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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgtataatgaattgaaaatcctacgttgagttgagtttctctattgtgtataaagagcccagactaatatgttggttgattagggaccttttttaatcttgagcagtgatttcctcgtttttgattgattagtttctttgaactaaagtattagtgatggtatcataatttcttgaatgtcgtttgcagATGGATTACATAAACACTTCACATCCAAATTTTATTGGTGGAACCAAGGCCGTGGAAGCTGCAATGCATCAAGTGAAGTCTTCGAGGATTCCCCATCCTG

Basic information

species Arabidopsis thaliana
transcript AT4G33650.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G33650.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: LOC_Os04g31190.1 (Oryza sativa), 3'ss of exon 12
gtctgtataatgaattgaaaatcctacgttgagttgagtttctctattgtgtataaagagcccagactaatatgttggttgattagggaccttttttaatcttgagcagtgatttcctcgtttttgattgattagtttctttgaactaaagtattagtgatggtatcataatttcttgaatgtcgtttgcagATGGATTACATAAACACTTCACATCCAAATTTTATTGGTGGAACCAAGGCCGTGGAAGCTGCAATGCATCAAGTGAAGTCTTCGAGGATTCCCCATCCTG
                                                                     |  |    |||| || |     ||   | ||  ||   ||| |  |    || |||  ||||||   |||||     ||| |         |  || || | | |||||        || ||||||||||||||||| |||||||||||||| ||| |||| || | |||||  || ||   ||| | |||  || |     || | |     ||     |||
--------------------------------------------------------------------gaagtacctgttggtttg-----ttcaatgattgtgcatagtaaagtatctgtgttttgttgatt---ttcttatgggtaatg-------agtaataccaca-tatcttg--------ttacagATGGATTACATAAATACTTCACATCCAAACTTTGTTGGAGGCAACAAGGTTGTTGAGCTTGCTAGGCAAGAAATTTTACCTCCCAAAGCACCAACCTCTG

upper sequence: AT4G33650.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GRMZM2G129155_T01 (Zea mays), 3'ss of exon 12
gtctgtataatgaattgaaaatcctacgttgagttgagtttctctattgtgtataaagagcccagactaatatgttggttgattagggaccttttttaatcttgagcagtgatttcctcgtttttgattgattagtttctttgaactaaagtattagtgatggtatcataatttcttgaatgtcgttt--gcagATGGATTACATAAACACTTCACATCCAAATTTTATTGGTGGAACCAAGGCCGTGGAAGCTGCAATGCATCAAGTGAAGTCTTCGAGGATTCCCCATCCTG
                                                                                        |||   | |||  ||     || || |       | | |||| ||  || | |||| ||    | ||     |  |     | |  |   |||||   ||  ||||   |||||||||||||| ||||| ||||||||||||||||| | |||||| || ||    |||  ||| ||||| | |||| | |  ||  |     | |
----------------------------------------------------------------------------------------accggctataagtttatttggtcatctg------tataattgtttgcttgcattgacctttcttgttttccttattcattcactagcaacaatgttaattgtgcagGAAGATTACATAAACACGTCACACCCAAATTTTATTGGTGGCAGCAAGGCTGTTGAGCAAGCACAGCAGCAAGTTAGGTCTGCCAAAATGTCAGCAGCGG

upper sequence: AT4G33650.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA13G32940.1 (Glycine max), 3'ss of exon 12
gtctgtataatgaattgaaaatcctacgttgagttgagtttctctattgtgtataaagagcccagactaatatgttggttgattagggaccttttttaatcttgagcagtgatt-tcctcgtttttgattgattagtttctttgaactaaagtattagtgatggtatcataatttcttgaatgtcgtttgcagATGGATTACATAAACACTTCACATCCAAATTTTATTGGTGGAACCAAGGCCGTGGAAGCTGCAATGCATCAAGTGAAGTCTTCGAGGATTCCCCATCCTG
                                                                                  | ||  | ||| || |    | |   |||||  ||    | || || ||| || |   ||| ||         |    ||| | || || ||     | |    | |||||||||| |||||||||||||| || ||||||||||||||||||| ||||||  | |||   ||   ||| ||    ||||| || ||| || |    || |
----------------------------------------------------------------------------------tcagtcagcttattca--tatcaattgtgatggtcagtctattagagtgaataatcaatttcaa---------tgtccatgatttcttatttgaactactcaattatgcagATGGACTACATAAACACTTCCCACCCAAATTTTATTGGTGGAAGCAAGGCATTAGAAATAGCTGCGCAACAGACCAAGTCCTCTAGGGTTGCTATACCAG

upper sequence: AT4G33650.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA15G06380.1 (Glycine max), 3'ss of exon 12
gtctgtataatgaattgaaaatcctacgttgagttgagtttctctattgtgtataaagagcccagactaatatgttggttgattagggaccttttttaatcttgagcagtgatttcctcgtttttgattgattagtttctttgaactaaagtattagtgatggtatcataatttcttgaatgtcgtttgcagATGGATTACATAAACACTTCACATCCAAATTTTATTGGTGGAACCAAGGCCGTGGAAGCTGCAATGCATCAAGTGAAGTCTTCGAGGATTCCCCATCCTG
                                                                                    ||  | ||| || |    | |   | |||   |  || | |    || |   |  |   || |    | |   ||||    |  | |  |  | |||    | |||||||||| |||||||||||||| || ||||||||||||||||||| ||||||  | |||   ||    || ||    ||||| || ||| || |    || |
-----------------------------------------------------------------------------------cagtcagcttattca--tgtcaattgcgatggtca-gtctctatcagagtgaatcatc--aatttccatgtccatgatttctttttgaactactcaat----tctgcagATGGACTACATAAACACTTCCCACCCAAATTTTATTGGTGGAAGCAAGGCATTAGAAATAGCTGCACAGCAGACCAAGTCGTCTAGGGTTGCTATACCAG

