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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcagcactgtgatttgcttggtacagacactgatgttgtacacacttgaccaattttcatattgcagGTTTTGGAGGAGCTTGAACTCACTATGGACCAATTCATTGACTTGTGCATCCTATCTGGATGTGACTATTGTGATAGCATTAAAG

Basic information

species Oryza sativa
transcript LOC_Os05g46270.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g46270.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G121262_T01 (Zea mays), 3'ss of exon 11
gtatgcagcactgtgatttgcttggtacagacactgatgttgtacacacttgaccaattttcatattgcagGTTTTGGAGGAGCTTGAACTCACTATGGACCAATTCATTGACTTGTGCATCCTATCTGGATGTGACTATTGTGATAGCATTAAAG
|| || | ||| || |||| || || |||||||| | | | |||| |||| | ||| ||||||||||||||||||||||||| |||||||| |||||||| ||||||||||| | |||||||||||||||||||||||| ||||
gtgtgtatttttgtcatgtgctcaataattaccttgatgttgcatatatgccacca-tttttttgttgtagGTTTTGGAGGAGCTTGAACTCACCATGGACCAGTTCATTGATTTGTGCATCCTGTGTGGATGTGACTATTGTGATAGCATCAAAG

upper sequence: LOC_Os05g46270.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA10G28200.2 (Glycine max), 3'ss of exon 10
--gtatgcagcactgtgatttgcttggtacagacactgat-gttgtacacacttgaccaattttcatattgcagGTTTTGGAGGAGCTTGAACTCACTATGGACCAATTCATTGACTTGTGCATCCTATCTGGATGTGACTATTGTGATAGCATTAAAG
|| ||| | | || ||| |||| | | | | | || | | || | || ||| ||||||||||||| | | || ||||||||||| |||||||| ||||| || ||||| ||||| |||||||| |||||| ||
gtccttgtagcgttcaacatacttttgtatttttactgtttgatctgctcattgtggtatttatttggtttcagATTTTGGAGGAGCTAAATATGACCATGGACCAATTTATTGACTTATGCATTCTTTCTGGCTGTGATTATTGTGACAGCATTCGAG

upper sequence: LOC_Os05g46270.1 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA20G22190.2 (Glycine max), 3'ss of exon 10
--gtatgcagcactgtgatttgcttg-gtacagacactg-atgttgtacacacttgaccaattttcatattgcagGTTTTGGAGGAGCTTGAACTCACTATGGACCAATTCATTGACTTGTGCATCCTATCTGGATGTGACTATTGTGATAGCATTAAAG
|| ||| | | | |||| || || | ||| | | | || | | || | || ||| ||||||||||||| | | || ||||||||||| |||||||| ||||| || ||||| ||||| |||||||| |||||| ||
gttcttgaagc-tttcaacatacttgagtttttttaccgtatgatctgctcattgtggtatttatttggtttcagATTTTGGAGGAGCTAAATATGACCATGGACCAATTTATTGACTTATGCATTCTTTCTGGCTGTGATTATTGTGACAGCATTCGAG

upper sequence: LOC_Os05g46270.1 (Oryza sativa), 3'ss of exon 10
lower sequence: AT5G26680.2 (Arabidopsis thaliana), 3'ss of exon 10
---------gtatgcagcactgtgatttgcttggtacag-acactgatgttgtacacacttgaccaattttcatattgcagGTTTTGGAGGAGCTTGAACTCACTATGGACCAATTCATTGACTTGTGCATCCTATCTGGATGTGACTATTGTGATAGCATTAAAG
| || |||| | ||| | | | | ||| | | ||| | || || ||| |||| || |||||| |||| || ||||| || ||||| |||||||| || | |||||||||||||||||||| ||||| ||
gtttgtctctcacaca-cactattctttcttcaacgtattaagttaatgaactg-atccttatattgtggtctcgtttcagATTTTAGAAGAGCTTCAACTTACCATGGATCAGTTCATCGACTTGTGTATATTGTCTGGATGTGACTATTGTGACAGCATCCGAG

upper sequence: LOC_Os05g46270.1 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv14s0060g00210.t01 (Vitis vinifera), 3'ss of exon 10
gtatgcagcactgtgatttgcttggtacagacactgatgttgtacacacttgaccaattt-tcatattgcagGTTTTGGAGGAGCTTGAACTCACTATGGACCAATTCATTGACTTGTGCATCCTATCTGGATGTGACTATTGTGATAGCATTAAAG
|| | | | | | | ||||| || || | | | ||| | || || ||| ||||||||||||| | || || ||||| |||||||||||| ||||||| || || || ||||| |||||||| |||||| ||
gtgcttaaaaattttgaatatggaatctgattgctgatttttcactctttccaataatgaattatgtttcagATTTTGGAGGAGCTGAATCTTACCATGGATCAATTCATTGACCTGTGCATTCTTTCAGGGTGTGATTATTGTGACAGCATTCGAG

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|29634937|gb|CB639946.1|CB639946
EST:     TGGATCCAAGTTCCAAGAAAATTCCAGTTATGGAATTTGAAGTCGCGAAA                         GTTTTGGAGGAGCTTGAACTCACTATGGACCAATTCATTGACTTGTGCATC
genomic: TGGATCCAAGTTCCAAGAAAATTCCAGTTATGGAATTTGAAGTCGCGAAAgtatgcagca ... catattgcagGTTTTGGAGGAGCTTGAACTCACTATGGACCAATTCATTGACTTGTGCATC
EST: gi|27578355|gb|CB001050.1|CB001050
EST:     TGGATCCAAGTTCCAAGAAAATTCCAGTTATGGAATTTGAAGTCGCGAAA                         GTTTTGGAGGAGCTTGAACTCACTATGGACCAATTCATTGACTTGTGCATC
genomic: TGGATCCAAGTTCCAAGAAAATTCCAGTTATGGAATTTGAAGTCGCGAAAgtatgcagca ... catattgcagGTTTTGGAGGAGCTTGAACTCACTATGGACCAATTCATTGACTTGTGCATC
EST: gi|3107727|gb|D43467.1|D43467
EST:     TGGATCCAAGTTCCAAGAAAATTCCAGTTATGGAATTTNAAGTCGCGAAA                         GTTTTGGAGGAGCTTG
genomic: TGGATCCAAGTTCCAAGAAAATTCCAGTTATGGAATTTGAAGTCGCGAAAgtatgcagca ... catattgcagGTTTTGGAGGAGCTTG
EST: gi|66913640|gb|CX100488.1|CX100488
EST:     GGGATCCAAGTTCCAAGAAAATTCCAGTTATGGAATTTGAAGTCGCGAAA                         GTTTTGGAGGAGCTTGAACTCACTATGGACCAATTCATTGACTTGTGCATC
genomic: TGGATCCAAGTTCCAAGAAAATTCCAGTTATGGAATTTGAAGTCGCGAAAgtatgcagca ... catattgcagGTTTTGGAGGAGCTTGAACTCACTATGGACCAATTCATTGACTTGTGCATC
EST: gi|58682239|gb|CK070926.1|CK070926
EST:     TGGATCCAAGTTCCAAGAAAATTCCAGTTATGGAATTTGAAGTCGCGAAA                         GTTTTGGAGGAGCTTGAACTCACTATGG
genomic: TGGATCCAAGTTCCAAGAAAATTCCAGTTATGGAATTTGAAGTCGCGAAAgtatgcagca ... catattgcagGTTTTGGAGGAGCTTGAACTCACTATGG
EST: gi|27577153|gb|CA999847.1|CA999847
EST:     TGGATCCAAGTTCCAAGAAAATTCCAGTTATGGAATTTGAAGTCGCGAAA                         GTTTTGGAGGAGCTTGAACTCACTATGGACCAATTCATTGACTTGTGCATC
genomic: TGGATCCAAGTTCCAAGAAAATTCCAGTTATGGAATTTGAAGTCGCGAAAgtatgcagca ... catattgcagGTTTTGGAGGAGCTTGAACTCACTATGGACCAATTCATTGACTTGTGCATC

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: 66 (upstream exon), 48 (downstream exon)
Score: 38

AGATATGGACTCTCTTACTTTTGGAGCTCCACGGTTTCTTCGTCATTTGATGGATCCAAGTTCCAAGAAAATTCCAGTTATGGAATTTGAAGTCGCGAAAgtatgcagca ... catattgcagGTTTTGGAGGAGCTTGAACTCACTATGGACCAATTCATTGACTTGTGCATCCTATCTGGATGTGACTATTGTGATAGCATTAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgcttggtacagacactgatgttgtacacacttgaccaattttcatattgcagGTTTTGGAGGAGCTTGAACTCACTATGGACCAATTCATTGACTTGTGCATCCTATCTGGATGTGACTATTGTGATAGCATTAAAG
                                         ttttcat  CT-rich tract
 aattttcatatt  TA-rich tract