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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcttcacttcaaatctttaatctcaagatccagatgcaaatattttgtgatagtaaaatgattgattacttcttaatgcattttttcagGTTGGTCAAGAGCAATTCTCTCCTAGTTCACCTGGATGGCCTCCCTTTATGAGGGTGAATCCTATATTGGATTGGTCCTACAG

Basic information

species Arabidopsis thaliana
transcript AT5G03430.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G03430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os01g15490.3 (Oryza sativa), 3'ss of exon 4
-----------------------------------------gttagcttcact---tcaaatctttaatctca-aga---tccagatgcaaatattttgtgatagtaaaatgattgattacttcttaatgcattt--tttcagGTTGGTCAAGAGCAATTCTCTCCTAGTTCACCTGGATGGCCTCCCTTTATGAGGGTGAATCCTATATTGGATTGGTCCTACAG
                                         | |||  |   |   || |||| | |  | || |||   | ||  |    || |     ||      |   |   |||||||  ||  |  |    ||  |||||||||||||||| ||||| |||||||||||||| |||||||| || |||||||| |||||||||||||| ||||| |||||
gtaattttcttgttcccttgtttagttgctcttcaaatctcgatagacttgttatgtccaatcctcatgcccatagacctttcacttattgatgtccctagactcccgataaacctattacttactacagtttgggattatagGTTGGTCAAGAGCAGTTCTCGCCTAGTTCACCTGGCTGGCCTCCTTTCATGAGGGTCAATCCTATATTGGACTGGTCATACAG

upper sequence: AT5G03430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G381933_T03 (Zea mays), 3'ss of exon 4
-----------------------------------------gttagcttcacttca---aatctttaatctcaagat----ccagatgcaaatattttgtgatagtaaaatga---ttgattacttcttaatgcattttttcagGTTGGTCAAGAGCAATTCTCTCCTAGTTCACCTGGATGGCCTCCCTTTATGAGGGTGAATCCTATATTGGATTGGTCCTACAG
                                          ||      | |  |   |||  |||  | || | |    |||| | |  | | ||| || ||    | |||   |||| ||      | |      |   ||||||||||||| || |||||||||||||||||||| |||||||| ||||||||||||||||| || ||||||||||| |||||
gtgattttcttttaccattgctcatttgttgttaacaaccccttgcacctattgtacgcaatgattatgcccatggtgttcccagttccttacagttt-tggtatctcactgaactttgagtaaacacaattttgaaatgatagGTTGGTCAAGAACAGTTCTCTCCTAGTTCACCTGGCTGGCCTCCTTTTATGAGGGTGAATCCAATCTTGGATTGGTCATACAG

upper sequence: AT5G03430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G028010_T01 (Zea mays), 3'ss of exon 5
-------------------------------------------------------------------------gttagctt--cacttcaaatctttaatctcaagatccagatgcaaatattttgtgatagtaaaatgattgattacttcttaatgcattttttcagGTTGGTCAAGAGCAATTCTCTCCTAGTTCACCTGGATGGCCTCCCTTTATGAGGGTGAATCCTATATTGGATTGGTCCTACAG
                                                                         | |||  |     ||||   | ||  |   |   |   |  ||     |  ||  ||   |   | ||||      |   ||   ||  ||  ||||||||||| |  | ||||| ||||| || ||||  |||||||| || ||||||||||| ||||| |||||||||||||||||
gtgactccccttgaattgagtgctcccgttttagtctacttcactgtcgtcattctacacctctatcgatctagctagtatactggttcatgccattc-tgcaacattttgggggccgggttcatgacatgtgatggtaattg-cggtgtggaaaaaaatacttgtagGTTGGTCAACAAGAGTTCTCCCCTAGCTCGCCTGACTGGCCTCCTTTCATGAGGGTGAACCCTATCTTGGATTGGTCCTACAG

upper sequence: AT5G03430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G149609_T01 (Zea mays), 3'ss of exon 4
---gttagcttcacttcaaat----ctttaatctcaagatccagatgcaaatattttgtgatagtaaaatgat--tgattacttcttaatgc--------attttttcagGTTGGTCAAGAGCAATTCTCTCCTAGTTCACCTGGATGGCCTCCCTTTATGAGGGTGAATCCTATATTGGATTGGTCCTACAG
     |  | |    || |||    | |   |  ||  ||| |    ||| | |||| |||  ||  | ||||  | ||    ||    ||         |||  |  |||| |||||| |  | ||||| ||||| || || || |||||||| || ||||||||||| || || |||||||||||||||||
gtgacttcccttgaatcgaatgacgcctgcctgacataatcgaatgacaatttttttttgagggttcattgatggtaatctaatcgcggtgtgaatgaaaattgctgtagGTCGGTCAACAAGAGTTCTCCCCTAGCTCGCCCGGCTGGCCTCCTTTCATGAGGGTGAACCCAATCTTGGATTGGTCCTACAG

upper sequence: AT5G03430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA19G36860.1 (Glycine max), 3'ss of exon 5
gttagctt---cacttcaaatctttaatctcaagatccagatgcaa-atattttgtgatagtaaaatgattgattacttctta-atgcattt---tttcagGTTGGTCAAGAGCAATTCTCTCCTAGTTCACCTGGATGGCCTCCCTTTATGAGGGTGAATCCTATATTGGATTGGTCCTACAG
||  ||||     ||| ||| |  || | | |  | |  | |  || | |   ||  ||| | | ||  |  |||  | | |   |||   |   || |||||||||||||| |||||||| |||||||| ||||| ||||| || || |||||||||||||| || || |||||||| |||||
gtatgcttttgttctttaaaccaata-tttgattaccatggtttaataaaagctggaatattgacatattatattcatacgtgtgtgctcctaccttacagGTTGGTCAAGAACAATTCTCCCCTAGTTCGCCTGGGTGGCCACCTTTCATGAGGGTGAATCCCATTTTAGATTGGTCATACAG

upper sequence: AT5G03430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA03G34140.1 (Glycine max), 3'ss of exon 4
------gttagct--tcacttcaaatctttaatctcaagatccagatgcaaatattttgtgatagtaaaatgattgattacttcttaatgcattttttcagGTTGGTCAAGAGCAATTCTCTCCTAGTTCACCTGGATGGCCTCCCTTTATGAGGGTGAATCCTATATTGGATTGGTCCTACAG
      ||| |||  | |   |||   || | |  || | |  |     || |    | |     ||  || ||| ||   |   |  | |    || |||||||||||||| |||||||| |||||||||||||| ||||| || || |||||| ||||||| || || |||||||| |||||
gtatgtgtttgctctttaaaccaatatttaattaccatggtttaatgaaaactggactattggcatattat-attcatacatgtgtgctcctaccttacagGTTGGTCAAGAACAATTCTCCCCTAGTTCACCTGGGTGGCCACCTTTCATGAGGCTGAATCCCATTTTAGATTGGTCATACAG

upper sequence: AT5G03430.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv08s0007g04980.t01 (Vitis vinifera), 3'ss of exon 5
--------------------------------------------------------gttagcttcacttcaaatctttaatctcaagatccagatgcaaatattttgtgatagtaaaatgattgattac-ttcttaatgcattttttcagGTTGGTCAAGAGCAATTCTCTCCTAGTTCACCTGGATGGCCTCCCTTTATGAGGGTGAATCCTATATTGGATTGGTCCTACAG
                                                          ||| ||  |||| |   ||   | | |   | ||   | | ||     ||||||       |  |  |||  || ||||     | || ||||| |||||||| ||||||||||||||||||||||||||||| || |||||||| ||||| || || ||||||||||| |||||
gtatatttgatgctctacctcaaaaagctatatgtctgctacatattttgcctcatactagattatcttccagatttc--tgtaagattgcattagaagattcaaagtgataagtgttagtatatttatatttttaacattatcttgcagGTAGGTCAAGAACAATTCTCTCCTAGTTCACCTGGATGGCCACCTTTTATGAGAGTGAACCCAATCTTGGATTGGTCTTACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcaaatattttgtgatagtaaaatgattgattacttcttaatgcattttttcagGTTGGTCAAGAGCAATTCTCTCCTAGTTCACCTGGATGGCCTCCCTTTATGAGGGTGAATCCTATATTGGATTGGTCCTACAG
                                    tcttaat  putative branch site (score: 3)
                                            cattttttc  CT-rich tract
                   taaaatgattgatta  TA-rich tract