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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagacacacaacataattttttttttcagtaagacacgcacgattattaaggcatgctaaattcttggccttttttttttttgtctatgatttgcctttttcaccagATGCTGATACCTCAGCTCGATCCACTGACGGAGCAGCAGCTGATGGGGATGTGCAGCCTGCAGCAGTCGTCGGAGCAGACCGAGGAGGCGCTCGCGCAGG

Basic information

species Oryza sativa
transcript LOC_Os05g37170.4
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g37170.4 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G000842_T04 (Zea mays), 3'ss of exon 9
---gtagacacacaacataattttttttttcagta-agacacgcacgattattaaggcatgctaaattcttggccttttttttttttgtctatgatttgcctttttcaccagATGCTGATACCTCAGCTCGATCCACTGACGGAGCAGCAGCTGATGGGGATGTGCAGCCTGCAGCAGTCGTCGGAGCAGACCGAGGAGGCGCTCGCGCAGG
      | | |     ||   |   |  || | || | |   |||  |   |          ||| |  ||   |      | |||| | |||| ||||  |    || |||||||||||||| |||||||| || ||  |||||| ||||||||| ||||||| ||  ||||| | ||||||||||||||||||||||||||||| ||   
gtttccggctctttttatttctccgtggtttattatatattagcagcacgctgttaattaattaattaattaatcgccgggtcttttatatatg-tttgtgtgac-cagCAGATGCTGATACCGCAGCTCGACCCTCTCGCGGAGCCGCAGCTGATAGGGATGTACAATCTGCAACGGTCGTCGGAGCAGACCGAGGAGGCGCTCGTGC---

upper sequence: LOC_Os05g37170.4 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G000842_T03 (Zea mays), 3'ss of exon 10
---gtagacacacaacataattttttttttcagta-agacacgcacgattattaaggcatgctaaattcttggccttttttttttttgtctatgatttgcctttttcaccagATGCTGATACCTCAGCTCGATCCACTGACGGAGCAGCAGCTGATGGGGATGTGCAGCCTGCAGCAGTCGTCGGAGCAGACCGAGGAGGCGCTCGCGCAGG
      | | |     ||   |   |  || | || | |   |||  |   |          ||| |  ||   |      | |||| | |||| ||||  |    || |||||||||||||| |||||||| || ||  |||||| ||||||||| ||||||| ||  ||||| | ||||||||||||||||||||||||||||| |||||
gtttccggctctttttatttctccgtggtttattatatattagcagcacgctgttaattaattaattaattaatcgccgggtcttttatatatg-tttgtgtgac-cagcagATGCTGATACCGCAGCTCGACCCTCTCGCGGAGCCGCAGCTGATAGGGATGTACAATCTGCAACGGTCGTCGGAGCAGACCGAGGAGGCGCTCGTGCAGG

upper sequence: LOC_Os05g37170.4 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ22847 (Selaginella moellendorffii), 3'ss of exon 4
gtagacacacaacataattttttttttcagtaagacacgcacgat-tattaaggcatgctaaattcttggccttttttttttttgtctatgatttgcctttttc-accagATGCTGATACCTCAGCTCGATCCACTGACGGAGCAGCAGCTGATGGGGATGTGCAGCCTGCAGCAGTCGTCGGAGCAGACCGAGGAGGCGCTCGCGCAGG
                                      | | | | |||     |   || ||   |||||           |     |  |||||  ||||||    ||||  |||| || ||||| || || || || |||||||||||||||||||| |||| ||| ||||| || ||| ||||| ||||||| ||  |  ||||||
--------------------------------------gtaagctgtatcgtatcgatcttaag--ttggctgacgagaagatgaa--aaaatttgtttttttctgttagATCTTGATTCCACAGCTGGAGCCCCTCACCGAGCAGCAGCTGATGGGGATTTGCAACCTCCAGCAATCCTCGCAGCAGGCCGAGGACGCTTTGTCGCAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgctaaattcttggccttttttttttttgtctatgatttgcctttttcaccagATGCTGATACCTCAGCTCGATCCACTGACGGAGCAGCAGCTGATGGGGATGTGCAGCCTGCAGCAGTCGTCGGAGCAGACCGAGGAGGCGCTCGCGCAGG
  tgctaaa  putative branch site (score: 2)
                ccttttttttttttgt  putative PPT
                  ttttttttttttgtct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagacacacaacataattttttttttcagtaagacacgcacgattattaaggcatgctaaattcttggccttttttttttttgtctatgatttgcctttttcaccagATGCTGATACCTCAGCTCGATCCACTGACGGAGCAGCAGCTGATGGGGATGTGCAGCCTGCAGCAGTCGTCGGAGCAGACCGAGGAGGCGCTCGCGCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG