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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTCGCAATGGTTCACCTGTCAGGCTTCCTGTTGCCCATATGGTGTGTAATCAGACCCCACCAGTTGGTGATAAACCCAGTCTTATGACCTTCCGTGAGgtaagcaataataaatatggcaatggtaaattattccagatagtctccaatgtatgagtattctgttacatcaatatgtggaaaactgtacactaaagta...

Basic information

species Oryza sativa
transcript LOC_Os02g58340.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58340.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G133919_T01 (Zea mays), 5'ss of exon 10
TGCTCGCAATGGTTCACCTGTCAGGCTTCCTGTTGCCCATATGGTGTGTAATCAGACCCCACCAGTTGGTGATAAACCCAGTCTTATGACCTTCCGTGAGgtaagcaata--------ataaatatggcaatggtaaattattccaga-----tagtctccaatgtatgagtattctgttac-atcaatatgtggaaaactgtacactaaagta----------
 |||||||||||||   |||  ||||| |||||||||||||| ||||| |||||||| ||||||||||| || || |||||||| |||||||||||||||||||| ||||        | |  ||||  |||    |  |||     |     |||    |    | |   |||| || ||| || ||  |||| |||    | |       |           
AGCTCGCAATGGTTTGGCTGCTAGGCTGCCTGTTGCCCATATAGTGTGCAATCAGACTCCACCAGTTGGCGAGAAGCCCAGTCTCATGACCTTCCGTGAGgtaagtaatacatctgtgacatgtatgtgaataaggatatatggagaaagcagtagctctctgcctctccttattatggtactatgaagttgtgtaaattctttctgctgtatgttgcctgtag

upper sequence: LOC_Os02g58340.1 (Oryza sativa), 5'ss of exon 10
lower sequence: AT5G65620.1 (Arabidopsis thaliana), 5'ss of exon 10
TGCTCGCAATGGTTCACCTGTCAGGCTTCCTGTTGCCCATATGGTGTGTAATCAGACCCCACCAGTTGGTGATAAACCCAGTCTTATGACCTTCCGTGAGgtaagcaataataaat--atggcaatggtaaattattccagatagtctccaatgtatgagtattctgttacatcaatatgtggaaaactgtacactaaagta
 ||||  || || ||  |||| ||||| |||||||| || ||||| || || || || |||||||| ||||| || || || |||||||| |||||||||||||   | || | ||  || ||| | | | ||   |     ||   |  ||| |   |  || || |    |  |       |  ||| |    || ||  
GGCTCAGAAAGGCTCTTCTGTTAGGCTGCCTGTTGCACACATGGTCTGCAACCAAACTCCACCAGTAGGTGACAAGCCAAGCCTTATGACATTCCGTGAGgtaaatgaaaaaacatccattgcacttgcacatatctaagcgtaacatgaaatct-caaaaatcctttcttgttgactataacatcactctgatttacag--

upper sequence: LOC_Os02g58340.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv06s0061g01070.t01 (Vitis vinifera), 5'ss of exon 10
TGCTCGCAATGGTTCACCTGTCAGGCTTCCTGTTGCCCATATGGTGTGTAATCAGACCCCACCAGTTGGTGATAAACCCAGTCTTATGACCTTCCGTGAGgtaagcaataataaatatggcaatggtaaattattccagatagtctccaatgtatgagtattctgttac--atcaatatgtggaaaactgtacactaaagta--------
| |  |  ||||| || ||   ||| | ||| |||| ||||| ||||| ||||| || |||||| | ||||| || || ||||||||||||||||||||||||   |     ||| |     |  | |  | |   |   |||| |   |  | ||  | |   ||||   ||  | |||||    |   |  |||| | ||        
TTCATGTGATGGTGCATCTCCTAGGTTGCCTATTGCACATATAGTGTGCAATCAAACACCACCAATGGGTGACAAGCCAAGTCTTATGACCTTCCGTGAGgtacata----caaacac----actgcatctcaggtccagtagttt--gacttctggctttcaggttaataattcaaatgtgagtgataattgactagattaaatgagta

upper sequence: LOC_Os02g58340.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv00s0211g00060.t01 (Vitis vinifera), 5'ss of exon 10
TGCTCGCAATGGTTCACCTGTCAGGCTTCCTGTTGCCCATATGGTGTGTAATCAGACCCCACCAGTTGGTGATAAACCCAGTCTTATGACCTTCCGTGAGgtaagcaataataaatatggcaatggtaaattattccagatagtctccaatgtatgagtat---tctgttacatcaatatgtggaaaactgtacactaaagta-
  | ||  ||||| |    |  ||| | ||| |||| ||||||||||| ||||| || |||||||| ||  ||||||| || |||||||| |||||||||||||    ||| |  ||   || || |    |||  ||    | ||  ||| | |   | |   ||| ||   |   | | ||     || |    |    |  
GTCACGTGATGGTACCAAAGCTAGGTTGCCTATTGCTCATATGGTGTGCAATCAAACACCACCAGTGGGAAATAAACCAAGCCTTATGACATTCCGTGAGgtaaatggtaa-acctaacacattgctt--ctatctcaagctg-ctttaatctctctctctctctctcttgtttttttctttgcttttctttttttttttttgt

upper sequence: LOC_Os02g58340.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv00s0211g00060.t01 (Vitis vinifera), 5'ss of exon 13
TGCTCGCAATGGTTCACCTGTCAGGCTTCCTGTTGCCCATATGGTGTGTAATCAGACCCCACCAGTTGGTGATAAACCCAGTCTTATGACCTTCCGTGAGgtaagcaataataaatatggcaatggtaaattattccagatagtctccaatgtatgagtat---tctgttacatcaatatgtggaaaactgtacactaaagta-
  | ||  ||||| |    |  ||| | ||| |||| ||||||||||| ||||| || |||||||| ||  ||||||| || |||||||| |||||||||||||    ||| |  ||   || || |    |||  ||    | ||  ||| | |   | |   ||| ||   |   | | ||     || |    |    |  
GTCACGTGATGGTACCAAAGCTAGGTTGCCTATTGCTCATATGGTGTGCAATCAAACACCACCAGTGGGAAATAAACCAAGCCTTATGACATTCCGTGAGgtaaatggtaa-acctaacacattgttt--ctatctcaagctg-ctttaatctctctctctctctctcttgtttttttctttgcttttctttttttttttttgt

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|29685086|gb|CB681361.1|CB681361
EST:     ATAAACCCAGTCTTATGACCTTCCGTGAG                         GTTGAAACTGTGTTCCATGAATTTGGTCATGCGCTGCAGCACATGCTTACC
genomic: ATAAACCCAGTCTTATGACCTTCCGTGAGgtaagcaata ... tcttttgtagGTTGAAACTGTGTTCCATGAATTTGGTCATGCGCTGCAGCACATGCTTACC
EST: gi|58676094|gb|CK064781.1|CK064781
EST:     ATCAGACCCCACCAGTTGGTGATAAACCCAGTCTTATGACCTTCCGTGAG                         GTTGAAACTGTGTTCCATGAATTTGGTCATGCGCTGCAGCACATGCTTACC
genomic: ATCAGACCCCACCAGTTGGTGATAAACCCAGTCTTATGACCTTCCGTGAGgtaagcaata ... tcttttgtagGTTGAAACTGTGTTCCATGAATTTGGTCATGCGCTGCAGCACATGCTTACC
EST: gi|58587575|gb|CF985883.1|CF985883
EST:     ATCAGACCCCACCAGTTGGTGATTAACCCAGTCTTATGACCTTCCGTGAG                         GTTGAAACTGTGTTCCATGAATTTGGTCATGCGCTGCAGCACATGCTTACC
genomic: ATCAGACCCCACCAGTTGGTGATAAACCCAGTCTTATGACCTTCCGTGAGgtaagcaata ... tcttttgtagGTTGAAACTGTGTTCCATGAATTTGGTCATGCGCTGCAGCACATGCTTACC
EST: gi|27577497|gb|CB000192.1|CB000192
EST:     ATCAGACCCCACCAGTTGGTGATAAACCCAGTCTTATGACCTTCCGTGAG                         GTTGAAACTGTGTTCCATGAATTTGGTCATGCGCTGCAGCACATGCTTACC
genomic: ATCAGACCCCACCAGTTGGTGATAAACCCAGTCTTATGACCTTCCGTGAGgtaagcaata ... tcttttgtagGTTGAAACTGTGTTCCATGAATTTGGTCATGCGCTGCAGCACATGCTTACC
EST: gi|38471500|gb|CF955631.1|CF955631
EST:     GACCTTCCGTGAG                         GTTGAAACTGTGTTCCATGAATTTTGTCATGCGCTGCAGCACATGCTTACC
genomic: GACCTTCCGTGAGgtaagcaata ... tcttttgtagGTTGAAACTGTGTTCCATGAATTTGGTCATGCGCTGCAGCACATGCTTACC
EST: gi|87011355|gb|CI289625.1|CI289625
EST:     ATCAGACCCCACCAGTTGGTGATAAACCCAGTCTTATGACCTTCCGTGAG                         GTTGAAACTGTGTTCCATGAATTTGGTCATGCGCTGCAGCACATGCTTACC
genomic: ATCAGACCCCACCAGTTGGTGATAAACCCAGTCTTATGACCTTCCGTGAGgtaagcaata ... tcttttgtagGTTGAAACTGTGTTCCATGAATTTGGTCATGCGCTGCAGCACATGCTTACC

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: 56 (upstream exon), 72 (downstream exon)
Score: 37

TGCTCGCAATGGTTCACCTGTCAGGCTTCCTGTTGCCCATATGGTGTGTAATCAGACCCCACCAGTTGGTGATAAACCCAGTCTTATGACCTTCCGTGAGgtaagcaata ... tcttttgtagGTTGAAACTGTGTTCCATGAATTTGGTCATGCGCTGCAGCACATGCTTACCAAACAAGATGAAGGATTTGTTTCTGGTATTCGTGGAGTAGAATGGGATG




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