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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcgattttgttccttacatttgcttggcatagtttttgcatttctaacatttcttggtctggatttgaatgtggtgcccttatttaatttcagGTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCAAAAGGTGTCAATTGTGTTGATTACTTTACTGGTGGTGATCGCCCATACT

Basic information

species Oryza sativa
transcript LOC_Os02g11830.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G141587_T01 (Zea mays), 3'ss of exon 6
gtttgcg-attttgttccttaca---tttgcttggcatagtttttgcatttctaacatttcttggtctg-----gatttgaatgtggtgcccttatttaatt---tcagGTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCAAAAGGTGTCAATTGTGTTGATTACTTTACTGGTGGTGATCGCCCATACT
||||| | | | | | | ||| |   | || ||||      | ||| |||  |     |  || |  |        |||||  ||| |  ||| ||||   |   |||| ||||||||||||||||||||||||| ||||||||| ||||||||||||| |||||||| || |||||||||||||| ||||||||||| || |||||||
gtttgtgtaatctctgctttaaaagttctggttggtcacaatgttgtattatttgtcgtcattagctttttcatagtttgatggtgatatcctaatttctgtctatcagATATGGAGTCTTGGTTCCCCTGATCCAAATTTCACACTAGATGGCCATTCGAAAGGTGTGAACTGTGTTGATTACTTCACTGGTGGTGACCGACCATACT

upper sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 6
gtttgcgat-tttgttccttaca---tttgcttggcatagtttttgcatt-tctaacattt-----------cttggtctggatttgaatgtggtgcccttattt-----aatttcagGTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCAAAAGGTGTCAATTGTGTTGATTACTTTACTGGTGGTGATCGCCCATACT
||||| | | | |   | ||| |   | || |||||     | ||||||| | |   |              |||  ||     ||||  ||| |  |||  |||     ||| |||| |||||||||||||||| ||||| || ||||||||| ||||||||||||| |||||||| || |||||||||||||| |||||||||||||| |||||| 
gtttgtgttatctccgctttaaaaattctggttggccacaatgttgcattatttggtaccgacaggcgacagctttttcatagcttgatggtgatatcctattttttgtcaatatcagATATGGAGTCTTGGTTCTCCTGACCCAAATTTCACACTAGATGGCCATTCCAAAGGTGTGAACTGTGTTGATTACTTCACTGGTGGTGATCGACCATACC

upper sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA07G03890.1 (Glycine max), 3'ss of exon 6
----gtttgcgattttgttccttacatttgcttggcatagtttttgc--atttctaacatttcttggtctggatttgaatgtggtgcccttatttaattt-------cagGTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCAAAAGGTGTCAATTGTGTTGATTACTTTACTGGTGGTGATCGCCCATACT
       || | | || || ||    | ||    ||||  | ||||   ||||| ||       || |    |||  || ||  ||   | || | || |       ||| | |||| |||||| || ||||| || ||||| ||||| ||||  |||  |||||| || |||||||||||||||||||| ||||||||    || ||  
gtatacatgtgttcttcttgctagt-tgtgtcctgcattttctttgtttatttccaaacacctatgataaaaattaaaaagtaatgtattaatgttatcttttcttgcagATTTGGAATCTTGGCTCTCCTGACCCCAATTTTACATTGGATGCGCATCAAAAAGGAGTGAATTGTGTTGATTACTTTACAGGTGGTGACAAGCCTTATC

upper sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 6
gtttgcgattttgttccttacatttgcttggcatagtttttgcatttctaacatttcttggtctggatttgaatgtggtgcccttatttaatttcagGTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCAAAAGGTGTCAATTGTGTTGATTACTTTACTGGTGGTGATCGCCCATACT
                  || | ||   ||   | |||  ||  | | |   ||    |  |       || |  || || | |   |   |||||| | |||| |||||| || |||||||||||||| || || ||||  |||   ||||| || |||||||||||||| ||||| ||||||||    |||||  
-----------------gtagaatta--tgttcttgttcctggttgtttcctatgatataatgcattaatgcacctgttgtcttctct---tttcagATTTGGAATCTTGGCTCTCCTGATCCTAATTTTACTTTGGATGCTCATCAGAAAGGAGTGAATTGTGTTGATTATTTTACAGGTGGTGACAAACCATATC

upper sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 6
gtttgcgattttgttccttacatt-----tgcttggcatagtttttgc--atttctaacatttcttggtctggatttgaatgtggtgcccttat-------ttaatttcagGTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCAAAAGGTGTCAATTGTGTTGATTACTTTACTGGTGGTGATCGCCCATACT
|| |     | ||||| |  |  |     ||    | ||  | ||||   ||||| |    |   || |    |||| || ||  ||   | ||       | |||| ||| | |||| |||||| || ||||| || ||||| || || |||| ||||  |||||| || |||||||||||||||||||| ||||||||    || ||| 
gtatatacatgtgttcttctcgctagttgtgtcctgaattttctttgtttatttccatacatctatgataaaaatttaaaagtaatgtattaatgttatcttcaattgcagATTTGGAATCTTGGCTCTCCTGACCCCAATTTTACGTTGGATGCCCATCAAAAAGGAGTGAATTGTGTTGATTACTTTACAGGTGGTGACAAACCTTACC

upper sequence: LOC_Os02g11830.2 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 6
----gtttgcgattttgttccttacatttgcttggcatagttttt-gcatttctaacatttcttggtctggatttgaatgtggtgccct-----tatttaattt--cagGTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCAAAAGGTGTCAATTGTGTTGATTACTTTACTGGTGGTGATCGCCCATACT
    | |   |||||| |       | ||| |      | |||||  |   | |  | |      || ||  | ||    |  ||| ||     ||| |  |||  ||| |||||| |||||| || || || |||||||| ||| | |||| ||||   ||||| || |||||||||||||||||||| || ||||||   |||||  
gtatgatctggattttctgttggcaacttgttaactgcatttttttaccaattttgcttcatcaagtatgagtgtgctatttatgctctgatgatatctccttttccagATATGGAATCTTGGCTCTCCAGACCCTAATTTTACACTGGATGCCCATCAGAAAGGGGTAAATTGTGTTGATTACTTTACAGGCGGTGATAAACCATATC

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|300215876|gb|HO088502.1|HO088502
EST:     CGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAG                         GTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCA
genomic: CGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAGgtttgcgatt ... ttaatttcagGTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCA
EST: gi|29680637|gb|CB676912.1|CB676912
EST:     ATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAG                         GTATGGAGTCTTGGTTCCCNTGATCCTAATTTCACATTAGATGGCCATTCA
genomic: ATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAGgtttgcgatt ... ttaatttcagGTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCA
EST: gi|29613909|gb|CB618922.1|CB618922
EST:     CGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAG                         GTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCA
genomic: CGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAGgtttgcgatt ... ttaatttcagGTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCA
EST: gi|29671007|gb|CB667282.1|CB667282
EST:     CGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAG                         GTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCA
genomic: CGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAGgtttgcgatt ... ttaatttcagGTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCA
EST: gi|29613910|gb|CB618923.1|CB618923
EST:     CGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAG                         GTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCA
genomic: CGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAGgtttgcgatt ... ttaatttcagGTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCA
EST: gi|29680636|gb|CB676911.1|CB676911
EST:     CGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAG                         GTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCA
genomic: CGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAGgtttgcgatt ... ttaatttcagGTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCA
EST: gi|29671006|gb|CB667281.1|CB667281
EST:     CGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAG                         GTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCA
genomic: CGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAGgtttgcgatt ... ttaatttcagGTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCA

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: 70 (upstream exon), 73 (downstream exon)
Score: 40

TCAAATCTTCGAGGGGCATTCTCACTATGTTATGCAAGTCACATTTAACCCGAAAGATACCAATACTTTTGCTAGTGCTTCACTTGATCGCACAGTAAAGgtttgcgatt ... ttaatttcagGTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCAAAAGGTGTCAATTGTGTTGATTACTTTACTGGTGGTGATCGCCCATACT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttctaacatttcttggtctggatttgaatgtggtgcccttatttaatttcagGTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCAAAAGGTGTCAATTGTGTTGATTACTTTACTGGTGGTGATCGCCCATACT
                                      cccttattt  CT-rich tract
                                         ttatttaatttca  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgcgattttgttccttacatttgcttggcatagtttttgcatttctaacatttcttggtctggatttgaatgtggtgcccttatttaatttcagGTATGGAGTCTTGGTTCCCCTGATCCTAATTTCACATTAGATGGCCATTCAAAAGGTGTCAATTGTGTTGATTACTTTACTGGTGGTGATCGCCCATACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG