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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgccatgttcctatttctttgttatgaaatccccttgttctgtcaactcccttccttacttcatatgtgatgttttattcagGGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAG

Basic information

species Oryza sativa
transcript LOC_Os12g05650.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g05650.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G109785_T02 (Zea mays), 3'ss of exon 7
gtatgccatgttcctatttctttgttatgaaatccccttgttctgtcaactcccttccttacttcatatgtgatgttttattcagGGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAG
|||||| | ||| |     |||  || | | |   |||    |  | ||  ||     |||  | |||| ||   || | | ||||| |||||||| |||||||| || ||||| ||||||||||||| |||| | |||||||| |||||||||
gtatgctacgtttcacccccttgctttttatagttcctaagaccattaaagcct---gttagatgatatttggcattctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTAAACAGCTCCTTATCTCAG

upper sequence: LOC_Os12g05650.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM5G825902_T02 (Zea mays), 3'ss of exon 8
gtatgccatgttcctatttctttg-ttatgaaatccccttgttctgtcaactcccttccttacttcatatgtgatgttttattcagGGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAG
|||||| | ||| |     | ||| || | | |  | ||    |  | ||  ||     |||  | |||| ||   || | | ||||| |||||||| |||||||| || ||||| ||||||||||||| |||| | |||||||| |||||||||
gtatgctacgtttcaccccccttgctttttatagtcgctaagaccattaaagcct---gttagatgatatttggcattctgtacagGGTTTGGTTGCGAAGGACAAGTTTCATGTAAGTTACAGAGGTGGAAAACTAAACAGCTCCTTATCTCAG

upper sequence: LOC_Os12g05650.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G066496_T01 (Zea mays), 3'ss of exon 8
gtatgccatgttcctatttctttg--ttatgaaatccccttgttctgtcaactcccttccttacttcatatgtgatgttttattcagGGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAG
|||||| |||||||  |  | |||  || |  | |  |   |  | || ||  |      | |  | |||| ||    | ||| ||||| |||||||| |||||||| ||||||||||||||||||||||||||| | |||||||| | |||||||
gtatgctatgttccactccccttgctttttctagtttctaagaccagtaaaacct----atcagatgatatctggcactgtatacagGGTTTGGTTGCGAAGGACAAGTTCCATGTGAGTTACAGAGGTGCAAAACTAAACAGCTCCTCATCTCAG

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|27577338|gb|CB000033.1|CB000033
EST:     TCATCACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAA                         GGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTG
genomic: TCATCACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAAgtatgccatg ... ttttattcagGGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTG
EST: gi|88490918|gb|CI428190.1|CI428190
EST:     CGTTGATGTGGAATCAGCTGAGATAGATACTGAA                         GGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGGTGCAAAATT
genomic: CGTTGATGTGGAATCAGCTGAGATAGATACTGAAgtatgccatg ... ttttattcagGGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGA-GGTGCAAAATT
EST: gi|86255014|gb|CI017134.1|CI017134
EST:     TCATCACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAA                         GGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTG
genomic: TCATCACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAAgtatgccatg ... ttttattcagGGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTG
EST: gi|87026460|gb|CI252414.1|CI252414
EST:     TCATCACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAA                         GGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTG
genomic: TCATCACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAAgtatgccatg ... ttttattcagGGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTG
EST: gi|88241583|gb|CI241432.1|CI241432
EST:     TCATCACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAA                         GGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTG
genomic: TCATCACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAAgtatgccatg ... ttttattcagGGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTG
EST: gi|86823074|gb|CI253990.1|CI253990
EST:     TCATCACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAA                         GGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTG
genomic: TCATCACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAAgtatgccatg ... ttttattcagGGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTG
EST: gi|86823113|gb|CI254016.1|CI254016
EST:     TCATCACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAA                         GGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTG
genomic: TCATCACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAAgtatgccatg ... ttttattcagGGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTG
EST: gi|88240853|gb|CI238704.1|CI238704
EST:     TCATCACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAA                         GGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTG
genomic: TCATCACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAAgtatgccatg ... ttttattcagGGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTG
EST: gi|55408732|gb|CV721108.1|CV721108
EST:     TCATCACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAA                         GGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTG
genomic: TCATCACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAAgtatgccatg ... ttttattcagGGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTG
EST: gi|86540849|gb|CI181055.1|CI181055
EST:     CACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAA                         GGCTTGGTTGCAAAGGACGAATTCCATGTGAGTTACAGAGGTGCAAAATTG
genomic: CACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAAgtatgccatg ... ttttattcagGGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTG
EST: gi|8335146|gb|BE040130.1|BE040130
EST:     CTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAA                         GGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTG
genomic: CTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAAgtatgccatg ... ttttattcagGGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTG
EST: gi|5900741|gb|AU078396.1|AU078396
EST:     CCATCACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAA                         GGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTG
genomic: -CATCACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAAgtatgccatg ... ttttattcagGGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTG
EST: gi|89188397|gb|CI115646.1|CI115646
EST:     TCATCACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAA                         GGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCTAAATTG
genomic: TCATCACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAAgtatgccatg ... ttttattcagGGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTG
EST: gi|86259447|gb|CI008124.1|CI008124
EST:     TCATCACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAA                         GGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTG
genomic: TCATCACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAAgtatgccatg ... ttttattcagGGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTG
EST: gi|88205440|gb|CI205289.1|CI205289
EST:     TCATGACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAA                         GGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTG
genomic: TCATCACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAAgtatgccatg ... ttttattcagGGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTG
EST: gi|89165417|gb|CI102507.1|CI102507
EST:     TCATCACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAA                         GGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTG
genomic: TCATCACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAAgtatgccatg ... ttttattcagGGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTG
EST: gi|86251590|gb|CI016879.1|CI016879
EST:     TCATCACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAA                         GGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTG
genomic: TCATCACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAAgtatgccatg ... ttttattcagGGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 74 (upstream exon), 52 (downstream exon)
Score: 57

GTACATAGAGACAGCTGATCGGCCTGGTCTACTTCTGGAAATAGTGAAGATCATCACTGACGTGAACGTTGATGTGGAATCAGCTGAGATAGATACTGAAgtatgccatg ... ttttattcagGGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatccccttgttctgtcaactcccttccttacttcatatgtgatgttttattcagGGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAG
                         tccttac  putative branch site (score: 57)
                                             ttttattc  putative PPT
                                          atgttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgccatgttcctatttctttgttatgaaatccccttgttctgtcaactcccttccttacttcatatgtgatgttttattcagGGCTTGGTTGCAAAGGACAAATTCCATGTGAGTTACAGAGGTGCAAAATTGAACAGCTCATTATCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA