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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgcgccttgtatcttgttatttctcagatggttctctaagtcgtccctaatataatttctattgcttatttgcagCATGGCCAATGTATTCATCGTTGCTCCTGAAAGTCTAGCTTCCTTATTTGAAGGAACCCCCAGTATCCGGAAAGATGCCTTGCG

Basic information

species Oryza sativa
transcript LOC_Os12g13590.2
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g13590.2 (Oryza sativa), 3'ss of exon 19
lower sequence: GRMZM5G823484_T01 (Zea mays), 3'ss of exon 8
gtgagtgcgccttgtatcttgttatttctcagatggttctctaagtcgtccctaatataatttctattgcttatttgcagCATGGCCAATGTATTCATCGTTGCTCCTGAAAGTCTAGCTTCCTTATTTGAAGGAACCCCCAGTATCCGGAAAGATGCCTTGCG
|| ||||  |  ||| |  | |  |      |||| |||| | |    | | | |||     | |||    |||||||||  |||| || || ||||| |||||||| |||||| |||| ||| | ||||||||||||||||| ||||| || ||||||||| |
gtaagtgttctatgtgtagtttcgtcat---gatgcttctgtcaactctgc-tgata----ctgtatcttgtatttgcagTGTGGCGAACGTCTTCATTGTTGCTCCAGAAAGTTTAGCATCCCTGTTTGAAGGAACCCCCAGCATCCGAAAGGATGCCTTGAG
















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|33689209|gb|CF317448.1|CF317448
EST:     CGTAGCTTCAATGCCCCATCGATAGATGAAAAGTTTGAACTGCTTGGAAT                         CATGGCCAATGTATTCATCGTTGCTCCTGAAAGTCTAGCTTCCTTATTTGA
genomic: CGTAGCTTCAATGCCCCATCGATAGATGAAAAGTTTGAACTGCTTGGAATgtgagtgcgc ... ttatttgcagCATGGCCAATGTATTCATCGTTGCTCCTGAAAGTCTAGCTTCCTTATTTGA
EST: gi|87029720|gb|CI274401.1|CI274401
EST:     CGTAGCTTCAATGCCCCATCGATAGATGAAAAGTTTGAACTGCTTGGAAT                         CATGGCCAATGTATTCATCGTTGCTCCTGAAAGTCTAGCTTCCTTATTTGA
genomic: CGTAGCTTCAATGCCCCATCGATAGATGAAAAGTTTGAACTGCTTGGAATgtgagtgcgc ... ttatttgcagCATGGCCAATGTATTCATCGTTGCTCCTGAAAGTCTAGCTTCCTTATTTGA
EST: gi|88546679|gb|CI476345.1|CI476345
EST:     TGAACTGCTTGGAAT                         CATGGCCAATGTATTCATCGTTGCTCCTGAAAGTCTAGCTTCCTTATTTGA
genomic: TGAACTGCTTGGAATgtgagtgcgc ... ttatttgcagCATGGCCAATGTATTCATCGTTGCTCCTGAAAGTCTAGCTTCCTTATTTGA
EST: gi|66920327|gb|CX107175.1|CX107175
EST:     CGTAGCTTCAATGCCCCATCGATAGATGAAAAGTTTGAACTGCTTGGAAT                         CATGGCCAATGTATTCATCGTTGCTCCTGAAAGTCTAGCTTCCTTATTTGA
genomic: CGTAGCTTCAATGCCCCATCGATAGATGAAAAGTTTGAACTGCTTGGAATgtgagtgcgc ... ttatttgcagCATGGCCAATGTATTCATCGTTGCTCCTGAAAGTCTAGCTTCCTTATTTGA
EST: gi|88980840|gb|CI022530.1|CI022530
EST:     ATGCCCCATCGATAGATGAAAAGTTTGAACTGCTTGGAAT                         CATGGCCAATGTATTCATCGTTGCTCCTGAAAGTCTAGCTTCCTTATTTGA
genomic: ATGCCCCATCGATAGATGAAAAGTTTGAACTGCTTGGAATgtgagtgcgc ... ttatttgcagCATGGCCAATGTATTCATCGTTGCTCCTGAAAGTCTAGCTTCCTTATTTGA
EST: gi|88974506|gb|CI022047.1|CI022047
EST:     CGTAGCTTCAATGCCCCATCGATAGATGAAAAGTTTGAACTGCTTGGAAT                         CATGGCCAATGTATTCATCGTTGCTCCTGAAAGTCTAGCTTCCTTATTTGA
genomic: CGTAGCTTCAATGCCCCATCGATAGATGAAAAGTTTGAACTGCTTGGAATgtgagtgcgc ... ttatttgcagCATGGCCAATGTATTCATCGTTGCTCCTGAAAGTCTAGCTTCCTTATTTGA
EST: gi|27577943|gb|CB000638.1|CB000638
EST:     CGTAGCTTCAATGCCCCATCGATAGATGAAAAGTTTGAACTGCTTGGAAT                         CATGGCCAATGTATTCATCGTTGCTCCTGAAAGTCTAGCTTCCTTATTTGA
genomic: CGTAGCTTCAATGCCCCATCGATAGATGAAAAGTTTGAACTGCTTGGAATgtgagtgcgc ... ttatttgcagCATGGCCAATGTATTCATCGTTGCTCCTGAAAGTCTAGCTTCCTTATTTGA
EST: gi|58666677|gb|CK055363.1|CK055363
EST:     CGTAGCTTCAATGCCCCATCGATAGATGAAAAGTTTGAACTGCTTGGAAT                         CATGGCCAATGTATTCATCGTTGCTCCTGAAAGTCTAGCTTCCTTATTTGA
genomic: CGTAGCTTCAATGCCCCATCGATAGATGAAAAGTTTGAACTGCTTGGAATgtgagtgcgc ... ttatttgcagCATGGCCAATGTATTCATCGTTGCTCCTGAAAGTCTAGCTTCCTTATTTGA
EST: gi|33689213|gb|CF317452.1|CF317452
EST:     CGTAGCTTCAATGCCCCATCGATAGATGAAAAGTTTGAACTGCTTGGAAT                         CATGGCCAATGTATTCATCGTTGCTCCTGAAAGTCTAGCTTCCTTATTTGA
genomic: CGTAGCTTCAATGCCCCATCGATAGATGAAAAGTTTGAACTGCTTGGAATgtgagtgcgc ... ttatttgcagCATGGCCAATGTATTCATCGTTGCTCCTGAAAGTCTAGCTTCCTTATTTGA
EST: gi|88508860|gb|CI436366.1|CI436366
EST:     CGTAGCTTCAATGCCCCATCGATAGATGAAAAGTTTGAACTGCTTGGAAT                         CATGGCCAATGTATTCATCGTTGCTCCTGAAAGTCTAGCTTCCTTATTTGA
genomic: CGTAGCTTCAATGCCCCATCGATAGATGAAAAGTTTGAACTGCTTGGAATgtgagtgcgc ... ttatttgcagCATGGCCAATGTATTCATCGTTGCTCCTGAAAGTCTAGCTTCCTTATTTGA
EST: gi|27576853|gb|CA999547.1|CA999547
EST:     CGTAGCTTCAATGCCCCATCGATAGATGAAAAGTTTGAACTGCTTGGAAT                         CATGGCCAATGTATTCATCGTTGCTCCTGAAAGTCTAGCTTCCTTATTTGA
genomic: CGTAGCTTCAATGCCCCATCGATAGATGAAAAGTTTGAACTGCTTGGAATgtgagtgcgc ... ttatttgcagCATGGCCAATGTATTCATCGTTGCTCCTGAAAGTCTAGCTTCCTTATTTGA
EST: gi|29632379|gb|CB637388.1|CB637388
EST:     CGTAGCTTCAATGCCCCATCGATAGATGAAAAGTTTGAACTGCTTGGAAT                         CATGGCCAATGTATTCATCGTTGCTCCTGAAAGTCTAGCTTCCTTATTTGA
genomic: CGTAGCTTCAATGCCCCATCGATAGATGAAAAGTTTGAACTGCTTGGAATgtgagtgcgc ... ttatttgcagCATGGCCAATGTATTCATCGTTGCTCCTGAAAGTCTAGCTTCCTTATTTGA
EST: gi|87029773|gb|CI274454.1|CI274454
EST:     CGTAGCTTCAATGCCCCATCGATAGATGAAAAGTTTGAACTGCTTGGAAT                         CATGGCCAATGTATTCATCGTTGCTCCTGAAAGTCTAGCTTCCTTATTTGA
genomic: CGTAGCTTCAATGCCCCATCGATAGATGAAAAGTTTGAACTGCTTGGAATgtgagtgcgc ... ttatttgcagCATGGCCAATGTATTCATCGTTGCTCCTGAAAGTCTAGCTTCCTTATTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctcagatggttctctaagtcgtccctaatataatttctattgcttatttgcagCATGGCCAATGTATTCATCGTTGCTCCTGAAAGTCTAGCTTCCTTATTTGAAGGAACCCCCAGTATCCGGAAAGATGCCTTGCG
                        ccctaat  putative branch site (score: 3)
                                            cttattt  putative PPT
                           taatataatttctatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgcgccttgtatcttgttatttctcagatggttctctaagtcgtccctaatataatttctattgcttatttgcagCATGGCCAATGTATTCATCGTTGCTCCTGAAAGTCTAGCTTCCTTATTTGAAGGAACCCCCAGTATCCGGAAAGATGCCTTGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG