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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCCTTTTCAGAGACTGAAGTCCGAAATTGGTGTTTTCAGATATTTCAAGCTTTGAGTCACATGCATCAGCGTGGATATTTTCACCGCGACCTTAAGCCTGgtatggctggtgggctgttatttttaaacctggcatgctttctaatgcttgagactgggagttgtttatgatgttctgttgtgcaatgcggcattaagtg...

Basic information

species Oryza sativa
transcript LOC_Os06g02550.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g02550.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM5G864414_T02 (Zea mays), 5'ss of exon 8
CCCTTTTCAGAGACTGAAGTCCGAAATTGGTGTTTTCAGATATTTCAAGCTTTGAGTCACATGCATCAGCGTGGATATTTTCACCGCGACCTTAAGCCTGgtatg-gctggtgggctgttatttttaaacctggcatgctttctaatgcttgagactgggagttgtttatgatgttctgttgtgcaatgcggcattaagtg----------
|||||||||||||||||| ||||||| ||||| ||||| |||||||||||| ||||||||||||| |||||||||||||||||||| |||||||||||||||||| | |  ||   |  |  ||||  || |  ||||  ||  |||| ||||          | |   |  |  | ||||| | ||   |  | ||  |           
CCCTTTTCAGAGACTGAAATCCGAAACTGGTGCTTTCAAATATTTCAAGCTCTGAGTCACATGCACCAGCGTGGATATTTTCACCGTGACCTTAAGCCTGgtatgtggttttgcatttgttcttttttacatt-catg--ttgcaatggttgat--------ctatcctttcttgtttgttgcgaaacaagttactagttccagtcgtttt

upper sequence: LOC_Os06g02550.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA16G08080.1 (Glycine max), 5'ss of exon 5
CCCTTTTCAGAGACTGAAGTCCGAAATTGGTGTTTTCAGATATTTCAAGCTTTGAGTCACATGCATCAGCGTGGATATTTTCACCGCGACCTTAAGCCTGgta-tggctggtgggctgttatttttaaacctggcatgctttctaatgcttgagactgggagttgtttatgatgttctgttgtgca-atgcggcattaagtg
|  ||||| || | ||||||  ||||||||||||||||  | || |||| |||   | ||||||| ||||||||||| ||||| || || ||||||||||||| | | |  |        | || |      ||  |    |  |||  | | |  |   | || | |   ||    ||   || | || |   || |  | 
CTGTTTTCTGAAAATGAAGTTAGAAATTGGTGTTTTCAAGTTTTCCAAGGTTTAGCTTACATGCACCAGCGTGGATACTTTCATCGTGATCTTAAGCCTGgtacttgtttatcattgtgcaattgtgtttagggtttatgatgaaataatcgggtttc--acttatattatatagcatggaatgtatatactatataatata

upper sequence: LOC_Os06g02550.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA01G35190.2 (Glycine max), 5'ss of exon 5
CCCTTTTCAGAGACTGAAGTCCGAAATTGGTGTTTTCAGATATTTCAAGCTTTGAGTCACATGCATCAGCGTGGATATTTTCACCGCGACCTTAAGCCTGgtatggctggtgggctgttattttta-aacctggcatgctttctaatgcttgagactgggagttgtttatg-atgttctgttg--tgcaatgcggcattaagtg-
|  ||||| ||   ||||||  ||||||||||||||||  | || ||||   |   | ||||||| ||||||||||| || || |||||||| ||||||||||   ||  |    | ||   |  | || |||| |   | |    |       |||||| || ||| ||| || ||   | |  |||||||    |||   |  
CTGTTTTCTGAAGGTGAAGTTAGAAATTGGTGTTTTCAAGTTTTCCAAGGCCTTGCTTACATGCACCAGCGTGGATACTTCCATCGCGACCTGAAGCCTGgta---cttattttttatttcatccacaatctggtagattatggtttaggatgaactgggtgt-gttcatgtatattacatagcatgcaatgta-tattgtctta

