACAATTACTGAATATCTCA
||| |    |||      ||||||||| ||| |||||||||      ||  ||| |||| ||     || | ||||  || |||  ||||||||||| |||||||| ||||||| ||||||||| ||||| |||||||| ||||| || ||||| ||||||||||||||||||||  ||||||| ||||
gtacctattttactgctagtatctctgatgcaaatcaagtgctggtcatgctctatgtt-attgaatacatctcatc-gaactttccagGACTTCGGGATCAAATACAACATGGGAAATGGTGGGCCTGCTCCTGAATCTGTTACCGACAAGATTTTCTCTAATACAACGACAATCTCTGAATACCTCA

upper sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 5
gtatcacagttatgat--gtatctctgctgctaatcaagtggcacg-attttctgtgtttatcagcaacttttcatttgatcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCGGTTACTGATAAGATCTTCTCTAATACAACGACAATTACTGAATATCTCA
||| ||   |||      || ||| || ||| ||||||||| |||  ||  ||| |||| ||     ||   ||| | || |||  |||||||| || |||||||| || |||| |||||||||||||||||||||||| ||||| || ||||| ||||||||||||||||||||  ||||||| ||||
gtaccaagtttactgctagtgtctttgttgcaaatcaagtgccacacatgctctatgtt-attgaatacgcctcact-gaactttccagGACTTTGGTATCAAATACAATATGGGAAATGGTGGACCTGCCCCTGAATCCGTTACCGACAAGATTTTCTCTAATACAACGACAATCTCTGAATACCTCA

upper sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G70730.1 (Arabidopsis thaliana), 3'ss of exon 5
---------------------------------------------------------gtatcacagttatgat-gtatctctgctgctaatcaagtggcacgattttctgtgtttatcagcaacttttcatttgatct--tggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCGGTTACTGATAAGATCTTCTCTAATACAACGACAATTACTGAATATCTCA
                                                         |||| |     ||  | | |||  |  || ||| | |   |  |   | ||||  |  ||  ||   ||| |   |  |||  |  ||||| |||||||| || || || ||||||||||||||||| || ||||||||  | ||||||||||| | |   || |||| |||||| |  || || |  |
gtcagttctctttttgttctcactcttttgtgcttgttcattcgataccctcacttagtattatttgaatcctagcatcagttttgttaaactatatgttcatctctctgcttccatatgctgatttcctgctattctattcacagGATTTCGGAATTAAGTACAATATGGAAAATGGTGGACCAGCTCCTGAATCAATCACTGATAAGATTTACGAGAACACAAAGACAATCAAGGAGTACCCAA

upper sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 5
------------------------------------------------------------gtatcacagttatgatgtatctctgctgctaatcaagtggcacgattttctgtgtttatcagcaacttttcatttgatcttg-gcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCGGTTACTGATAAGATCTTCTCTAATACAACGACAATTACTGAATATCTCA
                                                            ||||| |  ||||  |||   | |  |  |||| |  |  |  |||      |     | ||      |||  |    ||||  ||||| || ||||||||||| || ||||||||||| |||||||| ||||||||  | |||||||| || | |   || || | |||||| |  || || |  |
gtccgttctgttcttgttccatctctactgtgctatcctttcatttgaactattcgttttgtatctct-ttatt-tgttctttttttaataataagatatctagatggataataagactaagaggtgattccataccccttgtacagGATTTTGGAATCAAATACAATATGGAAAATGGAGGACCTGCTCCTGAATCAATCACTGATAAAATTTACGAGAACACTAAGACAATCAAGGAGTACCCAA

upper sequence: LOC_Os03g50480.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 6
--------------gtatcacagttatgatgtatctctgctgctaatcaagtggcacgattttctgtgtttatcagcaacttttcatttgatcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCGGTTACTGATAAGATCTTCTCTAATACAACGACAATTACTGAATATCTCA
                || | | ||||  | | |   |     | ||      ||| |||| |   | |||||      |  |   ||    | | |||||| || ||||| || || ||||||||||||||||||||||| |  ||  |  |||||||||||||||     || ||||   | || |  || ||| | |
tgaacgtttgaagcagataaaatttattttatttgattcggatttatggtagtgcatgattcttgttctttatttttttccctgtgttcttcccttgcagGATTTTGGAATTAAGTACAACATGGAAAATGGTGGACCTGCTCAAGAGGCAATTACTGATAAGATCTATGAGAACACAAAATCCATAAAGGAGTATATAA

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|58668595|gb|CK057281.1|CK057281
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATA
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATA
EST: gi|58675297|gb|CK063984.1|CK063984
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|29664693|gb|CB660968.1|CB660968
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|58654844|gb|CK043524.1|CK043524
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCGGAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|58682481|gb|CK071168.1|CK071168
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|58666397|gb|CK055083.1|CK055083
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|87015499|gb|CI303105.1|CI303105
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAAT
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAAT
EST: gi|58590938|gb|CF989246.1|CF989246
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|58667790|gb|CK056476.1|CK056476
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
EST: gi|58666319|gb|CK055005.1|CK055005
EST:     CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAG                         GACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG
genomic: CTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCG

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: 63 (upstream exon), 75 (downstream exon)
Score: 177

GGATCAAAGGCTACTGGTGCCTTCATTTTAACAGCTAGTCACAACCCTGGTGGTCCTACTGAGgtatcacagt ... atcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCGGTTACTGATAAGATCTTCTCTAATACAACGACAATTACTGAATATCTCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcaagtggcacgattttctgtgtttatcagcaacttttcatttgatcttggcagGACTTCGGAATCAAATATAACATGGAAAATGGTGGACCTGCCCCTGAATCGGTTACTGATAAGATCTTCTCTAATACAACGACAATTACTGAATATCTCA
                                   ttttcattt  TA-rich tract