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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacctatttagtttaatttgtttatgtcagctactcagttataaaagttcaaccttatggtactgacagatctatgttggttcttggccttaatatgcagTCAGCTGGTGGTTTTCCGGCTTCGCTTAGACCTGGTCGATGGTTAGACTTGTATAGTGGTACTGGATCTGTTGGAATTGAGGCTATGAGCCGTGGATGTT

Basic information

species Oryza sativa
transcript LOC_Os03g52640.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g52640.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G010801_T01 (Zea mays), 3'ss of exon 3
gtacctatttagtttaatttgtttatgtcagctactcagttataaaagttcaaccttatggtactgacagatctatgttggttcttggccttaatatgcagTCAGCTGGTGGTTTTCCGGCTTCGCTTAGACCTGGTCGATGGTTAGACTTGTATAGTGGTACTGGATCTGTTGGAATTGAGGCTATGAGCCGTGGATGTT
||| | || ||      |  ||| ||| ||  |      || |     | |    ||    |||| | ||| ||   ||| ||| || || ||   |||||||||||||||||| ||| ||||| || ||||| ||||| ||| ||||||||||||||||||||||||| ||||||||||| ||||||||||| |||||||
gtatccatcta------tcggttgatgccactttaatcattgt-----tccccttttgatttactcatagaccttccttgattcatgaccataccttgcagTCAGCTGGTGGTTCTCCTGCTTCACTCAGACCGGGTCGGTGGCTAGACTTGTATAGTGGTACTGGATCCGTTGGAATTGAAGCTATGAGCCGAGGATGTT

upper sequence: LOC_Os03g52640.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA13G04900.1 (Glycine max), 3'ss of exon 4
--------------------------------gtacctatttagtt-taatttgtttatgtcagct---actcagt-tataaaagttcaaccttatggtactgacagatctatgttggttcttggccttaatatgcagTCAGCTGGTGGTTTTCCGGCTTCGCTTAGACCTGGTCGATGGTTAGACTTGTATAGTGGTACTGGATCTGTTGGAATTGAGGCTATGAGCCGTGGATGTT
                                   | | |||  |  | | || || || |  | |   |   ||| | || || |||     |       |      |     |   ||       | || |   || |||||||||| | ||| ||  |  | ||||||||||| ||||||||||||||||| ||||| || |||||||||||||| ||  | ||||| |||||||
gtaccggttttatgttttatttcctatgtagcacgcttgtttgctaattaattattgatattgggtttcatctagtctgtacaatttccttgctgcaacttttttgtttactaatcattttactttttcaacaccaagGCAGCTGGTGGCTGTCCTGCAGCATTGAGACCTGGTCGCTGGTTAGACTTGTATAGCGGTACAGGTTCTGTTGGAATTGAAGCACTTAGCCGAGGATGTT

upper sequence: LOC_Os03g52640.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA19G02060.1 (Glycine max), 3'ss of exon 2
--------------------------------gtacctatttagtt-taatttgtttatgtcagct---actcagt-tataaaagttcaaccttatggtactgacagatctatgttggttcttggcctt-aatatgcagTCAGCTGGTGGTTTTCCGGCTTCGCTTAGACCTGGTCGATGGTTAGACTTGTATAGTGGTACTGGATCTGTTGGAATTGAGGCTATGAGCCGTGGATGTT
                                  || | |||  |  | | || || || |  | |   |   ||| | || || |||  | |  ||  |||  |   |   |  |  || |     || || |   || |||||||||| | ||| ||  | || ||||||||||  ||||||||||||||||||||||| || |||||||||||||| ||  | ||||| |||||||
gtaccagtttcatgttttatttcctatgtagcacacttgtttgctaattaattattgatattgggtttcatctagtctgtacaatttc--cttgctgcaactttcttgttactaataattttactttttcaacaccaagGCAGCTGGTGGCTGTCCTGCAGCTCTGAGACCTGGTCACTGGTTAGACTTGTATAGTGGTACAGGTTCTGTTGGAATTGAAGCACTCAGCCGAGGATGTT

upper sequence: LOC_Os03g52640.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv14s0066g02200.t01 (Vitis vinifera), 3'ss of exon 4
-gtacctatttagtttaatttgttta--tgtcagctactcagttataaaagttcaaccttatggtactgacagatctatgttggttcttggccttaatatgcagTCAGCTGGTGGTTTTCCGGCTTCGCTTAGACCTGGTCGATGGTTAGACTTGTATAGTGGTACTGGATCTGTTGGAATTGAGGCTATGAGCCGTGGATGTT
  |   |||  | | ||     ||||  ||| |  |     | |  |||   | |  |||    || ||| | |  ||  || ||| ||    ||  | |  ||   |||||||| | ||| || ||  | || ||||| || ||||||||||||||||||||||| ||||||||||| ||||| ||| | |||||||||||||
aattgatatgaaatctagaaattttacttgttaattttgacgctgaaaagaattattctttaattattgaaaaa--taaattagttgttctggtt--tgtttagGTGGCTGGTGGCTGTCCTGCATCTTTGAGGCCTGGGCGCTGGTTAGACTTGTATAGTGGTACAGGATCTGTTGGGATTGAAGCTCTTAGCCGTGGATGTT

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: 61 (upstream exon), 65 (downstream exon)
Score: 19

AGGAGGAAAAGTACGCAGAAGAAAATTACTTTCACCAAAAGATAGGAATGTTCGTCCAATGATGGAAGTTGTACGAGGGGCAGCCTTTGACATTTTACAGgtacctattt ... taatatgcagTCAGCTGGTGGTTTTCCGGCTTCGCTTAGACCTGGTCGATGGTTAGACTTGTATAGTGGTACTGGATCTGTTGGAATTGAGGCTATGAGCCGTGGATGTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttcaaccttatggtactgacagatctatgttggttcttggccttaatatgcagTCAGCTGGTGGTTTTCCGGCTTCGCTTAGACCTGGTCGATGGTTAGACTTGTATAGTGGTACTGGATCTGTTGGAATTGAGGCTATGAGCCGTGGATGTT
                                            ttaatat  TA-rich tract