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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttgctggaccatgtcaaagtactcagccgattcattttttcaatgctagcatgccgaatttccattgtgagcactgatagctatatattttccttgcagCCAACTTACCTGCAGAAAACTTCTCCGACGTACTATCAGAGCATACATCAGGGGTATACTTTGGCTGGGCTGGACTTTCAACGCGAGGTATATTTAAGAT

Basic information

species Oryza sativa
transcript LOC_Os10g32730.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g32730.1 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G027115_T01 (Zea mays), 3'ss of exon 9
tttgctggaccatgtcaaagtactcagccg-attcattttttcaatgctagcatgc-cgaatttccattgtgagcactgatagctatatattttccttgcagCCAACTTACCTGCAGAAAACTTCTCCGACGTACTATCAGAGCATACATCAGGGGTATACTTTGGCTGGGCTGGACTTTCAACGCGAGGTATATTTAAGAT
  |  |  ||||     | |||      |  |||  ||| ||| ||||||  |  |  |  ||| | |   ||||| |||| ||| |   | |    | |||| || ||||| || || || || ||||||||| | ||||| ||||||||||||||||||||||||||||| |||||||||||||| ||||||| ||||||
--tagtataccaccattatgtatgagttcatatttgtttcttctatgctactacacgtggtttttcgtctggagcattgatggctttgcttctgtactacagCAAATTTACCCGCGGAGAATTTTTCCGACGTAGTGTCAGAACATACATCAGGGGTATACTTTGGCTGGGCAGGACTTTCAACGCGTGGTATATATAAGAT
















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|29623339|gb|CB628350.1|CB628350
EST:     TGTGATTAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATTCCAACAG                         CCAACTTACCTGCAGAAAACTTCTCCGATGTACTATCAGAGCATACATCAG
genomic: TGTGATTAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATTCCAACAGgtatggtgga ... ttccttgcagCCAACTTACCTGCAGAAAACTTCTCCGACGTACTATCAGAGCATACATCAG
EST: gi|29613709|gb|CB618722.1|CB618722
EST:     ATTAAAGGATTTGGCCGTGG-TCTAAAGTACTAGG-ATTCCAACAG                         CCAACTTACCTGCAGAAAACTTCTCCGATGTACTATCAGAGCATACATCAG
genomic: ATTAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATTCCAACAGgtatggtgga ... ttccttgcagCCAACTTACCTGCAGAAAACTTCTCCGACGTACTATCAGAGCATACATCAG
EST: gi|29671819|gb|CB668094.1|CB668094
EST:     TGTGATTAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATTCCAACAG                         CCAACTTACCTGCAGAAAACTTCTCCGACGTACTATCAGAGCATACATCAG
genomic: TGTGATTAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATTCCAACAGgtatggtgga ... ttccttgcagCCAACTTACCTGCAGAAAACTTCTCCGACGTACTATCAGAGCATACATCAG
EST: gi|29629324|gb|CB634335.1|CB634335
EST:     TGTGATTAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATTCCAACAG                         CCAACTTACCTGCAGAAAACTTCTCCGATGTACTATCAGAGCATACATCAG
genomic: TGTGATTAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATTCCAACAGgtatggtgga ... ttccttgcagCCAACTTACCTGCAGAAAACTTCTCCGACGTACTATCAGAGCATACATCAG
EST: gi|29671820|gb|CB668095.1|CB668095
EST:     AAAGTACTAGGAATTCCAACAG                         CCAACTTACCTGCAGAAAACTTCTCCGACGTACTATCAGAGCATACATCAG
genomic: AAAGTACTAGGAATTCCAACAGgtatggtgga ... ttccttgcagCCAACTTACCTGCAGAAAACTTCTCCGACGTACTATCAGAGCATACATCAG
EST: gi|29684882|gb|CB681157.1|CB681157
EST:     TGTGATTAAAGGATTTGGCCGTGGATCTAAAGTACTAAGAATTCCAACAG                         CCAACTTACCTGCAGAAAACTTCTCCAACGTACTATCATATCATACATCAC
genomic: TGTGATTAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATTCCAACAGgtatggtgga ... ttccttgcagCCAACTTACCTGCAGAAAACTTCTCCGACGTACTATCAGAGCATACATCAG
EST: gi|29623338|gb|CB628349.1|CB628349
EST:     TGTGATTAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATTCCAACAG                         CCAACTTACCTGCAGAAAACTTCTCCGATGTACTATCAGAGCATACATCAG
genomic: TGTGATTAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATTCCAACAGgtatggtgga ... ttccttgcagCCAACTTACCTGCAGAAAACTTCTCCGACGTACTATCAGAGCATACATCAG
EST: gi|33680484|gb|CF308723.1|CF308723
EST:     TGTGATTAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATTCCAACAG                         CCAACTTACCTGCAGAAAACTTCTCCGACGTACTATCAGAGCATACATCAG
genomic: TGTGATTAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATTCCAACAGgtatggtgga ... ttccttgcagCCAACTTACCTGCAGAAAACTTCTCCGACGTACTATCAGAGCATACATCAG
EST: gi|29629325|gb|CB634336.1|CB634336
EST:     ATTAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATTCCAACAG                         CCAACTTACCTGCAGAAAACTTCTCCGATGTACTATCAGAGCATACATCAG
genomic: ATTAAAGGATTTGGCCGTGGTTCTAAAGTACTAGGAATTCCAACAGgtatggtgga ... ttccttgcagCCAACTTACCTGCAGAAAACTTCTCCGACGTACTATCAGAGCATACATCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctagcatgccgaatttccattgtgagcactgatagctatatattttccttgcagCCAACTTACCTGCAGAAAACTTCTCCGACGTACTATCAGAGCATACATCAGGGGTATACTTTGGCTGGGCTGGACTTTCAACGCGAGGTATATTTAAGAT
                           cactgat  putative branch site (score: 3)
                                         tattttcctt  putative PPT
                                atagctatatatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttgctggaccatgtcaaagtactcagccgattcattttttcaatgctagcatgccgaatttccattgtgagcactgatagctatatattttccttgcagCCAACTTACCTGCAGAAAACTTCTCCGACGTACTATCAGAGCATACATCAGGGGTATACTTTGGCTGGGCTGGACTTTCAACGCGAGGTATATTTAAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA