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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctatttcttctgctctagtagatactttgaattgctttagtatcgctttcgtgttgatcgtaatcaaaaccattcactgaacactcttgtactttatgatcgatttagGTGGTAGCAATTGGTGAATGTGGATTGGATTATGACAGGCTTCAATTTTGCTCAGTTGATATCCAGAAGAA

Basic information

species Arabidopsis thaliana
transcript AT3G52390.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G52390.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G051032_T01 (Zea mays), 3'ss of exon 7
---------------------gtgctatttcttctgctctagtagatactttgaattgctttagtatcgctttcgtgttgatcgtaatcaaaaccattcactgaaca-ctcttgtacttt---atga---tcgattt----agGTGGTAGCAATTGGTGAATGTGGATTGGATTATGACAGGCTTCAATTTTGCTCAGTTGATATCCAGAAGAA
                        |  || ||  ||  | |     | |    ||   || ||  |||   ||   ||      |    |  | | | ||  ||| | | || | | | |   ||||    | | ||    |||| || || |||||||||||||| |||||||||||||| ||||| || ||  | |  |             
actgcattccccttctccccttctcccttcctgttgtgcaaagtcgtgccccaaacc-ctctaccatcttatttcagtccccactctctaccatcctacagGGAAAAACACTAGCAATCTTACATGAGTTCCAAGTTTTGCAGGTCGTTGCTATTGGTGAATGTGGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAG-------------

upper sequence: AT3G52390.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM2G095969_T01 (Zea mays), 3'ss of exon 5
gtgctatttcttctgctctagtagatactttgaattgctttagtatcgctttcgtgttgatcgtaatcaaaaccattcactgaacactcttgtact--ttatgatcgatttagGTGGTAGCAATTGGTGAATGTGGATTGGATTATGACAGGCTTCAATTTTGCTCAGTTGATATCCAGAAGAA
          || ||   |     | ||  ||  ||  || |||  |   |   |      |   |   |||  |  |||| | || ||||  |    ||   |    |  |||| || ||  ||||||||||||| |||||||||||||| ||||| || ||  | |  ||||| || |||||
---------tttttgtagtgagccacacagtgc-ttatttcagtccccactctctaccatcctccagggaaaaaa--cact-agcaatcttacatgagttccaagttttgcagGTCGTTGCTGTTGGTGAATGTGGTTTGGATTATGACAGACTTCAGTTCTGTCCGGCAGATATGCAAAAGAA

upper sequence: AT3G52390.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GRMZM5G894029_T01 (Zea mays), 3'ss of exon 14
-----------------------------------------------------------------------------------------gtgctatttcttctgctctagtagatactttgaattgctttagtatcgctttcgtgttgatcgtaatcaaaaccattcactgaaca-ctcttgtacttt---atga---tcgattt----agGTGGTAGCAATTGGTGAATGTGGATTGGATTATGACAGGCTTCAATTTTGCTCAGTTGATATCCAGAAGAA
                                                                                            |  || || |||  | |     | |    ||   || ||  |||   ||   ||      |    |  | | | ||  ||| | | || | | | |   ||||    | | ||    |||| || ||  ||||||||||||| |||||||||||||| ||||| || ||  |    |             
gttcctaaaaatcgtttgacttcaaatactaaactaacacaatgttgctctattgtagggatttttgaagcactgactgcattcccctttctcccttcctgctgtgcgaagccgtgccccaaacc-ctctaccatcttatttcagtccccactctctaccatcttccagGGAAAAACACTAGCAATCTTACATGAGTTCCAAGTTTTGCAGGTCGTTGCTGTTGGTGAATGTGGTTTGGATTATGACAGACTTCAGTTCTGTCCGACAG-------------

upper sequence: AT3G52390.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA19G38780.1 (Glycine max), 3'ss of exon 6
gtgctatttcttctgctctagtagatactttgaattgctttagtatcgctttcgtgttgatcgtaatcaaaaccattcactgaac-actcttgtactttatgatcgatttagGTGGTAGCAATTGGTGAATGTGGATTGGATTATGACAGGCTTCAATTTTGCTCAGTTGATATCCAGAAGAA
       ||||  |    | | |||   | ||   |  || || | |   | | |  | | | |  | | || ||     |   | | ||||    ||  | ||      ||||||| |||||||| |||||||||||||| |||||||||||||| |||||| |||  || || || |||||
------gttctcatctagttgcagaacttgtgttctagttcagaaac---tacctaataaccat--ttagaaacaactgttatgctattcttacttttcttcatatgca-agGTGGTTGCAATTGGAGAATGTGGATTGGACTATGACAGGCTTCATTTTTGCCCAGCAGAGATTCAAAAGAA

upper sequence: AT3G52390.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv08s0032g01170.t01 (Vitis vinifera), 3'ss of exon 6
gtgctatttcttctgctctagtagatactttgaattgctttagtatcgctttcgtgttgatcgtaatcaaaaccattcactgaacactcttgtactttatgatcgatttagGTGGTAGCAATTGGTGAATGTGGATTGGATTATGACAGGCTTCAATTTTGCTCAGTTGATATCCAGAAGAA
           ||   ||| |   ||  || |||  |   | || || | |   ||    ||  |    |  |||  |  |     ||  |||   |  |  || | | ||||||| |||||||||||||||||||||||||| ||||||||||| |||||| ||  |||  | ||||||||
----------ctcaagtcttgagaatg-ttagaaaagtacttgtgtcacatctctgggcttcagaggatattccaaactgttttatcttctgtttatattcttcaaataagGTGGTGGCAATTGGTGAATGTGGATTGGATTACGACAGGCTTCACTTTTGCCCATCTGAGGTTCAGAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatcgtaatcaaaaccattcactgaacactcttgtactttatgatcgatttagGTGGTAGCAATTGGTGAATGTGGATTGGATTATGACAGGCTTCAATTTTGCTCAGTTGATATCCAGAAGAA
 tgttgat  putative branch site (score: 4)
       taatcaaaa  TA-rich tract