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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTGATGAAGAACCAAACTACGCAAAGCTTATTTCCCTTTTTGATGAATTGATTGAGCCCCAGCATTTGAGGCCTATTAGAATCGATGGTGCTCTAAAGgttattttacatcagaaattttttttcttcatattacagtatcagctagtcaatccacccaattttaatataattcacatgatttgacattgaatggtttctatatgcag

Basic information

species Oryza sativa
transcript LOC_Os01g56580.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56580.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G116086_T01 (Zea mays), 5'ss of exon 11
ATTTGATGAAGAACCAAACTACGCAAAGCTTATTTCCCTTTTTGATGAATTGATTGAGCCCCAGCATTTGAGGCCTATTAGAATCGATGGTGCTCTAAAGgtt-attttacatcagaaattttttttcttcatattacagtat-cagctagtca-----atccacccaattttaatataattcacatgatttgacattgaatggtttctatatgcag
|||||||||||||||||| ||| ||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||| ||||||||  | ||||||  |||| ||  | ||    |     ||| ||||    ||| ||  || |       ||      ||||     |||  |  | | ||||  ||||  ||   ||| ||| | ||
ATTTGATGAAGAACCAAATTACTCAAAGCTTATTTCCCTTTTCGATGAATTGATTGAGCCCCAGCATTTGAGGCCTATTAGAATTGATGGTGCATTGAAGgtttgtttttcactacaaggaatgacatttcctattttgttatacaattatttttatgcatttctgtaattactggatatctggcttaattttgcatttgattacttccatacgtag
















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|4714662|gb|AU055779.1|AU055779
EST:     TGATTGAGCCCCAGCATTTGAGGCCTATTAGAATCGATGGTGCTCTAAAG                         GCTGGACAAAAACGTGGAAGGTTGCTTGTAAATCTTGAAGAAGATGAACAA
genomic: TGATTGAGCCCCAGCATTTGAGGCCTATTAGAATCGATGGTGCTCTAAAGgttattttac ... ctatatgcagGCTGGACAAAAACGTGGAAGGTTGCTTGTAAATCTTGAAGAAGATGAACAA
EST: gi|58609933|gb|CK037966.1|CK037966
EST:     TGATTGAGCCCCAGCATTTGAGGCCTATTAGAATCGATGGTGCTCTAAAG                         GCTGGACAAAAACGTGGAAGGTTGCTTGTAAATCTTGAAGAAGATGAACAA
genomic: TGATTGAGCCCCAGCATTTGAGGCCTATTAGAATCGATGGTGCTCTAAAGgttattttac ... ctatatgcagGCTGGACAAAAACGTGGAAGGTTGCTTGTAAATCTTGAAGAAGATGAACAA
EST: gi|58609726|gb|CK037759.1|CK037759
EST:     TGATTGAGCCCCAGCATTTGAGGCCTATTAGAGTCGATGGTGCTCTAAAG                         GCTGGACAAAAACGTGGAAGGTTGCTTGTAAATCTT
genomic: TGATTGAGCCCCAGCATTTGAGGCCTATTAGAATCGATGGTGCTCTAAAGgttattttac ... ctatatgcagGCTGGACAAAAACGTGGAAGGTTGCTTGTAAATCTT
EST: gi|66914155|gb|CX101003.1|CX101003
EST:     TGATTGAGCCCCAGCATTTGAGGCCTATTAGAATCGATGGTGCTCTAAAG                         GCTGGACAAAAACGTGGAAGGTTGCTTGTAAATCTTGAAGAAGATGAACAA
genomic: TGATTGAGCCCCAGCATTTGAGGCCTATTAGAATCGATGGTGCTCTAAAGgttattttac ... ctatatgcagGCTGGACAAAAACGTGGAAGGTTGCTTGTAAATCTTGAAGAAGATGAACAA
EST: gi|702121|gb|D48412.1|D48412
EST:     TGATTGAGCCCCAGCATTTGAGGCCTATTAGAATCGATGGTGCTCTAAAG                         GCTGGACAAAAACGTGGAAGGTTGCTTGTAAATCTTGAAGGAAGATGNACA
genomic: TGATTGAGCCCCAGCATTTGAGGCCTATTAGAATCGATGGTGCTCTAAAGgttattttac ... ctatatgcagGCTGGACAAAAACGTGGAAGGTTGCTTGTAAATCTTGAAG-AAGATGAACA
EST: gi|5005377|gb|AU070539.1|AU070539
EST:     TGATTGAGCCCCAGCATTTGAGGCCTATTAGAATCGATGGTGCTCTAAAG                         GCTGGACAAAAACGTGGAAGGTTGCTTGTAAATCTTGAAGAAGATGAACAA
genomic: TGATTGAGCCCCAGCATTTGAGGCCTATTAGAATCGATGGTGCTCTAAAGgttattttac ... ctatatgcagGCTGGACAAAAACGTGGAAGGTTGCTTGTAAATCTTGAAGAAGATGAACAA

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: 73 (upstream exon), 75 (downstream exon)
Score: 45

ATTTGATGAAGAACCAAACTACGCAAAGCTTATTTCCCTTTTTGATGAATTGATTGAGCCCCAGCATTTGAGGCCTATTAGAATCGATGGTGCTCTAAAGgttattttac ... ctatatgcagGCTGGACAAAAACGTGGAAGGTTGCTTGTAAATCTTGAAGAAGATGAACAACCAAAGAAGAAAGTTCGACTTGGAAGCCCAGCAAATCAGTGGATATCAG




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