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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctgtgaataatcagaaacagcttctgttcattacttatcccatgcatctcttactttcggaagtctctctgactagtgactactgctaaaaaattgcagATTGTAACATTAGAAGATGTTGTGGAAGAAATAGTTGGAGAAATCTTCGATGAGAATGATTCAAAG

Basic information

species Oryza sativa
transcript LOC_Os03g39640.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g39640.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G153928_T03 (Zea mays), 3'ss of exon 3
tctgtgaataatcagaaacagcttctgttca-ttacttatcccatgcatctcttactttcggaagtctct---ctgactagtgactactgctaaaaaattgcagATTGTAACATTAGAAGATGTTGTGGAAGAAATAGTTGGAGAAATCTTCGATGAGAATGATTCAAAG
  | |      | |||||  | || ||  || ||  | ||  | |   | | | |||    | |  ||      |   |  ||| |  ||  ||||||| ||||||| ||||||||||||| || ||||||||||||||||| ||||||||||||||||||||||| |||
--tattg-cgtttagaaaatgtttatgcacagtttgtaatttcgtatgtttatcactgcatggacactaggaattacttgctgaattttgtcaaaaaat-gcagATT-TAACATTAGAAGACGTAGTGGAAGAAATAGTTGGTGAAATCTTCGATGAGAATGATTCCAAG

upper sequence: LOC_Os03g39640.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA02G46780.1 (Glycine max), 3'ss of exon 10
tctgtgaataatcagaaacagcttctgttca--ttacttat---cccatgcatctcttactttcggaagtctctctgactagtgactactgctaaaaaattgcagATTGTAACATTAGAAGATGTTGTGGAAGAAATAGTTGGAGAAATCTTCGATGAGAATGATTCAAAG
  |   | |  || ||||    |||  |  |   | |||||     |   || || | | |||   || |||   || ||  |   |  ||| |   ||   |||||||||||| | ||||||||||| || ||||| ||||| ||||| || ||||| ||||| ||||||
--tccaagtcttctgaaatccattccatgtaatctgcttataagttctaacaactttcagtttatcaaatctagatgtcttattgattttgccatctaa---cagATTGTAACACTCGAAGATGTTGTTGAGGAAATTGTTGGTGAAATATTTGATGAAAATGACTCAAAG

upper sequence: LOC_Os03g39640.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GLYMA14G01920.1 (Glycine max), 3'ss of exon 10
tctgtgaataatcagaaacagcttctgttcattacttat---cccatgcatctcttactttcggaagtctctctgactagtgactactgctaaaaaattgcagATTGTAACATTAGAAGATGTTGTGGAAGAAATAGTTGGAGAAATCTTCGATGAGAATGATTCAAAG
||   |  |  | | |  ||     |||    | |||||     |   ||  | | | |||   || | |   || ||  |   || ||| |   ||   |||||||||||  | ||||||||||| || ||||| ||||| |||||||| ||||| ||||| ||||||
tccaagtcttctgaaatccattccttgtaatctgcttataagttctaacaattttcagtttatcaaatataaatgtcttattgatattgccatctaa---cagATTGTAACTCTTGAAGATGTTGTTGAGGAAATTGTTGGTGAAATCTTTGATGAAAATGACTCAAAG

upper sequence: LOC_Os03g39640.2 (Oryza sativa), 3'ss of exon 10
lower sequence: Vv19s0090g01820.t01 (Vitis vinifera), 3'ss of exon 10
tctgtgaataatcagaaaca-gcttctgttcattacttatcccatgca-tctcttactttcgg-----aagtctctctgactagtgactactgctaaaaaattgcagATTGTAACATTAGAAGATGTTGTGGAAGAAATAGTTGGAGAAATCTTCGATGAGAATGATTCAAAG
       || || |||   | ||  || | ||  |         |||| | | |||  ||| |      |  ||   |   |  | |    | ||  |  |   ||||| |||||  | |||||||| || || ||||| || || |||||||||||||||||||||||||| 
-----atattatgagatttatgccactatccaacatcctctttgtgcacttttttatattctgtgtcagaaccttatttcttccttatcttttctgtatga--acagATAGTAACCCTGGAAGATGTGGTTGAGGAAATTGTCGGTGAAATCTTCGATGAGAATGATTCAAAA

