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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttgacaaatatgcatcacttccttttatatcaaatgttcatcttactgcatgcataataatcttttaccgccaattctgaattctttgtcatttccagGATAATTTGAAGCTGATGGATGATCTGGCTGCACTGAGACCAACAGTATTTTCTAGCGTACCCCGGCTATATAACAGAATTTATGCTGC

Basic information

species Oryza sativa
transcript LOC_Os11g04980.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g04980.2 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 3
--acttgacaaatatgcatcacttcct-tttatatcaaatgttcatcttactgcatgcataataatcttttaccgccaattctgaattctttgtcat-ttccagGATAATTTGAAGCTGATGGATGATCTGGCTGCACTGAGACCAACAGTATTTTCTAGCGTACCCCGGCTATATAACAGAATTTATGCTGC
  |   |   |   | ||  | |   |  ||  |||  ||  |  | |  ||  |    ||  |   | | |||      ||||  | |||||| |  |||||||||||||||||||| |||||||||||||||||  ||||||| ||| ||||  | || || |||||| ||||||||||||||||| ||||
gtatgggttcagcttccaataatctgtacttgcatcccataattgtttacctataaatctacca--ttatgaccctttcatctg--tcctttgttaaattccagGATAATTTGAAGCTCATGGATGATCTGGCTGCTTTGAGACCGACAATATTCGCAAGTGTTCCCCGGTTATATAACAGAATTTATACTGC
















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|29679209|gb|CB675484.1|CB675484
EST:     ACCAGATTGCACTGCTTCACTATGGAGTTGCCATTGGATTCTACCAAGGG                         GATAATTTGAAGCTGATGGATGATCTGGCTGCACTGAGACCAACAGTATTT
genomic: ACCAGATTGCACTGCTTCACTATGGAGTTGCCATTGGATTCTACCAAGGGgtatgcagat ... tcatttccagGATAATTTGAAGCTGATGGATGATCTGGCTGCACTGAGACCAACAGTATTT
EST: gi|29679207|gb|CB675482.1|CB675482
EST:     ACCAGATTGCACTGCTTCACTATGGAGTTGCCATTGGATTCTACCAAGGG                         GATAATTTGAAGCTGATGGATGATCTGGCTGCACTGAGACCAACAGTATTT
genomic: ACCAGATTGCACTGCTTCACTATGGAGTTGCCATTGGATTCTACCAAGGGgtatgcagat ... tcatttccagGATAATTTGAAGCTGATGGATGATCTGGCTGCACTGAGACCAACAGTATTT
EST: gi|29671403|gb|CB667678.1|CB667678
EST:     ACCAGATTGCACTGCTTCACTATGGAGTTGCCATTGGATTCTACCAAGGG                         GATAATTTGAAGCTGATGGATGATCTGGCTGCACTGAGACCAACAGTATTT
genomic: ACCAGATTGCACTGCTTCACTATGGAGTTGCCATTGGATTCTACCAAGGGgtatgcagat ... tcatttccagGATAATTTGAAGCTGATGGATGATCTGGCTGCACTGAGACCAACAGTATTT
EST: gi|58663800|gb|CK052486.1|CK052486
EST:     ACCAGATTGCACTGCTTCACTATGGAGTTGCCATTGGATTCTACCAAGGG                         GATAATTTGAAGCTGATGGATGATCTGGCTGCACTGAGACCAACAGTATTT
genomic: ACCAGATTGCACTGCTTCACTATGGAGTTGCCATTGGATTCTACCAAGGGgtatgcagat ... tcatttccagGATAATTTGAAGCTGATGGATGATCTGGCTGCACTGAGACCAACAGTATTT
EST: gi|58688175|gb|CK076862.1|CK076862
EST:     ACCAGATTGCACTGCTTCACTATGGAGTTGCCATTGGATTCTACCAAGGG                         GATAATTTGAAGCTGATGGATGATCTGGCTGCACTGAGACCAACAGTATTT
genomic: ACCAGATTGCACTGCTTCACTATGGAGTTGCCATTGGATTCTACCAAGGGgtatgcagat ... tcatttccagGATAATTTGAAGCTGATGGATGATCTGGCTGCACTGAGACCAACAGTATTT
EST: gi|29670550|gb|CB666825.1|CB666825
EST:     ACCAGATTGCACTGCTTCACTATGGAGTTGCCATTGGATTCTACCAAGGG                         GATAATTTGAAGCTGATGGATGATCTGGCTGCACTGAGACCAACAGTATTT
genomic: ACCAGATTGCACTGCTTCACTATGGAGTTGCCATTGGATTCTACCAAGGGgtatgcagat ... tcatttccagGATAATTTGAAGCTGATGGATGATCTGGCTGCACTGAGACCAACAGTATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactgcatgcataataatcttttaccgccaattctgaattctttgtcatttccagGATAATTTGAAGCTGATGGATGATCTGGCTGCACTGAGACCAACAGTATTTTCTAGCGTACCCCGGCTATATAACAGAATTTATGCTGC
 atcttac  putative branch site (score: 3)
                                      ttctttgtcatttcc  putative PPT
          ataataatctttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttgacaaatatgcatcacttccttttatatcaaatgttcatcttactgcatgcataataatcttttaccgccaattctgaattctttgtcatttccagGATAATTTGAAGCTGATGGATGATCTGGCTGCACTGAGACCAACAGTATTTTCTAGCGTACCCCGGCTATATAACAGAATTTATGCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC