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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtttcttcatgtgttgattatttatactattattgcatttccatgatttattcagcgtgtaattaatttgggtacattagacatatggttatcttctgctattcttttgaaatgccctgataaatcttgttgactattgtgcagTGATGTCATCAAATCATTCATCCAAGGTTTTCTTCCAGGAATTGCTTTGAAGGTCTTCCTTATATTGCTTCCAACTATACTGATGTTTATGTCTAAGTTT

Basic information

species Oryza sativa
transcript LOC_Os05g51630.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g51630.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G456000_T01 (Zea mays), 3'ss of exon 8
gtaagtgtttcttcatgtgttgattatttatactattattgcatttccatgatttattcagcgtgtaattaatttgggtacattagacatatggttatcttctgctattcttttgaaatgccctgataaat-cttgttgactattgtgcagTGATGTCATCAAATCATTCATCCAAGGTTTTCTTCCAGGAATTGCTTTGAAGGTCTTCCTTATATTGCTTCCAACTATACTGATGTTTATGTCTAAGTTT
|||||| |   | ||| |||||||  |||||          ||||||  |||||| ||    |  ||  | ||    |||  ||  |               ||   || |  ||| ||||||||||   | |||||  ||| || |||||     |||| ||||||||||||||||| |||||||| ||||||||||||||| ||||||||||| ||||||||||||||||||||||||||||||| |||
gtaagtctacatccatatgttgatactttatgt--------catttctttgatttctta---gcatagcttatggtagtattttgaa---------------tgtccttttggtgacatgccctgatttctgcttgtaaactgttatgcagGCCATTCATTAAATCATTCATCCAAGGGTTTCTTCCTGGAATTGCTTTGAAGATCTTCCTTATAGTGCTTCCAACTATACTGATGTTTATGTCTAAATTT

upper sequence: LOC_Os05g51630.2 (Oryza sativa), 3'ss of exon 7
lower sequence: Vv12s0059g01090.t01 (Vitis vinifera), 3'ss of exon 7
gtaagtgtttcttcatgtgttgattatttatactattattgcatttccatgatttattcagcgtgta-attaatttgggtacat-tagacatatggttatcttctgctattcttttgaa-atgccctgataaatcttgttgact--attgtgcagTGATGTCATCAAATCATTCATCCAAGGTTTTCTTCCAGGAATTGCTTTGAAGGTCTTCCTTATATTGCTTCCAACTATACTGATGTTTATGTCTAAGTTT
                                                       | |     | || || ||| |   || || || | ||||   ||| |     |||   | |  | ||    | || ||     ||| ||   |  |||||  |  ||||||| ||| ||||||||||||||||||| || |||||| | ||| |||| || || || || ||| | ||| ||||| | |||||||| |||
-------------------------------------------------------actttaaatatatataaatatatatatatatatatatatatatatatatatatatatatatatatatatatttattaacagcattgtctttgtcatgcagCCACTTCATCAAGTCAATCATCCAAGGTTTTCTTCCTGGGATTGCTCTAAAGATCTTTCTCATTTTTCTACCATCAATATTGATGCTAATGTCTAAATTT
















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|33675054|gb|CF303293.1|CF303293
EST:     CTTGAAGGAATAGAAAAGGCGCTTCCATTTCTGAAACCCTTAATCAAAAT                         TGATGTCATCAAATCATTCATCCAAGGTTTTCTTCCAGGAATTGCTTTGAA
genomic: CTTGAAGGAATAGAAAAGGCGCTTCCATTTCTGAAACCCTTAATCAAAATgtaagtgttt ... tattgtgcagTGATGTCATCAAATCATTCATCCAAGGTTTTCTTCCAGGAATTGCTTTGAA
EST: gi|29678912|gb|CB675187.1|CB675187
EST:     CTTGAAGGAATAGAAAAGGCGCTTCCATTTCTGAAACCCTTAATCAAAAT                         TGATGTCATCAAATCATTCATCCAAGGTTTTCTTCCAGGAATTGCTTTGAA
genomic: CTTGAAGGAATAGAAAAGGCGCTTCCATTTCTGAAACCCTTAATCAAAATgtaagtgttt ... tattgtgcagTGATGTCATCAAATCATTCATCCAAGGTTTTCTTCCAGGAATTGCTTTGAA
EST: gi|58693113|gb|CK081800.1|CK081800
EST:     C-TGAAGGAATAGAAAAGGCGCTTCCATTTCTGAAACCCTTAATCAAAAT                         TGATGTCATCAAATCATTCATCCAAGGTTTTCTTCCAGGAATTGCTTTGAA
genomic: CTTGAAGGAATAGAAAAGGCGCTTCCATTTCTGAAACCCTTAATCAAAATgtaagtgttt ... tattgtgcagTGATGTCATCAAATCATTCATCCAAGGTTTTCTTCCAGGAATTGCTTTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcttctgctattcttttgaaatgccctgataaatcttgttgactattgtgcagTGATGTCATCAAATCATTCATCCAAGGTTTTCTTCCAGGAATTGCTTTGAAGGTCTTCCTTATATTGCTTCCAACTATACTGATGTTTATGTCTAAGTTT
                                      tgttgac  putative branch site (score: 3)
          tattcttttgaaat  TA-rich tract