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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatgaatatgaattgtgcatagccgcaaatgtcatctgagctaggacagacgacctaaaatgtaccagtttctgttaaatatcctcctgtaagctagttctgattgatttatacgtaacatcatgttattccatactgttgagtttggatggtaattatggttagctttctgatggctcatagTTGACTGTTTACAGTTCCAAGGAGATCACAAGGAAAGCTTGTATTGGGGTACCTACAGGCCGAATGTATATCTTGGAATTCGTGCAAG

Basic information

species Oryza sativa
transcript LOC_Os01g69210.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g69210.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G126468_T01 (Zea mays), 3'ss of exon 1
gtaaaatgaatatgaattgtgcatagccgcaaatgtcatctgagctaggacagacgacctaaaatgtaccagtttctgttaaatatcctcctgtaagctagttctgattgatttatacgtaacatcatgttattccatactgttgagtttggatggtaattatggttagctttctgatggctcatagTTGACTGTTTACAGTTCCAAGGAGATCACAAGGAAAGCTTGTATTGGGGTACCTACAGGCCGAATGTATATCTTGGAATTCGTGCAAG
                                                                                             |||| || |  |   | || |   |   | |||||   |  ||| ||      |    ||  |||| || | || ||||||| |||| ||||   | | || || ||||| |||    | ||||||||||| ||||||||||| || || || || ||||| || || ||||||||||||||
--------------------------------------------------------------------------------------------ataagtta-tattatataatctgggc---agatcata--aacccaaacaaacatgcactga--gtaactacg-ttggctttctcatggttcatgcctaaatgattgcagTTTCAAAATAACCACAAGGAAAGTTTGTATTGGGGCACTTATAGACCAAATGTGTACCTCGGAATTCGTGCAAG

upper sequence: LOC_Os01g69210.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT1G24320.1 (Arabidopsis thaliana), 3'ss of exon 1
gtaaaatgaatatgaattgtgcatagccgcaaatgtcatctgagctaggacagacgacctaaaatgtaccagtttctgttaaatatcctcctgtaagctagttctgattgatttatacgtaacatcatgttattccatactgttgagtt-tggatggtaattatggttagctttctgatggctcatagTTGACTGTTTACAGTTCCAAGGAGATCACAAGGAAAGCTTGTATTGGGGTACCTACAGGCCGAATGTATATCTTGGAATTCGTGCAAG
                                                                                                                      |||||    | ||      |  | |||  || |   ||| || |    ||  |||| ||    ||  |  ||   |    |||||| ||||| || ||||||||||||||||||||||| || ||  | ||  |  | ||| ||||| |||| || ||
----------------------------------------------------------------------------------------------------------------------gtaactctctttttgcttttcttcttgttttctcagtggaaagt----ttgactttttgg-aactttttttttttttgcaacagTTTCAAGGTGAGCACAAGGAAAGCTTGTATTGGGGAACTTATCGTCCTCAGATGTATTTTGGAGTTCGAGCCAG

upper sequence: LOC_Os01g69210.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv01s0010g03300.t01 (Vitis vinifera), 3'ss of exon 1
gtaaaatgaatatgaattgtgcatagccgcaaatgtcatctgagctaggacagacgacctaaaatgtaccagtttctgttaaatatcctcctgtaagctagttctgattgatttatacgtaacatcatgttattccatactgttgagtttggatggt--aattatggttagctttctgatggctcat-agTTGACTGTTTACAGTTCCAAGGAGATCACAAGGAAAGCTTGTATTGGGGTACCTACAGGCCGAATGTATATCTTGGAATTCGTGCAAG
                                                                                                                            | | |||  |    | | || | |||   |  |  | || |   |   ||| |||    | || | | || | ||  ||||||||||| || |||||||| |||||||||||||| || ||  | ||  | || ||||||||||||||||| ||
---------------------------------------------------------------------------------------------------------------------------gtaaagttgctttcgatttttcaattttttttttcgatttttaaatttttttttgagacttgatgaatcgagtatt-gcagTTCCAAGGCGAGCACAAGGAGAGCTTGTATTGGGGAACATATCGCCCTCAGGTTTATCTTGGAATTCGTGCCAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccatactgttgagtttggatggtaattatggttagctttctgatggctcatagTTGACTGTTTACAGTTCCAAGGAGATCACAAGGAAAGCTTGTATTGGGGTACCTACAGGCCGAATGTATATCTTGGAATTCGTGCAAG
                                       ttctgat  putative branch site (score: 3)
                        taattat  TA-rich tract