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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aataggtttcatgcacaattatgttttgccatttagtatcacatggtgaagcattcactttttatgctgctgctcattgtactactttgatattttgaagGTGGTCATGAACTCAGTAAAACAACAGGAAATGCAGGAGCAAGAATTGGATGCG

Basic information

species Oryza sativa
transcript LOC_Os03g11960.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g11960.3 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G891739_T01 (Zea mays), 3'ss of exon 5
aataggtttcatgcacaattatgttttgccatttagtatcaca-tggtgaagcat--tcactttttatgctgctgctcattgtactactttgatattttgaagGTGGTCATGAACTCAGTAAAACAACAGGAAATGCAGGAGCAAGAATTGGATGCG
      |     ||||| ||  | ||    | |   | |  || || ||| ||||  |||  | ||    |||| || |   |  |||||  ||||||||||||||| |||||||| |||||  |||||||||| |||||||| ||||||||||| |
---gaataatcagcacacttcagattcctgaatagttgttccagtgttgaggcatcctcatatgtttaattgctcctgaccatgttacttcaatattttgaagGTGGCCATGAACTGAGTAAGTCAACAGGAAACGCAGGAGCTAGAATTGGATGTG
















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|88503033|gb|CI430539.1|CI430539
EST:     ATTGGGAAGGGCAGTTGTTGTTCATGCTGATTCTGATGACCTAGGAAGGG                         GTGGTCATGAACTCAGTAAAACAACAGGAAATGCAGGAGCAAGAATTGGAT
genomic: ATTGGGAAGGGCAGTTGTTGTTCATGCTGATTCTGATGACCTAGGAAGGGgtaagcatta ... tattttgaagGTGGTCATGAACTCAGTAAAACAACAGGAAATGCAGGAGCAAGAATTGGAT
EST: gi|88518098|gb|CI445752.1|CI445752
EST:     ATTGGGAAGGGCAGTTGTTGTTCATGCTGATTCTGATGACCTAGGAAGGG                         GTGGTCATGAACTCAGTAAAACAACAGGAAATGCAGGAGCAAGAATTGGAT
genomic: ATTGGGAAGGGCAGTTGTTGTTCATGCTGATTCTGATGACCTAGGAAGGGgtaagcatta ... tattttgaagGTGGTCATGAACTCAGTAAAACAACAGGAAATGCAGGAGCAAGAATTGGAT
EST: gi|88906709|gb|CI375781.1|CI375781
EST:     CAGTTGTTGTTCATGCTGATTCTGATGACCTAGGAAGGG                         GTGGTCATGAACTCAGTAAAACAACAGGAAATGCAGGAGCAAGAATTGGAT
genomic: CAGTTGTTGTTCATGCTGATTCTGATGACCTAGGAAGGGgtaagcatta ... tattttgaagGTGGTCATGAACTCAGTAAAACAACAGGAAATGCAGGAGCAAGAATTGGAT
EST: gi|56158218|gb|C74673.2|C74673
EST:     ATTGGGAAGGGCAGTTGTTGTTCATGCTGATTCTGATGACCTAGGAAGGG                         GTGGTCATGAACTCAGTAAAACAACAGGAAATGCAGGAGCAAGAATTGGAT
genomic: ATTGGGAAGGGCAGTTGTTGTTCATGCTGATTCTGATGACCTAGGAAGGGgtaagcatta ... tattttgaagGTGGTCATGAACTCAGTAAAACAACAGGAAATGCAGGAGCAAGAATTGGAT
EST: gi|88480951|gb|CI418222.1|CI418222
EST:     ATT-GGAAGGGCAGTTGTTGTTCATGCTGATTCTGATGACCTAGGAAGGG                         GTGGTCATGAACTCAGTAAAACAACAGGAAATGCAGGAGCAAGAATTGGAT
