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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacgatgattcatttcatttagtgttctaatgttcttatatctatgttacgtcttttctgatcaaaatgttctatctttttctttttgtttcagCCGGTTTATGAACCAGTACTTTTTGTTGATTGCTTGCCTTCAGCTATGGTCACTTATCACCCCTGTGAATCCTGCAAGTACATGGGGTCCGTTAATATTC

Basic information

species Arabidopsis thaliana
transcript AT5G44240.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G44240.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os11g25980.1 (Oryza sativa), 3'ss of exon 2
----------gtaacgatgattcatttcatttagtgttctaatgttcttatatcta-tgttacgtctttt---------ctgatcaa--------aatgttctatctttttctttt-tgtttcagCCGGTTTATGAACCAGTACTTTTTGTTGATTGCTTGCCTTCAGCTATGGTCACTTATCACCCCTGTGAATCCTGCAAGTACATGGGGTCCGTTAATATTC
           | |     ||| |||| || |  | ||  ||||    | |||    | |||| || |||         ||||  ||        |       || | |   |||  |||||||| || || ||||| || || || ||| |||| || ||||| || || |||||||||||||| ||||| ||||||||||| |||||||| ||| | || || 
gtttgtacttattagatgcatttattttatgttctcttaaaatggaagtctattggcttttacatcatttggagaagcactgactaatagttagtagaagctgatatctccatttcatgtttcagGCGTTTCATGAATCAATATTTCTTGCTGATAGCATGCCTCCAACTGTGGTCACTTATCACTCCTGTAAATCCTGCAAGCACATGGGGCCCGCTTATTTTT

upper sequence: AT5G44240.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os04g28460.1 (Oryza sativa), 3'ss of exon 1
--gtaa---cgatgattcatttcatttagtgttctaatgttcttatatctatgttacgtcttttctgatcaaaatgttctatctttttctttttgt-ttcagCCGGTTTATGAACCAGTACTTTTTGTTGATTGCTTGCCTTCAGCTATGGTCACTTATCACCCCTGTGAATCCTGCAAGTACATGGGGTCCGTTAATATTC
  || |   |  || |  || |    ||     ||  | ||||| |||   ||| |      |   |||   ||| |   | |  |||||||   | ||||| || || ||||| ||||| ||| |  | || || ||||||||| ||||||||  |||||| ||||| | |||||||| ||||||||||||  |     ||
ccgtgaatccattggtatatctatgctaaaccacttttcttctt-tatgcgtgtcatagagatatcgattttaat-tataacccatttctttgaatattcagGCGTTTCATGAATCAGTATTTTCTTCTAATCGCCTGCCTTCAGTTATGGTCAAGTATCACACCTGTTAGTCCTGCAACTACATGGGGTCCACTTGCCATC

upper sequence: AT5G44240.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G411940_T01 (Zea mays), 3'ss of exon 4
gtaacgatgattcatttcatttagtgttcta-atgttcttatatctatgttacgtcttttct---gatcaaaatgttctatctttttctttttgtttcagCCGGTTTATGAACCAGTACTTTTTGTTGATTGCTTGCCTTCAGCTATGGTCACTTATCACCCCTGTGAATCCTGCAAGTACATGGGGTCCGTTAATATTC
 | |  |    ||||    |  ||  |  || |  || || ||  |   | |  |  ||  |    ||  |||   |   | ||| | ||  |||||||| || || ||||| || || || |||||||| ||||| || || ||||||||||||||||| ||||| |||||||||||||| ||||| ||  | ||||| 
ctgaaaaaatctcatgatttcaagcatgttagaccttgttgtaattgcataagttaattggtacgaatggaaaaagttactatttattttggtgtttcagGCGCTTCATGAATCAATATTTCTTGTTGATAGCTTGTCTGCAACTATGGTCACTTATCACTCCTGTAAATCCTGCAAGTACCTGGGGCCCACTTATATTT

upper sequence: AT5G44240.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA13G37090.1 (Glycine max), 3'ss of exon 1
-gtaacgatgattcatttcatttagtgttctaatgttcttatatctatgttacgtcttttctgatcaaaatgttctatct---ttttctttttgtttcagCCGGTTTATGAACCAGTACTTTTTGTTGATTGCTTGCCTTCAGCTATGGTCACTTATCACCCCTGTGAATCCTGCAAGTACATGGGGTCCGTTAATATTC
  |||  |  ||   |||    |   | |  ||  ||| | |   | |  ||  |        ||     |  || ||||   ||| |   || |||||||||||| ||||| |||||||||||| |||| |||||||| ||| ||||| | || || || || || |||||||  ||||||||||||||  | || || 
attaaacagaatgagtttttcctgcgggttaaactttcatgttcattttctaattaaacataaatttcgttaatccatctgattttaccccttttttcagCCGGTTCATGAATCAGTACTTTTTGCTGATAGCTTGCCTGCAGTTATGGCCTCTCATTACTCCGGTAAATCCTGTCAGTACATGGGGTCCTCTTATCTTT

upper sequence: AT5G44240.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA12G33340.1 (Glycine max), 3'ss of exon 1
gtaacgatgattcatttcatttagtgttctaatgttcttatatctatgttacg-tcttttctga-tcaaaatgttctatct---ttttctttttgtttcagCCGGTTTATGAACCAGTACTTTTTGTTGATTGCTTGCCTTCAGCTATGGTCACTTATCACCCCTGTGAATCCTGCAAGTACATGGGGTCCGTTAATATTC
 | |     | | | ||  |   ||||  |||  || | || |  || ||    ||     | | |     |  || ||||   ||| |   || |||||||||||| ||||| |||||||||||| |||| |||||||| ||| ||||| | || || || || || |||||||  ||||||||||||||  | || || 
attaaacaaaatgagtttgtcctgtgtgttaa-attttcatgttcattttctaatcgaacataactttcgttaatccatctgattttaccccttttttcagCCGGTTCATGAATCAGTACTTTTTGCTGATAGCTTGCCTGCAGTTATGGCCTCTCATTACTCCAGTAAATCCTGTCAGTACATGGGGTCCTCTTATCTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctatgttacgtcttttctgatcaaaatgttctatctttttctttttgtttcagCCGGTTTATGAACCAGTACTTTTTGTTGATTGCTTGCCTTCAGCTATGGTCACTTATCACCCCTGTGAATCCTGCAAGTACATGGGGTCCGTTAATATTC
                ttctgat  putative branch site (score: 3)
                            tgttctatctttttct  putative PPT
                                 tatctttttcttttt  TA-rich tract