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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattgggttgttggccaagtgtttatatgttccgatgctgtgtgctgtttctgaccttgaatgatttggataaacatacacctttttctgtattttgcagCAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCTGTTTTGTCTATTGGTGCTATAGCGGAGGGATGCATTACTGGGCTATATC

Basic information

species Oryza sativa
transcript LOC_Os04g59494.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g59494.4 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G312026_T01 (Zea mays), 3'ss of exon 12
tattgggt-tgttggccaagtgtttatatgtt-ccgatgctgtgtgctgtttctgaccttgaatgatttggataaacatacacctttttctgtattttgcagCAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCTGTTTTGTCTATTGGTGCTATAGCGGAGGGATGCATTACTGGGCTATATC
 | ||  | ||       | ||  | | |||| | | |  | ||||||| |  | |||||| ||  ||||| |||||||||| | ||||||||| ||||||||||||  |||||||||| || |||||| | ||||||||||||||| |||||||||| | | | || |||||||| ||||| ||||||| ||| ||||| |
-agtgtatatgccttttgactgcctttgtgttactgttagtatgtgctgctcttaaccttgcatc-tttggttaaacatacatcattttctgtaatttgcagCAAAACTTGGCTCGAACAGATGATGATTCTTGGAAGGAGAGGGAAACTGCTGTTTTATGTCTAGGCGCTATAGCAGAGGGGTGCATTAGTGGTCTATACC

upper sequence: LOC_Os04g59494.4 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G376731_T01 (Zea mays), 3'ss of exon 12
tattgggttgttggccaagtgtttatatgttccgatgctgtgtgctgtttctgaccttgaatgatttg---gataaacatacacctttttctgtattttgcagCAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCTGTTTTGTCTATTGGTGCTATAGCGGAGGGATGCATTACTGGGCTATATC
      ||   || |     | ||   | | | | |  | | ||||  |  | |||||| ||  || |    ||| ||||  ||| ||||||||| ||||||||||||  |||||||||| || ||  || | ||||||||||||||| |||||||||||| | | || |||||||| ||||| ||||||  ||| ||||| |
---aatgtatatgccttttggcttccttttactggtagtatatgctactcttaaccttgcatctttggttcaatatacatgtaccattttctgtaatttgcagCAAAACTTGGCTCGAACAGATGACAATTCTTGGAAGGAGAGGGAAACTGCTGTTTTGTGTCTAGGCGCTATAGCAGAGGGGTGCATTGGTGGTCTATACC

upper sequence: LOC_Os04g59494.4 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA20G24040.1 (Glycine max), 3'ss of exon 12
-tattgggttgttggccaagtgtttatatgttccgatgctgtgtgctgtttctgaccttgaatgatttggataaacatacacctttttctgtattttgcagCAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCTGTTTTGTCTATTGGTGCTATAGCGGAGGGATGCATTACTGGGCTATATC
  || ||  | |      |     | ||||      |    | ||  | |  |  |  || | |  ||   |      |  || || |     || |||||   ||  |  ||     ||  |||||||| ||||| || |||||||||||||| ||| || ||||||||||||  || || ||||| | ||| || ||||
acataggtgtatatatgtaagacatctatgaaa-actatattatgacgctaatttctctgcaagcctttctttttatgaggccattctaaaatttctgcagGCTAAGTTATCTGCTGGTGGGGATGATGCTTGGAAAGATAGGGAAGCTGCTGTCTTGGCTCTTGGTGCTATAGGCGAAGGTTGCATCAATGGTCTTTATC

upper sequence: LOC_Os04g59494.4 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA10G42960.1 (Glycine max), 3'ss of exon 12
-tattgggttgttggccaagtgtttatatgttccgatgctgtgtgctgtttctgaccttgaatgatttggataaacatacacctttttctgtattt-tgcagCAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCTGTTTTGTCTATTGGTGCTATAGCGGAGGGATGCATTACTGGGCTATATC
 |||      |    | | |      ||| ||  || |||  ||       |    |||   |  | ||   | | |   |  ||| |  | |||| |||||   ||  || ||     ||  |||||||| ||||| || |||||||||||||| ||| || ||||||||||||  || || ||||| | ||| || ||||
gtatatatgagacatctatgaaaac-tatattatgacgct-cgtttctccgcaaggctttctttttatgaggatatactaaaatttctgaggatttgtgcagGCTAAGTTGTCTGCTGGTGGGGATGATGCTTGGAAAGATAGGGAAGCTGCTGTCTTGGCTCTTGGTGCTATAGGTGAAGGTTGCATCAATGGTCTTTATC

upper sequence: LOC_Os04g59494.4 (Oryza sativa), 3'ss of exon 12
lower sequence: Vv03s0038g02830.t01 (Vitis vinifera), 3'ss of exon 12
tattgggttgttggccaagtgtt-tatatgttccgatgctgtgtgctgtttctg-accttgaatgatttg-gataaacatacacctttttctgta--ttttgcagCAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCTGTTTTGTCTATTGGTGCTATAGCGGAGGGATGCATTACTGGGCTATATC
        |    |  ||  ||| ||| |||  | |   |  ||     ||||   |    | | | ||| | | || |||    ||  |    |  || |||||   ||  |  |    ||||| |||||  | ||||| || ||||||||||| |||||  || |||||||| |||| ||||| ||||||||||| || ||||
-----aaatagaagttaaaagttatatgtgtctcaaccattagtttcacttctttgcaaccatttacttgtgtttaaaatatgatttccttaaaaatttctgcagGCTAAGTTATCAACTACTGATGATGAGACCTGGAAAGAAAGGGAAGCTGCCGTTTTAGCTCTTGGTGCTGTAGCTGAGGGTTGCATTACTGGTCTTTATC

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|58612862|gb|CK040574.1|CK040574
EST:     CTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAG                         CAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT
genomic: CTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAGgtaagttgta ... tattttgcagCAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT
EST: gi|29626307|gb|CB631318.1|CB631318
EST:     CTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAG                         CAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT
genomic: CTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAGgtaagttgta ... tattttgcagCAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT
EST: gi|33797567|gb|CF324643.1|CF324643
EST:     CTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAG                         CAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT
genomic: CTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAGgtaagttgta ... tattttgcagCAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT
EST: gi|58672477|gb|CK061163.1|CK061163
EST:     CTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAG                         CAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT
genomic: CTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAGgtaagttgta ... tattttgcagCAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT
EST: gi|33678128|gb|CF306367.1|CF306367
EST:     CTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAG                         CAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT
genomic: CTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAGgtaagttgta ... tattttgcagCAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT
EST: gi|58662574|gb|CK051260.1|CK051260
EST:     CTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAG                         CAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT
genomic: CTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAGgtaagttgta ... tattttgcagCAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT
EST: gi|58656826|gb|CK045506.1|CK045506
EST:     TAATGTTTTCGGTGATGACATTCTTGCCTACTTTAATGCCTTTGATACAG                         CAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT
genomic: TAATGTTTTCGGTGATGACATTCTT-CCTACTTTAATGCCTTTGATACAGgtaagttgta ... tattttgcagCAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT
EST: gi|58663523|gb|CK052209.1|CK052209
EST:     CTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAG                         CAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT
genomic: CTAATGTTTTCGGTGATGACATTCTTCCTACTTTAATGCCTTTGATACAGgtaagttgta ... tattttgcagCAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttctgaccttgaatgatttggataaacatacacctttttctgtattttgcagCAAAATCTGGCTCGAACTGACGATGATGCGTGGAAGGAGAGGGAAGCTGCTGTTTTGTCTATTGGTGCTATAGCGGAGGGATGCATTACTGGGCTATATC
   ttctgac  putative branch site (score: 2)
                                   cctttttctgtatttt  putative PPT
                                     tttttctgtatttt  TA-rich tract