upper sequence: LOC_Os06g02550.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA16G17580.1 (Glycine max), 5'ss of exon 5
CCCTTTTCAGAGACTGAAGTCCGAAATTGGTGTTTTCAGATATTTCAAGCTTTGAGTCACATGCATCAGCGTGGATATTTTCACCGCGACCTTAAGCCTGgtatggctggtgggctgttatttttaaacctggcatgctttctaatgcttgagactgggagttgtttatgatgttctgttgtgcaatgcg-gcatta-agtg---
|  ||||| || | ||||||  ||||||||||||||||  | || |||| |||   | ||||||| ||||||||||| ||||| || || |||||||||||||    |       |||    |||     | |   | ||| | |||        ||||  |   || |  | |  |    |  ||||     | || | |    
CTGTTTTCTGAAAATGAAGTTAGAAATTGGTGTTTTCAAGTTTTCCAAGGTTTAGCTTACATGCACCAGCGTGGATACTTTCATCGTGATCTTAAGCCTGgtacttgtttataattgt-gcatttgtgtttag---ggtttatgatgaaaatagttgggtttcacttgtattata-taacatagaatgtatatactataatataa

upper sequence: LOC_Os06g02550.2 (Oryza sativa), 5'ss of exon 8
lower sequence: AT4G19110.1 (Arabidopsis thaliana), 5'ss of exon 7
CCCTTTTCAGAGACTGAAGTCCGAAATTGGTGTTTTCAGATATTTCAAGCTTTGAGTCACATGCATCAGCGTGGATATTTTCACCGCGACCTTAAGCC-------TGgtatggct----ggtgggctgt---tatttttaaac--ctggcatgctttctaatgctt--gagactgggagttgt--ttatgatgttc--tgttgtgcaatgcggcattaagtg------------------------
|  ||| ||||  ||||  ||  ||||||||| |||||  | || ||||   |   | |||||||||||||||| || || |||||||| ||||||||       || ||| ||     |||| |   |   ||  || ||||  |||   ||     ||    ||  |||  | |    |||  || | |   ||  ||||    | |  | || | | |                         
CTTTTTGCAGAAGCTGATATCAAAAATTGGTGCTTTCAAGTCTTCCAAGGCCTTTCTTACATGCATCAGCGTGGTTACTTCCACCGCGATCTTAAGCCAGgtaattgatatagccttgaggtgtgagatacatagcttcaaacatctgctctgaagattagcaattctgagtttagtcactgtctttctaacaatccttgtttaatagtttgtcactgaatatgtatattgtgttggttgttgcag

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|58674281|gb|CK062967.1|CK062967
EST:     TTTGAGTCACATGCATCAGCGTGGATATTTTCACCGCGACCTTAAGCCTG                         AAAATTTGCTAGTTACAAAGGAGCTCATCAAGATAGCAGATTTTGGACTTG
genomic: TTTGAGTCACATGCATCAGCGTGGATATTTTCACCGCGACCTTAAGCCTGgtatggctgg ... gatatttcagAAAATTTGCTAGTTACAAAGGAGCTCATCAAGATAGCAGATTTTGGACTTG
EST: gi|29638208|gb|CB643217.1|CB643217
EST:     TTTGAGTCACATGCATCAGCGTGGATATTTTCACCGCGACCTTAAGCCTG                         AAAATTTGCTAGTTACAAAGGAGCTCATCAAGATAGCAGATTTTGGACTTG
genomic: TTTGAGTCACATGCATCAGCGTGGATATTTTCACCGCGACCTTAAGCCTGgtatggctgg ... gatatttcagAAAATTTGCTAGTTACAAAGGAGCTCATCAAGATAGCAGATTTTGGACTTG
EST: gi|58662294|gb|CK050974.1|CK050974
EST:     TNTGAGTCACATGCATCAGCGTGGATATTTTCACCGCGACCTTAAGCCTG                         AAAATTTGCTAGTTACAAAGGAGCTCATCAAGATAGCAGATTTTGGACTTG
genomic: TTTGAGTCACATGCATCAGCGTGGATATTTTCACCGCGACCTTAAGCCTGgtatggctgg ... gatatttcagAAAATTTGCTAGTTACAAAGGAGCTCATCAAGATAGCAGATTTTGGACTTG
EST: gi|29641486|gb|CB646493.1|CB646493
EST:     TTTGAGTCACATGCATCAGCGTGGATATTTTCACCGCGACCTTAAGCCTG                         AAAATTTGCTAGTTACAAAGGAGCTCATCAAGATAGCAGATTTTGGACTTG
genomic: TTTGAGTCACATGCATCAGCGTGGATATTTTCACCGCGACCTTAAGCCTGgtatggctgg ... gatatttcagAAAATTTGCTAGTTACAAAGGAGCTCATCAAGATAGCAGATTTTGGACTTG
EST: gi|58677581|gb|CK066268.1|CK066268
EST:     TTTGAGTCACATGCATCAGCGTGGATATTTTCACCGCGACCTTAAGCCTG                         AAAATTTGCTAGTTACAAAGGAGCTCATCAAGATAGCAGATTTTGGACTTG
genomic: TTTGAGTCACATGCATCAGCGTGGATATTTTCACCGCGACCTTAAGCCTGgtatggctgg ... gatatttcagAAAATTTGCTAGTTACAAAGGAGCTCATCAAGATAGCAGATTTTGGACTTG
EST: gi|58657844|gb|CK046524.1|CK046524
EST:     -TTGAGTCACATGCATCAGCGTGGATATTTTCACCGCGACCTTAAGCCTG                         AAAATTTGCTAGTTACAAAGGAGCTCATCAAGATAGCAGATTTTGGACTTG
genomic: TTTGAGTCACATGCATCAGCGTGGATATTTTCACCGCGACCTTAAGCCTGgtatggctgg ... gatatttcagAAAATTTGCTAGTTACAAAGGAGCTCATCAAGATAGCAGATTTTGGACTTG
EST: gi|29658028|gb|CB654303.1|CB654303
EST:     TTGAGTCACATGCATCAGCGTGGATATTTTCACCGCGACCTTAAGCCTG                         AAAATTTGCCTAGTTACCAAGGAGCTCCTCAAGATAGCAGATTTTGGACTT
genomic: TTGAGTCACATGCATCAGCGTGGATATTTTCACCGCGACCTTAAGCCTGgtatggctgg ... gatatttcagAAAATTTG-CTAGTTACAAAGGAGCTCATCAAGATAGCAGATTTTGGACTT
EST: gi|58685041|gb|CK073728.1|CK073728
EST:     CCTTAAGCCTG                         AAAATTTGCTAGTTACAAAGGAGCTCATCAAGATAGCAGATTTTGGACTTG
genomic: CCTTAAGCCTGgtatggctgg ... gatatttcagAAAATTTGCTAGTTACAAAGGAGCTCATCAAGATAGCAGATTTTGGACTTG
EST: gi|29685601|gb|CB681876.1|CB681876
EST:     TTTGAGTCACATGCATCAGCGTGGATATTTTCACCGCGACCTTAAGCCTG                         AAAATTTGCTAGTTACAAAGGAGCTCATCAAGATAGCAGATTTTGGACTTG
genomic: TTTGAGTCACATGCATCAGCGTGGATATTTTCACCGCGACCTTAAGCCTGgtatggctgg ... gatatttcagAAAATTTGCTAGTTACAAAGGAGCTCATCAAGATAGCAGATTTTGGACTTG
EST: gi|58689016|gb|CK077703.1|CK077703
EST:     TTTGAGTCACATGCATCAGCGTGGATATTTTCACCGCGACCTTAAGCCTG                         AAAATTTGCTAGTTACAAAGGAGCTCATCAAGATAGCAGATTTTGGACTTG
genomic: TTTGAGTCACATGCATCAGCGTGGATATTTTCACCGCGACCTTAAGCCTGgtatggctgg ... gatatttcagAAAATTTGCTAGTTACAAAGGAGCTCATCAAGATAGCAGATTTTGGACTTG

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: 75 (upstream exon), 74 (downstream exon)
Score: 130

CCCTTTTCAGAGACTGAAGTCCGAAATTGGTGTTTTCAGATATTTCAAGCTTTGAGTCACATGCATCAGCGTGGATATTTTCACCGCGACCTTAAGCCTGgtatggctgg ... gatatttcagAAAATTTGCTAGTTACAAAGGAGCTCATCAAGATAGCAGATTTTGGACTTGCTCGTGAGATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCG




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