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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttctccataatgcgcaatgtgttttctacagaattcctagaatatagttaatacaatatgaaaccatttaacttaactagGTAATCCATGGAGCAGATCGAGATATTATTTGGCTTCAACGGGACTTTGGCATTTATGTCTGCAATCTTTTTGACACAGGACAG

Basic information

species Arabidopsis thaliana
transcript AT1G54440.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G54440.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os10g30100.1 (Oryza sativa), 3'ss of exon 3
-----------gttttctccataatgcgcaatgtgttttctacagaattcctagaatatagttaatacaatatgaaaccatttaacttaactagGTAATCCATGGAGCAGATCGAGATATTATTTGGCTTCAACGGGACTTTGGCATTTATGTCTGCAATCTTTTTGACACAGGACAG
             ||||  |||  |     |||||  |  |     || |    | | |      || | | | |   |  |||    |  |||||||| ||||| |||||||| ||||| || ||||||||||||||||||||||| ||||| ||||| |||||||||||||| |||
gtataacatgctctttcatcattttcatacatgtgcatattgttatatgctccaattgtg-----tagattctcattgctcttatggcacatagGTAATGCATGGTGCAGATCGTGATATAATATGGCTTCAACGGGACTTTGGCATATATGTATGCAACCTTTTTGACACAGGCCAG

upper sequence: AT1G54440.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os03g06190.1 (Oryza sativa), 3'ss of exon 3
gttttctccataatgcgcaatgtgttttctacagaattcctagaatatagttaatacaatatgaaaccat-------ttaacttaact---------------agGTAATCCATGGAGCAGATCGAGATATTATTTGGCTTCAACGGGACTTTGGCATTTATGTCTGCAATCTTTTTGACACAGGACAG
||||  ||     |   |||| |||||   |    |||    | | || ||| || || | ||||  ||        || ||||   |               ||||||| ||||| || ||||| |||||||| ||||| |||||||| ||   ||| ||||| ||||||||||||||||||||||||
gtttcttctgcgttctccaat-tgtttatcattttattgaggggaaattgtttat-cattgtgaactcaaatttctgtttacttggtttcttcttgtgcaaaaagGTAATGCATGGGGCTGATCGTGATATTATGTGGCTCCAACGGGATTTCCACATATATGTTTGCAATCTTTTTGACACAGGACAG

upper sequence: AT1G54440.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G000749_T01 (Zea mays), 3'ss of exon 3
gttttctccataatgcgcaatgtgttttctacagaattcctagaatatagttaatacaatatgaaaccatttaacttaactagGTAATCCATGGAGCAGATCGAGATATTATTTGGCTTCAACGGGACTTTGGCATTTATGTCTGCAATCTTTTTGACACAGGACAG
  ||| |  | | | |  |||      ||||   |    || |||| |   |  |    | | |  |    |   | || |||||||| ||||| || ||||| ||||| || ||||| || ||||||||   ||| ||||| ||||||||||||||||||||||||
-gtttttaaaaactacaaaataatgcctctatgta----ctcgaattt--ctggt----tttcattcgtccttggtcaaatagGTAATGCATGGTGCGGATCGTGATATAATGTGGCTCCAGCGGGACTTCCACATCTATGTGTGCAATCTTTTTGACACAGGACAG

upper sequence: AT1G54440.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G145704_T02 (Zea mays), 3'ss of exon 3
gttttctccataatgcgcaatgtgttttctacagaattcctagaatatagttaatacaatatgaaaccatttaacttaactagGTAATCCATGGAGCAGATCGAGATATTATTTGGCTTCAACGGGACTTTGGCATTTATGTCTGCAATCTTTTTGACACAGGACAG
||||| |  | | | |  |||      ||||   |    || |||| |   |  |    | | |  |  | |   | || |||||||| ||||| || ||||| ||||| || ||||| || ||||||||   ||| ||||| ||||||||||||||||||||||| 
gtttttttaaaactacaaaataatgcctctatgta----ctcgaattt--ctggt----tttcattcgttcttggtcaaatagGTAATGCATGGTGCGGATCGTGATATAATGTGGCTCCAGCGGGACTTCCACATCTATGTGTGCAATCTTTTTGACACAGGACAA