upper sequence: LOC_Os03g39640.2 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S147_55V6.1 (Physcomitrella patens), 3'ss of exon 12
-tctgtgaataatcagaaacagcttctgttca--ttacttatcccatgcatctcttactttcggaagtctctctgactagtgactactgctaaaaaattgcagATTGTAACATTAGAAGATGTTGTGGAAGAAATAGTTGGAGAAATCTTCGATGAGAATGATTCAAAG
 | |  |    || |     |  |    | ||  ||     |    |  || | ||  |||  | | ||  |   | || |||  |   |   | |||| ||| |||| ||| | ||||||||||||||||| || ||||| ||||| || ||||| |||||||| |||
ttgtaagggggattaattttaattcaactccaagttgaggttgtagtaaattttttgttttgtgcaatcaatacaaatactgatgaacac---agaattacagGTTGTGACACTGGAAGATGTTGTGGAAGAGATTGTTGGCGAAATTTTTGATGAAAATGATTCCAAG

upper sequence: LOC_Os03g39640.2 (Oryza sativa), 3'ss of exon 10
lower sequence: PP1S7_173V6.1 (Physcomitrella patens), 3'ss of exon 13
tctgtgaataa--tcagaaacagcttctgttcattacttatcccatgcatctcttactttcggaagtctctctgactagtgactactgctaaaaaat-tgcagATTGTAACATTAGAAGATGTTGTGGAAGAAATAGTTGGAGAAATCTTCGATGAGAATGATTCAAAG
 ||   | | |  |   |||      ||||   | | | ||   ||  || | | |       || |  |  ||   |   | |    | |     | |  || |||||||  | ||||||||||||||||| || ||||| || || |||||||| ||||||||||||
acttcaattcaactttaaaattaaggctgtgt-tgaatcatttgat--atttgtaatcaatacaaataccgatgctaacaaagttgcaccatgcgttatttagGTTGTAACGCTGGAAGATGTTGTGGAAGAGATTGTTGGGGAGATTTTCGATGAAAATGATTCAAAG

upper sequence: LOC_Os03g39640.2 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ38618 (Selaginella moellendorffii), 3'ss of exon 10
tctgtgaataatcagaaacagcttctgttcattacttatcccatgcatctcttactttcggaagtctctctgactagtgactactgctaaaaaattgcagATTGTAACATTAGAAGATGTTGTGGAAGAAATAGTTGGAGAAATCTTCGATGAGAATGATTCAAAG
                                           | | | || ||  |||| |  ||| |  |    | |  || | |      |||||||||||||||| | ||||||||||| || || || ||||||||||| || || || || ||||| |||
------------------------------------------gtacgtttcatatcttcgtagttcttttcgg---gagtataatacacttctattgcagATTGTAACACTGGAAGATGTTGTTGAGGAGATTGTTGGAGAAATTTTTGACGAAAACGATTCCAAG

upper sequence: LOC_Os03g39640.2 (Oryza sativa), 3'ss of exon 10
lower sequence: EFJ31527 (Selaginella moellendorffii), 3'ss of exon 10
tctgtgaataatcagaaacagcttctgttcattacttatcccatgcatctcttactttcggaagtctctctgactagtgactactgctaaaaaattgcagATTGTAACATTAGAAGATGTTGTGGAAGAAATAGTTGGAGAAATCTTCGATGAGAATGATTCAAAG
                                                    ||| ||    |||   | |    |||   || | |      |||||||||||||||| | ||||||||||| || || || ||||||||||| || || || || ||||| |||
---------------------------------------------------gtacgtttcatagttcttttcgggagta--taatacacttctattgcagATTGTAACACTGGAAGATGTTGTTGAGGAGATTGTTGGAGAAATTTTTGACGAAAACGATTCCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catctcttactttcggaagtctctctgactagtgactactgctaaaaaattgcagATTGTAACATTAGAAGATGTTGTGGAAGAAATAGTTGGAGAAATCTTCGATGAGAATGATTCAAAG
                                       tgctaaa  putative branch site (score: 2)
                                          taaaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctgtgaataatcagaaacagcttctgttcattacttatcccatgcatctcttactttcggaagtctctctgactagtgactactgctaaaaaattgcagATTGTAACATTAGAAGATGTTGTGGAAGAAATAGTTGGAGAAATCTTCGATGAGAATGATTCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA