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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctaacttatctgcaatatgttcagttgggattgaccatgattattgttgttagaatttaccaactatcttattggtcctgtaactttatgatatttcagAAAATTTGCTAGTTACAAAGGAGCTCATCAAGATAGCAGATTTTGGACTTGCTCGTGAGATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCG

Basic information

species Oryza sativa
transcript LOC_Os06g02550.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g02550.2 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM5G864414_T02 (Zea mays), 3'ss of exon 8
-gctaacttatctgcaatatgttcagttgggattgaccatgattattgttgttagaatttaccaactatctta-ttggtcctgtaac--tttatgatatttcagAAAATTTGCTAGTTACAAAGGAGCTCATCAAGATAGCAGATTTTGGACTTGCTCGTGAGATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCG
   |||||||  || |   | | ||  ||||  ||    || | | ||||||||| |   | |||| | | || ||| || ||  |    || ||  ||||||||||||||||| ||||||||||| |||||||||||||| |||||||| ||||||||||| ||||||||||| ||||| || || ||||||||||| |||||
atttaacttacatgtaccgtttccatctggggatg----tgttcagtgttgttagcaaacaacaacaaccataattgatcttggtataacttgtgcaatttcagAAAATTTGCTTGTTACAAAGGAACTCATCAAGATAGCGGATTTTGGGCTTGCTCGTGAAATTTCTTCTGAGCCACCTTATACGGAATATGTGTCCACTCG

upper sequence: LOC_Os06g02550.2 (Oryza sativa), 3'ss of exon 8
lower sequence: Vv02s0033g01110.t01 (Vitis vinifera), 3'ss of exon 5
gctaacttatctgcaatatgttcagttgggattgaccatgatt-attgttgttagaatttaccaactatcttattggtcctgtaactttatgata--tttcagAAAATTTGCTAGTTACAAAGGAGCTCATCAAGATAGCAGATTTTGGACTTGCTCGTGAGATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCG
    | |||| ||     | |    |    | |   |||  |  ||| |  ||| ||     || ||  | ||    | |  |   | |||| |   ||||||| || ||| | |||||||| ||  | || || || || |||||||| |||||||| |||||   |||| ||||||||||||| |||||||| || || ||
---tatttatatgtgggttatagtttctcaaatatgcatcttccattctgattaaaaaaatgcatcttccataaaaattccttccttgtatgtttcttttcagAGAACTTGTTGGTTACAAAAGATGTAATAAAAATTGCTGATTTTGGTCTTGCTCGGGAGATCAATTCTCAACCACCATACACGGAATATGTCTCTACACG
















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


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttgttagaatttaccaactatcttattggtcctgtaactttatgatatttcagAAAATTTGCTAGTTACAAAGGAGCTCATCAAGATAGCAGATTTTGGACTTGCTCGTGAGATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCG
                                 ctgtaac  putative branch site (score: 3)
                                    taactttatgatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctaacttatctgcaatatgttcagttgggattgaccatgattattgttgttagaatttaccaactatcttattggtcctgtaactttatgatatttcagAAAATTTGCTAGTTACAAAGGAGCTCATCAAGATAGCAGATTTTGGACTTGCTCGTGAGATTTCTTCTGAACCACCATACACAGAATATGTGTCAACTCG

- - - - atctgca
- - - - - - - - - - - - - - - - - - catgatt
- - - - - - - - - - - - - - - - - - - - - - ttgttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtcctg