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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatttgttggctcccttcgttttggtttagtactctctctttctctctcaacgggttattcactcttgaaccttttggatgaattttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAG

Basic information

species Arabidopsis thaliana
transcript AT1G78900.2
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: LOC_Os06g45120.1 (Oryza sativa), 3'ss of exon 16
gtaag--atttgttggctcccttcgttttggtttag---tactctctctttctctctcaacgggttatt-cactcttgaacct---tttggatgaattttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAG
|| ||  ||    | | |   |  | |||  |  ||   || |   | | ||| | | || |  | |      |||| |  ||     |   |  ||  |   ||||||||||||| |||||||| ||||||||||| || ||||||||||| |||||||| |||||| | |   |||| || |||
gtgagtcataccctagttttttctgatttaatacagatttattggttgtctctattttaatgattaaccattttctttagtctgatcatctctatataatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACATTATTCATTTCAATACATTAGCAAATCAG

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: LOC_Os06g45120.2 (Oryza sativa), 3'ss of exon 16
gtaag--atttgttggctcccttcgttttggtttag---tactctctctttctctctcaacgggttatt-cactcttgaacct---tttggatgaattttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAG---------------------
|| ||  ||    | | |   |  | |||  |  ||   || |   | | ||| | | || |  | |      |||| |  ||     |   |  ||  |   ||||||||||||| |||||||| ||||||||||| || ||||||||||| |||||||| |||||| | |   |||| || |||                     
gtgagtcataccctagttttttctgatttaatacagatttattggttgtctctattttaatgattaaccattttctttagtctgatcatctctatataatgaaacagATATGACAAGTTCTGTCCATTCTACAAGTCTGTTTGGATGATGCGCAACATTATTCATTTCAATACATTAGCAAATCAGGTAAATCTAACGTGTTTTTAC

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GRMZM2G421857_T02 (Zea mays), 3'ss of exon 16
gtaagatttgttggctcccttcgttttggtttagtactctctctttctctctcaacgggttattcactcttgaaccttttggatgaattttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAG
    || |      ||   |||       |||  | |||  | ||   |  |  |       |    | ||||    |   | | |||| |   | |||||||| || ||||| || |||||||| ||||| ||||||||||| |||||||| || ||| |||   | || || |||
--gtgagtcccctacttatttcaacaca-tttgatgctcatttttctccattatattttaagtatttttttgacaagtgctgtttaattat---atagATATGATAAGTTCTGCCCATTCTACAAATCCGTTTGGATGATGCGCAACATTATTCACTTCAACACATTGGCAAATCAG

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA08G23990.1 (Glycine max), 3'ss of exon 17
gtaagatttgttg-gctcccttcgttttggtttagtactctctctttctctctcaacgggttattcactcttgaaccttttggatgaattttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAG
|||||     |||   |   ||   ||   |    |    | | ||  | | |  |   ||| ||   |    | | |||||  ||     | ||| ||||||||||||||||| || ||||||||||| || ||||||||||| ||||||||||||||||||||  | || || |||
gtaagggaccttgtaattggttaacttctttaatatgtattatattattgtttttatttgttcttatgttggtacctttttgtgtgg---ctgtgatagATATGACAAATTCTGCCCCTTCTACAAGTCTGTTTGGATGATGCGCAACATTATCCATTTCTACAATTTGGCAAATCAG

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA07G00430.1 (Glycine max), 3'ss of exon 17
gtaagatttgttggctcccttcgttttggtttagtactct--ctctttctctctcaacgggttattcactcttgaaccttttggatgaattttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAG
         ||  |  |||||    |||||| | | || |  |  ||  | | | |  | ||| || |   | | ||||| ||  ||     | ||| |||||||| ||||| || || ||||||||||| || ||||||||||| ||||||||||||||||||||  | || || |||
---------gtaagggcccttgtaattggttaacttctttaacatttattatattattgtgttctt-atgttggtaccttctgtgtgg---ctgtgatagATATGATAAATTTTGCCCCTTCTACAAGTCTGTTTGGATGATGCGCAACATTATCCATTTCTACAATTTGGCAAATCAG

