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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcatggattttattcatgttgagcttttgctattcccgtttgattttgcatactggcattatctttgtaatatgttacactaacccttttgtattccagGGCCAATTTTGTGGAAGACCTGAAATTTCTGCAGATCAAAGGGAGAAGTACCTGCAAAGATTGCAGCAAGTACAACAACAAGGCAGCCTTCTTAATGTTT

Basic information

species Oryza sativa
transcript LOC_Os03g44900.3
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g44900.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G340749_T02 (Zea mays), 3'ss of exon 2
---atcatggattttattcatgttgagcttttgctattcccgtttgattttgcatactggcattatctttgtaatatgttacactaacccttttgtattccagGGCCAATTTTGTGGAAGACCTGAAATTTCTGCAGATCAAAGGGAGAAGTACCTGCAAAGATTGCAGCAAGTACAACAACAAGG---CAGCCTTCTTAATGTTT
      | | | |||||| || |||| |||    |  |      | |||  ||   |    | |   ||    |||| | ||  |   |  | |   |||||| | || ||| ||||||| ||||| |||||||| ||||| |||||||||||| | |||||| ||||||||||||| || |||||   ||||||||| || |   
tactgaaagaactttatttattttgaacttgatttgctaattcctcattgggctcgcaattacttgtttgcctatatatgacgtttttctctat---ttccagAGTCATTTTCGTGGAAGGCCTGAGATTTCTGCTGATCACAGGGAGAAGTACATACAAAGACTGCAGCAAGTACAGCAGCAAGGTGGCAGCCTTCTGAACG---

upper sequence: LOC_Os03g44900.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AC197122.3_FGT003 (Zea mays), 3'ss of exon 10
atcatggattttattcatgttgagcttttgct-attcccgtttgattttgcatactggcattatctttgtaatatgttacactaacccttttgtattccagGGCCAATTTTGTGGAAGACCTGAAATTTCTGCAGATCAAAGGGAGAAGTACCTGCAAAGATTGCAGCAAGTACAACAACAAGG---CAGCCTTCTTAATGTTT
  |    |    ||| || ||||  |||   |   |      | |||  ||  ||    | |   ||    |||||  |   |  | |  |    ||||||   || |   ||||||| ||||| |||||||| ||||| |||||||||||| | || ||| ||||||||||||| || |||||   ||||||||| ||||   
-actgaaagaacatttattttgaattttgatttgataattcctcattgggctcacaaatacttgtttgcctatatgacattttttctcgctgtatttccagAATCAGTACCGTGGAAGGCCTGAGATTTCTGCTGATCACAGGGAGAAGTACATACAGAGACTGCAGCAAGTACAGCAGCAAGGTGGCAGCCTTCTGAATG---
















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|88408656|gb|CI686162.1|CI686162
EST:     TTCAATGGAGGCCTCAAAACACTGCTGGTTTGCAAAATCAAAGTGAAGCG                         GGCCAATTTTGTGGAAGACCTGAAATTTCTGCAGATC
genomic: TTCAATGGAGGCCTCAAAACACTGCTGGTTTGCAAAATCAAAGTGAAGCGgtaagtacct ... tgtattccagGGCCAATTTTGTGGAAGACCTGAAATTTCTGCAGATC
EST: gi|88461701|gb|CI695545.1|CI695545
EST:     TTCAATGGAGGCCTCAAAACACTGCTGGTTTGCAAAATCAAAGTGAAGCG                         GGCCAATTTTGTGGAAGACCTGAAATTTCTGCAGATCAAAGGGA
genomic: TTCAATGGAGGCCTCAAAACACTGCTGGTTTGCAAAATCAAAGTGAAGCGgtaagtacct ... tgtattccagGGCCAATTTTGTGGAAGACCTGAAATTTCTGCAGATCAAAGGGA
EST: gi|58684868|gb|CK073555.1|CK073555
EST:     TTCAATGGAGGCCTCAAAACACTGCTGGTTTGCAAAATCAAAGTGAAGCG                         GGCCAATTTCGTGGAAG
genomic: TTCAATGGAGGCCTCAAAACACTGCTGGTTTGCAAAATCAAAGTGAAGCGgtaagtacct ... tgtattccagGGCCAATTTTGTGGAAG
EST: gi|88468945|gb|CI696953.1|CI696953
EST:     TTCAATGGAGGCCTCAAAACACTGCTGGTTTGCAAAATCAAAGTGAAGCG                         GGCCAATTTTGTGGAAGAC
genomic: TTCAATGGAGGCCTCAAAACACTGCTGGTTTGCAAAATCAAAGTGAAGCGgtaagtacct ... tgtattccagGGCCAATTTTGTGGAAGAC
EST: gi|58590602|gb|CF988910.1|CF988910
EST:     TTCAATGGAGGCCTCAAAACACTGCTGGTTTGCAAAATCAAAGTGAAGCG                         GGCCAATTTCGTGGAAGACCTGAAATTTCTGCAGATCAAAGGGAGAAGTAC
genomic: TTCAATGGAGGCCTCAAAACACTGCTGGTTTGCAAAATCAAAGTGAAGCGgtaagtacct ... tgtattccagGGCCAATTTTGTGGAAGACCTGAAATTTCTGCAGATCAAAGGGAGAAGTAC
EST: gi|88381712|gb|CI682382.1|CI682382
EST:     TTCAATGGAGGCCTCAAAACACTGCTGGTTTGCAAAATCAAAGTGAAGCG                         GGCCAATTTTGTGGAAGACCTGAAATTTCTGCAGATCAAAGGGAGAAGTAC
genomic: TTCAATGGAGGCCTCAAAACACTGCTGGTTTGCAAAATCAAAGTGAAGCGgtaagtacct ... tgtattccagGGCCAATTTTGTGGAAGACCTGAAATTTCTGCAGATCAAAGGGAGAAGTAC
EST: gi|88313396|gb|CI671509.1|CI671509
EST:     TTCAATGGAGGCCTCAAAACACTGCTGGTTTGCAAAATCAAAGTGAAGCG                         GGCCAATTTTGTGGAAGACC
genomic: TTCAATGGAGGCCTCAAAACACTGCTGGTTTGCAAAATCAAAGTGAAGCGgtaagtacct ... tgtattccagGGCCAATTTTGTGGAAGACC
EST: gi|58676955|gb|CK065642.1|CK065642
EST:     TTCAATGGAGGCCTCAAAACACTGCTGGTTTGCAAAATCAAAGTGAAGCG                         GGCCAATTTCGTGGAAGACCTGAAATTTCTGCAGATCAAAGGGAGAAGTAC
genomic: TTCAATGGAGGCCTCAAAACACTGCTGGTTTGCAAAATCAAAGTGAAGCGgtaagtacct ... tgtattccagGGCCAATTTTGTGGAAGACCTGAAATTTCTGCAGATCAAAGGGAGAAGTAC
EST: gi|88349186|gb|CI678160.1|CI678160
EST:     TTCAATGGAGGCCTCAAAACACTGCTGGTTTGCAAAATCAAAGTGAAGCG                         GGCCAATTTTGTGGAAGACCTGAAATTTCTGCAGATCAAAGG
genomic: TTCAATGGAGGCCTCAAAACACTGCTGGTTTGCAAAATCAAAGTGAAGCGgtaagtacct ... tgtattccagGGCCAATTTTGTGGAAGACCTGAAATTTCTGCAGATCAAAGG
EST: gi|88331342|gb|CI675672.1|CI675672
EST:     TTCAATGGAGGCCTCAAAACACTGCTGGTTTGCAAAATCAAAGTGAAGCG                         GGCCAATTTTGTGGAAGACCTGAAATTTCTGCAGATCAAAGGGAGAAG
genomic: TTCAATGGAGGCCTCAAAACACTGCTGGTTTGCAAAATCAAAGTGAAGCGgtaagtacct ... tgtattccagGGCCAATTTTGTGGAAGACCTGAAATTTCTGCAGATCAAAGGGAGAAG
EST: gi|88587352|gb|CI705090.1|CI705090
EST:     TTCAATGGAGGCCTCAAAACACTGGTGGTTTGCAAAATCAAAGTGAAGCG                         GGCCAATTTTGTGGAAGA
genomic: TTCAATGGAGGCCTCAAAACACTGCTGGTTTGCAAAATCAAAGTGAAGCGgtaagtacct ... tgtattccagGGCCAATTTTGTGGAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgcatactggcattatctttgtaatatgttacactaacccttttgtattccagGGCCAATTTTGTGGAAGACCTGAAATTTCTGCAGATCAAAGGGAGAAGTACCTGCAAAGATTGCAGCAAGTACAACAACAAGGCAGCCTTCTTAATGTTT
                                 cactaac  putative branch site (score: 1)
                                       cccttttgtattcc  CT-rich tract
             attatctttgtaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcatggattttattcatgttgagcttttgctattcccgtttgattttgcatactggcattatctttgtaatatgttacactaacccttttgtattccagGGCCAATTTTGTGGAAGACCTGAAATTTCTGCAGATCAAAGGGAGAAGTACCTGCAAAGATTGCAGCAAGTACAACAACAAGGCAGCCTTCTTAATGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG