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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCCAGCGCCTTCAAGGACCGTTCGAGGAAGAGACTCTTAAGGCACACTTCGAGAAAATAATATTCCTTGGTCAAAAGTTGCATCCAAATCGTAGAAAGgttagtttttttttggaaaagccttttacaggcttgactttgtattagtatattagaattgtaaattttcctacggcgtgtagtacataatggttattct...

Basic information

species Oryza sativa
transcript LOC_Os08g08000.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g08000.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G440951_T01 (Zea mays), 5'ss of exon 2
GTTCCAGCGCCTTCAAGGACCGTTCGAGGAAGAGACTCTTAAGGCACACTTCGAGAAAATAATATTCCTTGGTCAAAAGTTGCATCCAAATCGTAGAAAGgttagtttttt-tttggaaaagccttttacaggcttgactttgtattagtatattagaattgtaaattttc-ctacggcgtgtagtacataatggttattct
||| |||||||||||||||||||| ||||||| |||||| ||| |||||||||||||||||||||| ||||||||||| ||||||| || |||||||||||||||| || | |||   ||| | |  || | | ||  | | ||     | || ||   ||||||  | |  || |   ||    | || |    ||   ||
GTTTCAGCGCCTTCAAGGACCGTTTGAGGAAGGGACTCTCAAGACACACTTCGAGAAAATAATATTGCTTGGTCAAAAATTGCATCAAACTCGTAGAAAGgttagtgttatgtttttgaaaacatcataaatgatt--cgtggttgggatgtaatatgtttgtaatctcttgcttccatgttcccttcaaatcttttgagct

upper sequence: LOC_Os08g08000.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G349570_T01 (Zea mays), 5'ss of exon 2
GTTCCAGCGCCTTCAAGGACCGTTCGAGGAAGAGACTCTTAAGGCACACTTCGAGAAAATAATATTCCTTGGTCAAAAGTTGCATCCAAATCGTAGAAAGgttagtttttt-tttggaaaagccttttacaggcttgactttgtattagtatattagaattgtaaattttc-ctacggcgtgtagtacataatggttattct
||| |||||||||||||||||||| ||||||| |||||| ||| ||||||| |||||||||||||| ||||||||||| ||||||| || |||||||||||||||| || | |||   ||| | |  || | | ||  | | ||     | || ||   ||||||  | |  || |   ||    | || |    ||   ||
GTTTCAGCGCCTTCAAGGACCGTTTGAGGAAGGGACTCTCAAGACACACTTTGAGAAAATAATATTGCTTGGTCAAAAATTGCATCAAACTCGTAGAAAGgttagtgttatgtttttgaaaacatcataaatgatt--cgtggttgggatgtaatatgtttgtaatctcttgcttccatgttcccttcaaatcttttgagct
















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|88722150|gb|CI745660.1|CI745660
EST:     TCGAGAAAATAATATTCCTTGGTCAAAAGTTGCATCCAAATCGTAGAAAG                         GGTGAGAGCCAAGAGCTCAAGCAGATAAACCCACTCCATTCTTCTCATCTT
genomic: TCGAGAAAATAATATTCCTTGGTCAAAAGTTGCATCCAAATCGTAGAAAGgttagttttt ... ggtcatgcagGGTGAGAGCCAAGAGCTCAAGCAGATAAACCCACTCCATTCTTCTCATCTT
EST: gi|29634713|gb|CB639722.1|CB639722
EST:     TCGAGAAAATAATATTCCTTGGTCAAAAGTTGCATCCAAATCGTAGAAAG                         GGTGAGAGCCAAGAGCTCAAGCAGATAAACCCACTCCATTCTTCTCATCTT
genomic: TCGAGAAAATAATATTCCTTGGTCAAAAGTTGCATCCAAATCGTAGAAAGgttagttttt ... ggtcatgcagGGTGAGAGCCAAGAGCTCAAGCAGATAAACCCACTCCATTCTTCTCATCTT
EST: gi|29644348|gb|CB649355.1|CB649355
EST:     TCGAGAAAATAATATTCCTTGGTCAAAAGTTGCATCCAAATCGTAGAAAG                         GGTGAGAGCCAAGAGCTCAAGCAGATAAACCCACTCCATTCTTCTCATCTT
genomic: TCGAGAAAATAATATTCCTTGGTCAAAAGTTGCATCCAAATCGTAGAAAGgttagttttt ... ggtcatgcagGGTGAGAGCCAAGAGCTCAAGCAGATAAACCCACTCCATTCTTCTCATCTT
EST: gi|58654091|gb|CK042771.1|CK042771
EST:     TTGAGAAAATAATATTCCTTGGTCAAAAGTTGCATCCAAATCGTAGAAAG                         GGTGAGAGCCAAGAGCTCAAGCAGATAAACCCACTCCATTCTTCTCATCTT
genomic: TCGAGAAAATAATATTCCTTGGTCAAAAGTTGCATCCAAATCGTAGAAAGgttagttttt ... ggtcatgcagGGTGAGAGCCAAGAGCTCAAGCAGATAAACCCACTCCATTCTTCTCATCTT

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: 75 (upstream exon), 72 (downstream exon)
Score: 13

GTTCCAGCGCCTTCAAGGACCGTTCGAGGAAGAGACTCTTAAGGCACACTTCGAGAAAATAATATTCCTTGGTCAAAAGTTGCATCCAAATCGTAGAAAGgttagttttt ... ggtcatgcagGGTGAGAGCCAAGAGCTCAAGCAGATAAACCCACTCCATTCTTCTCATCTTCATGCACTTTCTCAAGCATGTGCACCTGGAGTCATTTTGAT




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