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 3'ss of exon 17
gtaagatttgttggctcccttcgttttggtttagtactctctctttctctctcaacgggttattcactcttgaaccttttggatgaattttt-------tgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAG
        | || |   |  | |   ||   | |     | | | |  ||  |||     | |||| | |    | |  |   ||| |||||       ||||||||||||||| || ||||| || |||||||| || ||||||||| | |||||||| |||||||| ||  | ||||| |||
-----cactcttagtcactgtaggactgacatgggttattttttgttacttccaatcaaattttcattatcttccatgattattgattttttggttggttgacagATATGACAAGTTTTGTCCCTTTTACAAGTCAGTTTGGATGATGAGGAACATTATTCATTTCTATAATTTGGCCAATCAG

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 3'ss of exon 17
-----------------------gtaagatttgttggctcccttcgttttggtttagt-actctctcttt--------ctctctcaacgggtt----attcactcttgaaccttttggatgaattt--------tttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAG
                        |   | || | | |    ||  |||| ||||| | ||| | || ||        || | |   | |||     | |   | ||  || |  |  ||| || |        | |||||||||||| || ||||| || ||||||||||| || ||||||||||| || |||||||||||||| ||  | ||||| |||
gtaagtcccagattaagtttttgattcaaattttcgtcctttttaatttttgtttacttactatttccttatgttcccctttttatgctggtctagaaattctttttccacttaatatatgtatctcatgtggctgtgacagATATGATAAGTTCTGCCCCTTCTACAAGTCGGTTTGGATGATGCGCAATATTATCCATTTCTATAATTTGGCCAATCAG

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: PP1S8_312V6.1 (Physcomitrella patens), 3'ss of exon 17
-------------------------gtaagat--ttgttggctcccttcgttttggtttagtac-tctctctttctctctcaacgggttattcactcttgaaccttttggatgaattttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAG
                         ||| |||  ||||||| |   |   |||   | |  |   || || ||   |  |     | || | ||    |||  |  |    | |  |   |||||| |||||||||||||| || ||||||||||| ||||||||||||||||| ||| |||| ||| |||  || || || |||
gtgagctttgttgaaattttgttgtgtaggatgtttgttgggtagatgtttttcattattctgtgtccctgttcgacgattgtgtgtttctccatgtctgattcggtcctctca--tacgtgacagTTATGACAAATTCTGCCCATTCTACAAGTCTGTGTGGATGATGCGTAATATTGTCCACTTCAACACTCTTGCAAATCAG

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: EFJ33015 (Selaginella moellendorffii), 3'ss of exon 16
gtaagatttgttggctcccttcgttttggtttagtactctctctttctctctcaacgggttattcactcttgaaccttttggatgaattttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAG
                                            | |    ||  ||||    |  ||||||    |     |  |  |  |   |||||| || || || ||||| |||||||||||||| ||||||||||| |||||  | ||||||| | ||||  |||  |||
-------------------------------------------gtacgtgttc--cgggc---ttgctcttgtttatcgctaacaatctgctc--cagATACGATAAGTTTTGTCCGTTCTACAAGTCCGTTTGGATGATGCGAAACATCGTTCATTTCTGCGACCTGTCCACTCAG

upper sequence: AT1G78900.2 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: EFJ30330 (Selaginella moellendorffii), 3'ss of exon 17
gtaagatttgttggctcccttcgttttggtttagtactctctctttctctctcaacgggttattcactcttgaaccttttggatgaattttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAG
                                            | |    ||  ||||    |  ||||||    |     |  |  |  |   |||||| || || || ||||| |||||||||||||| ||||||||||| |||||  ||||||||| | ||||  |||  |||
-------------------------------------------gtacgtgttc--cgggc---ttgctcttgtttatcgctaacaatctgctc--cagATACGATAAGTTTTGTCCGTTCTACAAGTCCGTTTGGATGATGCGAAACATCGTCCATTTCTGCGACCTGTCCACTCAG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|116463760|gb|EG506352.1|EG506352
EST:     ACAGCTAAGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACC                         ATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
genomic: ACAGCTAAGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACCgtaagatttg ... tttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
EST: gi|116484152|gb|EG526744.1|EG526744
EST:     AGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACC                         ATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
genomic: AGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACCgtaagatttg ... tttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
EST: gi|124822727|gb|EH907593.1|EH907593
EST:     CTTGCTCAAAACGCGTTTACACC                         ATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
genomic: CTTGCTCAAAACGCGTTTACACCgtaagatttg ... tttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
EST: gi|116484817|gb|EG527409.1|EG527409
EST:     ACAGCTAAGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACC                         ATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
genomic: ACAGCTAAGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACCgtaagatttg ... tttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
EST: gi|116423655|gb|EG466247.1|EG466247
EST:     ACAGCTAAGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACC                         ATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
genomic: ACAGCTAAGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACCgtaagatttg ... tttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
EST: gi|116423878|gb|EG466470.1|EG466470
EST:     AGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACC                         ATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
genomic: AGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACCgtaagatttg ... tttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
EST: gi|116423877|gb|EG466469.1|EG466469
EST:     AGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACC                         ATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
genomic: AGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACCgtaagatttg ... tttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
EST: gi|116467266|gb|EG509858.1|EG509858
EST:     AGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACC                         ATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
genomic: AGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACCgtaagatttg ... tttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
EST: gi|116484141|gb|EG526733.1|EG526733
EST:     AGCTATTGAGGGAAGATTACCTTCGCTCAAAACGCGTTTACACC                         ATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
genomic: AGCTATTGAGGGAAGATTACCTT-GCTCAAAACGCGTTTACACCgtaagatttg ... tttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
EST: gi|116452176|gb|EG494768.1|EG494768
EST:     AGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACC                         ATATGACAAATTCTGTCCTTTTTACAAGTCCGTGTGGATGATGCGTAACAT
genomic: AGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACCgtaagatttg ... tttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
EST: gi|116463788|gb|EG506380.1|EG506380
EST:     ACAGCTAAGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACC                         ATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
genomic: ACAGCTAAGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACCgtaagatttg ... tttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
EST: gi|125031712|gb|EL103981.1|EL103981
EST:     TTACCTTGCTCAAAACGCGTTTACACC                         ATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
genomic: TTACCTTGCTCAAAACGCGTTTACACCgtaagatttg ... tttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
EST: gi|164136381|gb|ES111995.1|ES111995
EST:     TGCTCAAAACGCGTTTACACC                         ATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
genomic: TGCTCAAAACGCGTTTACACCgtaagatttg ... tttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
EST: gi|116436722|gb|EG479314.1|EG479314
EST:     ACAGCTAAGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACC                         ATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
genomic: ACAGCTAAGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACCgtaagatttg ... tttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
EST: gi|116424281|gb|EG466873.1|EG466873
EST:     ACAGCTAAGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACC                         ATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
genomic: ACAGCTAAGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACCgtaagatttg ... tttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
EST: gi|116452175|gb|EG494767.1|EG494767
EST:     AGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACC                         ATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
genomic: AGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACCgtaagatttg ... tttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
EST: gi|116456041|gb|EG498633.1|EG498633
EST:     ACAGCTAAGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACC                         ATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
genomic: ACAGCTAAGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACCgtaagatttg ... tttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
EST: gi|116433583|gb|EG476175.1|EG476175
EST:     ACAGCTAAGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACC                         ATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
genomic: ACAGCTAAGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACCgtaagatttg ... tttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
EST: gi|116423654|gb|EG466246.1|EG466246
EST:     AGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACC                         ATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
genomic: AGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACCgtaagatttg ... tttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
EST: gi|116451304|gb|EG493896.1|EG493896
EST:     ACAGCTAAGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACC                         ATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
genomic: ACAGCTAAGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACCgtaagatttg ... tttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
EST: gi|116424219|gb|EG466811.1|EG466811
EST:     ACAGCTAAGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACC                         ATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
genomic: ACAGCTAAGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACCgtaagatttg ... tttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
EST: gi|116468179|gb|EG510771.1|EG510771
EST:     ACAGCTAAGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACC                         ATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT
genomic: ACAGCTAAGCTATTGAGGGAAGATTACCTTGCTCAAAACGCGTTTACACCgtaagatttg ... tttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctctctcaacgggttattcactcttgaaccttttggatgaattttttgacagATATGACAAATTCTGTCCTTTCTACAAGTCCGTGTGGATGATGCGTAACATTATCCATTTCTACAACCTAGCCAACCAG
                                            tttttt  CT-rich tract
                                       atgaatttttt  TA-rich tract