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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atccatcttacttactacatggattctttgccataataatcgtttacattcaatggattctttgccatatatctgatgtgtatattgttgttgtttctagGATAATTTGAAGCTGATGGATGATCTGGCTGCATTGAGACCAACAGTATTTCCTAGTGTGCCTCGGCTATATAATAGAATTTATGCTGC

Basic information

species Oryza sativa
transcript LOC_Os12g04990.3
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g04990.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 3
--atccatcttacttactacatggattctttgc-cataataatcgtttacattcaatggattctttgccatatatctgatgtgtatattgttgttgtttctagGATAATTTGAAGCTGATGGATGATCTGGCTGCATTGAGACCAACAGTATTTCCTAGTGTGCCTCGGCTATATAATAGAATTTATGCTGC
  ||   |    ||| | | |     |  ||||     ||||| |||||| |   ||  ||        ||    ||    | | |  | |  |   ||| |||||||||||||||| ||||||||||||||||| |||||||| ||| ||||  | ||||| || ||| ||||||| ||||||||| ||||
gtatgggttcagcttccaataatctgtacttgcatcccataattgtttacct---ataaatctaccattatgaccctttcatctgtcctttgttaaattccagGATAATTTGAAGCTCATGGATGATCTGGCTGCTTTGAGACCGACAATATTCGCAAGTGTTCCCCGGTTATATAACAGAATTTATACTGC
















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|58602340|gb|CK012868.1|CK012868
EST:     ACCAGGTCTCAGTGGTTCACTATGGTGTTGCCATTGGTTTCTACCAAGGG                         GATAATTTGAAGCTGATGGATGATCTGGCTGCATTGAGACCAACAGTATTT
genomic: ACCAGGTCTCAGTGGTTCACTATGGTGTTGCCATTGGTTTCTACCAAGGGgtatgcagat ... ttgtttctagGATAATTTGAAGCTGATGGATGATCTGGCTGCATTGAGACCAACAGTATTT
EST: gi|58693358|gb|CK082045.1|CK082045
EST:     TGGTGTTGCCATTGGTTTCTACCAAGGG                         GATAATTTGAAGCTGATGGATGATCTGGCTGCATTGAGACCAACAGTATTT
genomic: TGGTGTTGCCATTGGTTTCTACCAAGGGgtatgcagat ... ttgtttctagGATAATTTGAAGCTGATGGATGATCTGGCTGCATTGAGACCAACAGTATTT
EST: gi|58655107|gb|CK043787.1|CK043787
EST:     ACCAGGTCTCAGTGGTTCACTATGGTGTTGCCATTGGTTTCTACCAAGGG                         GATAATTTGAAGCTGATGGATGATCTGGCTGCATTGAGACCAACAGTATTT
genomic: ACCAGGTCTCAGTGGTTCACTATGGTGTTGCCATTGGTTTCTACCAAGGGgtatgcagat ... ttgtttctagGATAATTTGAAGCTGATGGATGATCTGGCTGCATTGAGACCAACAGTATTT
EST: gi|58694148|gb|CK082835.1|CK082835
EST:     ACCAGGTCTCAGTGGTTCACTATGGTGTTGCCATTGGTTTCTACCAAGGG                         GATAATTTGAAGCTGATGGATGATCTGGCTGCATTGAGACCAACAGTATTT
genomic: ACCAGGTCTCAGTGGTTCACTATGGTGTTGCCATTGGTTTCTACCAAGGGgtatgcagat ... ttgtttctagGATAATTTGAAGCTGATGGATGATCTGGCTGCATTGAGACCAACAGTATTT
EST: gi|33797098|gb|CF324415.1|CF324415
EST:     ACCAGGTCTCAGTGGTTCACTATGGTGTTGCCATTGGTTTCTACCAAGGG                         GATAATTTGAAGCTGATGGATGATCTGGCTGCATTGAGACCAACAGTATTT
genomic: ACCAGGTCTCAGTGGTTCACTATGGTGTTGCCATTGGTTTCTACCAAGGGgtatgcagat ... ttgtttctagGATAATTTGAAGCTGATGGATGATCTGGCTGCATTGAGACCAACAGTATTT
EST: gi|58689916|gb|CK078603.1|CK078603
EST:     ACCAGGTCTCAGTGGTTCACTATGGTGTTGCCATTGGTTTCTACCAAGGG                         GATAATTTGAAGCTGATGGATGATCTGGCTGCATTGAGACCAACAGTATTT
genomic: ACCAGGTCTCAGTGGTTCACTATGGTGTTGCCATTGGTTTCTACCAAGGGgtatgcagat ... ttgtttctagGATAATTTGAAGCTGATGGATGATCTGGCTGCATTGAGACCAACAGTATTT
EST: gi|58666789|gb|CK055475.1|CK055475
EST:     ACCAGGTCTCAGTGGTTCACTATGGTGTTGCCATTGGTTTCTACCAAGGG                         GATAATTTGAAGCTGATGGATGATCTGGCTGC
genomic: ACCAGGTCTCAGTGGTTCACTATGGTGTTGCCATTGGTTTCTACCAAGGGgtatgcagat ... ttgtttctagGATAATTTGAAGCTGATGGATGATCTGGCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acattcaatggattctttgccatatatctgatgtgtatattgttgttgtttctagGATAATTTGAAGCTGATGGATGATCTGGCTGCATTGAGACCAACAGTATTTCCTAGTGTGCCTCGGCTATATAATAGAATTTATGCTGC
                         atctgat  putative branch site (score: 4)
                                             ttgtttct  putative PPT
                                   tatattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atccatcttacttactacatggattctttgccataataatcgtttacattcaatggattctttgccatatatctgatgtgtatattgttgttgtttctagGATAATTTGAAGCTGATGGATGATCTGGCTGCATTGAGACCAACAGTATTTCCTAGTGTGCCTCGGCTATATAATAGAATTTATGCTGC

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