genomic: ATTGGGAAGGGCAGTTGTTGTTCATGCTGATTCTGATGACCTAGGAAGGGgtaagcatta ... tattttgaagGTGGTCATGAACTCAGTAAAACAACAGGAAATGCAGGAGCAAGAATTGGAT
EST: gi|88519428|gb|CI447082.1|CI447082
EST:     AAGGGCAGTTGTTGTTCATGCTGATTCTGATGACCTAGGAAGGG                         GTGGTCATGAACTCAGTAAAACAACAGGAAATGCAGGAGCAAGAATTGGAT
genomic: AAGGGCAGTTGTTGTTCATGCTGATTCTGATGACCTAGGAAGGGgtaagcatta ... tattttgaagGTGGTCATGAACTCAGTAAAACAACAGGAAATGCAGGAGCAAGAATTGGAT
EST: gi|86527707|gb|CI167913.1|CI167913
EST:     ATTGGGAAGGGCAGTTGTTGTTCATGCTGATTCTGATGACCTAGGAAGGG                         GTGGTCATGAACTCAGTAAAACAACAGGAAATGCAGGAGCAAGAATTGGAT
genomic: ATTGGGAAGGGCAGTTGTTGTTCATGCTGATTCTGATGACCTAGGAAGGGgtaagcatta ... tattttgaagGTGGTCATGAACTCAGTAAAACAACAGGAAATGCAGGAGCAAGAATTGGAT
EST: gi|88506655|gb|CI434161.1|CI434161
EST:     ATTGGGAAGGGCAGTTGTTGTTCATGCTGATTCTGATGACCTAGGAAGGG                         GTGGTCATGAACTCAGTAAAACAACAGGAAATGCAGGAGCAAGAATTGGAT
genomic: ATTGGGAAGGGCAGTTGTTGTTCATGCTGATTCTGATGACCTAGGAAGGGgtaagcatta ... tattttgaagGTGGTCATGAACTCAGTAAAACAACAGGAAATGCAGGAGCAAGAATTGGAT
EST: gi|86533503|gb|CI173709.1|CI173709
EST:     ATTGGGAAGGGCAGTTGTTGTTCATGCTGATTCTGATGACCTAGGAAGGG                         GTGGTCATGAACTCAGTAAAACAACAGGAAATGCAGGAGCAAGAATTGGAT
genomic: ATTGGGAAGGGCAGTTGTTGTTCATGCTGATTCTGATGACCTAGGAAGGGgtaagcatta ... tattttgaagGTGGTCATGAACTCAGTAAAACAACAGGAAATGCAGGAGCAAGAATTGGAT
EST: gi|88515699|gb|CI443353.1|CI443353
EST:     ATTGGGAAGGGCAGTTGTTGTTCATGCTGATTCTGATGACCTAGGAAGGG                         GTGGTCATGAACTCAGTAAAACAACAGGAAATCCAGGAGCAAGAATTGGAT
genomic: ATTGGGAAGGGCAGTTGTTGTTCATGCTGATTCTGATGACCTAGGAAGGGgtaagcatta ... tattttgaagGTGGTCATGAACTCAGTAAAACAACAGGAAATGCAGGAGCAAGAATTGGAT
EST: gi|88489650|gb|CI426922.1|CI426922
EST:     ATTGGGAAGGGCAGTTGTTGTTCATGCTGATTCTGATGACCTAGGAAGGG                         GTGGTCATGAACTCAGTAAAACAACAGGAAATGCAGGAGCAAGAATTGGAT
genomic: ATTGGGAAGGGCAGTTGTTGTTCATGCTGATTCTGATGACCTAGGAAGGGgtaagcatta ... tattttgaagGTGGTCATGAACTCAGTAAAACAACAGGAAATGCAGGAGCAAGAATTGGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgaagcattcactttttatgctgctgctcattgtactactttgatattttgaagGTGGTCATGAACTCAGTAAAACAACAGGAAATGCAGGAGCAAGAATTGGATGCG
                                       ctttgat  putative branch site (score: 5)
                                     tactttgatatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aataggtttcatgcacaattatgttttgccatttagtatcacatggtgaagcattcactttttatgctgctgctcattgtactactttgatattttgaagGTGGTCATGAACTCAGTAAAACAACAGGAAATGCAGGAGCAAGAATTGGATGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA