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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_Os05g51630.2
intron # 7
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

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 71 (upstream exon), 70 (downstream exon)
Score: 25

TCAACTTTTTTTATGTCATTCCAATAGCATTCGTGCAATCTCTTGCAAGCCTTGAAGGAATAGAAAAGGCGCTTCCATTTCTGAAACCCTTAATCAAAATgtaagtgttt ... tattgtgcagTGATGTCATCAAATCATTCATCCAAGGTTTTCTTCCAGGAATTGCTTTGAAGGTCTTCCTTATATTGCTTCCAACTATACTGATGTTTATGTCTAAGTTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatcttctgctattcttttgaaatgccctgataaatcttgttgactattgtgcagTGATGTCATCAAATCATTCATCCAAGGTTTTCTTCCAGGAATTGCTTTGAAGGTCTTCCTTATATTGCTTCCAACTATACTGATGTTTATGTCTAAGTTT
                                      tgttgac  putative branch site (score: 25)
          tattcttttgaaat  TA-rich tract