upper sequence: AT1G54440.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G118917_T02 (Zea mays), 3'ss of exon 3
gttttctccataatgcgcaatgtgttttctacagaatt----cctagaatatagttaatacaatatgaaaccatttaactta-----actagGTAATCCATGGAGCAGATCGAGATATTATTTGGCTTCAACGGGACTTTGGCATTTATGTCTGCAATCTTTTTGACACAGGACAG
           |||  ||    || || ||| | | ||      |  ||  |   ||| ||   |       |||   ||||     |  ||||||| ||||| |||| ||| ||||| || ||||||||||| |||||  |||| ||||| ||||| |||||||||||||| |||
-------gtgcaatatgct---tgcttcctatacatttatactttgtaacgtgtctaaaactgcagtttcttattggtcttatgacaaacagGTAATGCATGGTGCAGGTCGTGATATAATATGGCTTCAACGAGACTTCAGCATATATGTGTGCAACCTTTTTGACACAGGCCAG

upper sequence: AT1G54440.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G039096_T01 (Zea mays), 3'ss of exon 4
gttttctccataatgcgcaatgtgttttctacagaattcctagaatatagttaatacaatatgaaaccatttaacttaactagGTAATCCATGGAGCAGATCGAGATATTATTTGGCTTCAACGGGACTTTGGCATTTATGTCTGCAATCTTTTTGACACAGGACAG
  ||| |  | | | |  |||      ||||   |    || |||| |   |  |    | | |  |  |||   | || |||||||| ||||| || ||||| ||||| || ||||| || ||||||||   ||| ||||| ||||||||||||||||||||||| 
-gtttttaaaaactacaaaataatgcctctatgta----ctcgaattt--ctggt----tttcattcgtttttggtcaaatagGTAATGCATGGTGCGGATCGTGATATAATGTGGCTCCAGCGGGACTTCCACATCTATGTGTGCAATCTTTTTGACACAGGACAA

upper sequence: AT1G54440.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G452875_T01 (Zea mays), 3'ss of exon 3
gttttctccataatgcgcaatgtgttttctacagaattcctagaatatagttaatacaatatgaaaccatttaacttaactagGTAATCCATGGAGCAGATCGAGATATTATTTGGCTTCAACGGGACTTTGGCATTTATGTCTGCAATCTTTTTGACACAGGACAG
  ||| |  | | | |  |||      ||||   |    || |||| |   |  |    | | |  |  | |   | || |||||||| ||||| || ||||| ||||| || ||||| || || |||||   ||| ||||| ||||||||||||||||||||||||
-gtttttaaaaactacaaaataatgcctctatgta----ctcgaattt--ctggt----tttcattcgttcttggtcaaatagGTAATGCATGGTGCGGATCGTGATATAATGTGGCTCCAGCGAGACTTCCACATCTATGTGTGCAATCTTTTTGACACAGGACAG

upper sequence: AT1G54440.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G29260.1 (Glycine max), 3'ss of exon 3
gttttctccataatgcgcaatgtgttttctacagaattcctagaatatagttaatacaatatgaaaccatttaacttaactagGTAATCCATGGAGCAGATCGAGATATTATTTGGCTTCAACGGGACTTTGGCATTTATGTCTGCAATCTTTTTGACACAGGACAG
||    | || | ||    |||| | ||      ||||| |   |  |  ||  |    | |||    |||||    || ||||| || ||||||||||||||||| ||| | ||||| |||||||| |||||||||||||| |||||| | || || || || |||
gtcagatgcaca-tgtttgatgtttcttt-----aattcatcagactttcttctttttgt-tgactttatttattggaaatagGTCATGCATGGAGCAGATCGAGACATTGTGTGGCTGCAACGGGATTTTGGCATTTATGTTTGCAATATGTTCGATACTGGCCAG

upper sequence: AT1G54440.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv08s0056g01320.t01 (Vitis vinifera), 3'ss of exon 2
gttttctccataatgcgcaatgtgttttctacagaattcctagaatatagttaatacaatatgaaaccatttaacttaactagGTAATCCATGGAGCAGATCGAGATATTATTTGGCTTCAACGGGACTTTGGCATTTATGTCTGCAATCTTTTTGACACAGGACAG
  ||  ||  |     |     | ||||    |  ||     | || || || ||     |||| |  |  ||| |||| ||||| || || || |||||||| ||||| ||||||||||||||||| |||||||| ||  |||||||  | ||||| || ||||||
-gttgatctctgtcttgttgcttatttttggtattataat--ggatctacttcatttgtgatgatat-acctaa-ttaattagGTTATGCACGGGGCAGATCGGGATATCATTTGGCTTCAACGGGATTTTGGCATATACATCTGCAACATGTTTGATACCGGACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctacagaattcctagaatatagttaatacaatatgaaaccatttaacttaactagGTAATCCATGGAGCAGATCGAGATATTATTTGGCTTCAACGGGACTTTGGCATTTATGTCTGCAATCTTTTTGACACAGGACAG
                                        atttaac  putative branch site (score: 3)
               aatatagttaatacaa  TA-rich tract