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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacttcgaggacaacggatttgtactatttcttatacagcaagaaagaagaacaaaacctaatatctcgcttaggttattttgagtaacagctatttatatgtcttttaatagGTGGGAGAAGGATGGAAACAGTCCTTTGTATGGGTATGATTTCTGGTACCAACCTCGGCATAAGACGATGATCAGTACCTCATGGGGAGCCCCGGCCGCG

Basic information

species Arabidopsis thaliana
transcript AT3G23800.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G23800.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os01g68770.1 (Oryza sativa), 3'ss of exon 3
gtaacttcgaggacaacggatttgtactatttcttatacagcaagaaagaagaacaaaacctaatatctcgcttaggttattttgagtaacagctatt-tatatgtcttttaatagGTGGGAGAAGGATGGAAACAGTCCTTTGTATGGGTATGATTTCTGGTACCAACCTCGGCATAAGACGATGATCAGTACCTCATGGGGAGCCCCGGCCGCG
         |  |   |   |      ||| |   ||  |     ||   |    | |     |||| | || |   ||   ||||   | | | ||  ||| |  ||| |   || ||||| |||   ||  |||| || |||| ||| |||||||  ||||| |||||||| || ||||| ||||||||| | ||||||||||| || || || 
--------cataatgcccattccaggatatgttccatgaaatgtcaatttatgttacac----atattt-gcatgactt---ttgaaagataaccatagtatttcccttctcgcagTTGGGAAAAGCCAGGTCACAGCCCCTTGTTTGGCTATGATTATTGGTATCAACCTCGTCACAAGACAATGATCAGTTCATCATGGGGAGCACCTGCAGCT

upper sequence: AT3G23800.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G103812_T02 (Zea mays), 3'ss of exon 3
gtaacttcgaggacaacggatttgtactatttcttatacagcaagaaagaagaacaaaacctaatatctcgcttaggttattttgagtaacagctatttatatgtcttttaatagGTGGGAGAAGGATGGAAACAGTCCTTTGTATGGGTATGATTTCTGGTACCAACCTCGGCATAAGACGATGATCAGTACCTCATGGGGAGCCCCGGCCGCG
             ||   |  | |||  ||| |||  |||    |||| |   ||| |  | | |||   | |     | | || | ||     ||  | | ||     |   || ||||| |||   ||  ||||||| |||| ||| ||||| ||||||||||| ||||| || ||||||||||||||| | |||||||||||||| || |||
-----------tgcagatgtatggtaaaattgcttg-aca-tgtgaaaaacagacagattc-attatgatgatctcagtgtctttattacttattaagtttctgctacatg-cagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCAGCCTCGCCACAAGACGATGATCAGTTCGTCATGGGGAGCCCCTGCAGCG

upper sequence: AT3G23800.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G058930_T01 (Zea mays), 3'ss of exon 6
gtaacttcgaggacaacggatttgtactatttcttatacagcaagaaagaagaaca-aaacctaatatctcgcttaggttattttgagtaacagctatttatatgtcttttaatagGTGGGAGAAGGATGGAAACAGTCCTTTGTATGGGTATGATTTCTGGTACCAACCTCGGCATAAGACGATGATCAGTACCTCATGGGGAGCCCCGGCCGCG
              ||  | |   || | | |   | |  ||  || |   ||| | | |   | |||   | |     ||| |||| |||    ||    | ||     |   || ||||| |||   ||  ||||||| |||| ||| ||||| ||||||||||| |||||  ||||||| ||||||||| | |||||||||||||| || |||
--------------aatagctgcata-tgtatggcaaattgcttgacatgtgaagacagattcactatgctgatctcagtatcttgattaattattaagcctttgctacatg-cagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCAGCCTCGCTATAAGACTATGATCAGTTCATCATGGGGAGCCCCTGCAGCG

upper sequence: AT3G23800.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM5G837351_T01 (Zea mays), 3'ss of exon 3
gtaacttcgaggacaacggatttgtactatttcttatacagcaagaaagaagaacaaaacctaatatctcgcttaggttattttgagtaacagctatttatatgtcttttaatagGTGGGAGAAGGATGGAAACAGTCCTTTGTATGGGTATGATTTCTGGTACCAACCTCGGCATAAGACGATGATCAGTACCTCATGGGGAGCCCCGGCCGCG
                 | || ||||       ||      || |  | || |   | |   | |||   | |     ||| |||| |||    ||    | ||     |  ||| ||||| |||   ||  ||||||| |||| ||| ||||| ||||||||||| ||||  || ||||| ||||||||| | |||||||||||||| || |||
--------------gctgcatatgtatggcaaattgcttgacatgtgaaaacagacagattcactatgctgatctcagtatcttgattaattattaagcctttgctacatt-tagTTGGGAAAAGCCAGGTCACAGTCCCTTGTTTGGATATGACTTCTGGTACCAGCCTCACCACAAGACTATGATCAGTTCATCATGGGGAGCCCCTGCAGCG

upper sequence: AT3G23800.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA05G28400.1 (Glycine max), 3'ss of exon 3
gtaacttcgaggacaacggatttgtactatttcttatacagcaagaaagaagaacaaaacctaatatctcgcttaggttattttgagtaacagctatttatatgt-cttttaatagGTGGGAGAAGGATGGAAACAGTCCTTTGTATGGGTATGATTTCTGGTACCAACCTCGGCATAAGACGATGATCAGTACCTCATGGGGAGCCCCGGCCGCG
             || |  |||      |  |  ||   | |     | |     |  |  | |    | | |||  || |  | | ||     ||| |       | |||  ||||||||||||   |||  ||||||| |  | ||||||||| |||||||||||||| | ||||||||| ||||| ||  | |||||||| || || || || 
-------------cagcatattcaacaaaagttctacgaatctgatgaaatagttaccatttcag---tggattattttctagttattagtttgtatcttggcacacatttgttagGTGGGAGAAACCTGGGCACAGTCCATCATTTGGGTATGACTTCTGGTACCAACCACAGCATAAGACTATGATTAGCTCATCATGGGGTGCTCCTGCTGCT

upper sequence: AT3G23800.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G11400.1 (Glycine max), 3'ss of exon 3
gtaacttcgaggacaacggatttgtactatttcttatacagcaagaaagaagaacaaaacctaatatctcgcttaggttattttgagtaacagctatttatatgt-cttttaatagGTGGGAGAAGGATGGAAACAGTCCTTTGTATGGGTATGATTTCTGGTACCAACCTCGGCATAAGACGATGATCAGTACCTCATGGGGAGCCCCGGCCGCG
             || |  |||      |  |  ||   | | |   |       |  |  | |    | | |||  || |  | | ||     ||| |       | |||  ||||||||||||   |||  ||||||| |  | ||||||||| |||||||||||||| | ||||||||| ||||| ||  | |||||||| || || || || 
-------------cagcatattcaacaaaagttctacgaaactaatgaagtagttaccatttcag---tggattattttctagttactagtttgtatcttggcacacatttgttagGTGGGAGAAACCTGGGCACAGTCCATCATTTGGGTATGACTTCTGGTACCAACCACAGCATAAGACTATGATTAGCTCATCATGGGGTGCTCCTGCTGCT

upper sequence: AT3G23800.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv05s0029g00240.t01 (Vitis vinifera), 3'ss of exon 3
gtaacttcgaggacaacggatttgtactatttcttatacagcaagaaagaagaacaaa-acctaatatctcgcttaggttattttgagtaacagctatttatatgtcttttaatagGTGGGAGAAGGATGGAAACAGTCCTTTGTATGGGTATGATTTCTGGTACCAACCTCGGCATAAGACGATGATCAGTACCTCATGGGGAGCCCCGGCCGCG
           ||  | |     | | |  || |  || | || ||   ||   |  | |   |  |      ||   | | ||||| |  |  ||  || |  |   | ||  || ||||||||    ||  | ||||| |  | ||| || ||||||||||||||||| || || ||||| ||||||||| | ||||||||||| || || || 
-----------gaacatgtccagggaatggttttagtataacatgagccaacctctgacattgagcacagtattt---taagtttgattttccactcctttt--gatatatatcagATGGGAGAAACCAGGGCATAGTCCGTCTTTTGGCTACGATTTCTGGTACCAACCCCGTCACAAGACAATGATCAGTTCATCATGGGGAGCACCTGCAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctaatatctcgcttaggttattttgagtaacagctatttatatgtcttttaatagGTGGGAGAAGGATGGAAACAGTCCTTTGTATGGGTATGATTTCTGGTACCAACCTCGGCATAAGACGATGATCAGTACCTCATGGGGAGCCCCGGCCGCG
                        gagtaac  putative branch site (score: 2)
                                          tgtctttt  putative PPT
                                  tatttatatgtctttt  TA-rich tract