upper sequence: AT4G33650.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA08G07160.1 (Glycine max), 3'ss of exon 12
gtctgtataatgaattgaaaatcctacgttgagttgagtttctctattgtgtataaagagcccagactaatatgttggttgattagggaccttttttaatcttg--agcagtgatttcctcgtttttgattgattagtttctttgaactaaagtattagtgatggtatcataatttcttgaatgtcgtttgcagATGGATTACATAAACACTTCACATCCAAATTTTATTGGTGGAACCAAGGCCGTGGAAGCTGCAATGCATCAAGTGAAGTCTTCGAGGATTCCCCATCCTG
                                                                                       ||| |   ||| |  ||  |  |||||| ||    | | |||| ||  |  |||        ||    ||    ||  | || || |      |      ||| |||||||| ||||| |||||||| || |||||||||||||||||||  |||||  | ||||||||| |||| |||   | |||||| ||  ||      || |
-------------------------------------------------------------------------------------aagacttggcttattaatgtcaatagtgatgtcaatctatctgat-gaaaaacttc--------aattccttgtccataatttcttattcaaactacaccaatttacagATGGACTACATCAACACTTCCCACCCAAATTTTATTGGTGGAAGTAAGGCAATAGAAGCTGCAGTGCAACAAACCAGGTCTTCTAGAGTTGGTTTACCAG

upper sequence: AT4G33650.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: GLYMA07G30150.1 (Glycine max), 3'ss of exon 12
gtctgtataatgaattgaaaatcctacgttgagttgagtttctctattgtgtataaagagcccagactaatatgttggttgattagggaccttttttaatcttg--agcagtgatttcctcgtttttgattgattagtttctttgaactaaagtattagtgatggtatcataatttcttgaatgtcgtttgcagATGGATTACATAAACACTTCACATCCAAATTTTATTGGTGGAACCAAGGCCGTGGAAGCTGCAATGCATCAAGTGAAGTCTTCGAGGATTCCCCATCCTG
                                                                                       ||| |   ||| |  ||  |  |||||| ||    | | ||||  |  |      || || |      ||   |||  | || || |      |      ||| |||||||| |||||||||||||| || |||||||||||||| ||||  |||||  | ||||||||| |||| |||   | |||||| || ||| |    || |
-------------------------------------------------------------------------------------aagacttagcttattaatgtcaatagtgatgtcaatctatctgatgaaaaa-----cttaaatt----ccttgtcgataatttcttattcaaactacaccaatttacagATGGACTACATAAACACTTCCCACCCAAATTTTATTGGCGGAAGTAAGGCAATAGAAGCTGCAGTGCAACAAACCAGGTCTTCTAGAATTGCTTTACCAG

upper sequence: AT4G33650.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: Vv03s0038g00970.t01 (Vitis vinifera), 3'ss of exon 13
gtctgtataatgaattgaaaatcctacgttgagttgagtttctctattgtgtataaagagcccagactaatatgttggttgattagggaccttttttaatcttgagcagtgatttcctcgtttttgattgattagtttctttgaactaaagtattag--tgatggta-tcataatttcttgaatgtcgtt-tgcagATGGATTACATAAACACTTCACATCCAAATTTTATTGGTGGAACCAAGGCCGTGGAAGCTGCAATGCATCAAGTGAAGTCTTCGAGGATTCCCCATCCTG
                                                                                                 || |   |  |   |       ||      |  ||    ||| |  || | |||| ||    |||   |  ||  | | |    |||    || || ||||||| |||||||| |||||||| |||||||||||||||||||  || || |||||    ||| |||| ||  | ||||| || ||| | ||    ||||
------------------------------------------------------------------------------------------------caaaccaaaaaaagaaaaaaaaagtagcaattgtatgcacttcatcaaagttaagtgttttcttgacaatggtctcagtctaagcaattctattctgtagATGGACTACATAAATACTTCACACCCAAATTTTATTGGTGGAAGTAAAGCTGTGGAGATGGCATTGCAACAGATTAAGTCCTCTAGGCTGCCTGTACCTG

upper sequence: AT4G33650.1 (Arabidopsis thaliana), 3'ss of exon 12
lower sequence: PP1S187_100V6.2 (Physcomitrella patens), 3'ss of exon 14
gtctgtataatgaattgaaaatcctacgttgagttgagtttctctattgtgtataaagagcccagactaatatgttggttgattagggaccttttttaatcttgagcagtgatttcctcgtttttgattgattagtttctttgaactaaagtattagtgatggtatcataatttcttgaatgtcgtttgcagATGGATTACATAAACACTTCACATCCAAATTTTATTGGTGGAACCAAGGCCGTGGAAGCTGCAATGCATCAAGTGAAGTCTTCGAGGATTCCCCATCCTG
                                                                                            |||| ||||    |  | |  |   | || | || |    |||| | ||||   |||  | | |    |     | |||||     ||  |   | ||||||||||||||| ||||| ||||||||   |||||| ||||||| |||||| |||||    ||  || ||||    | |  | | | ||  |    | || 
----------------------------------------------------------------------------------------gtaattttaaatccaatgttgagcctatgttgtgtctgtt--gctagtgtttttgtgttaat-tgtcaactttctggccgtaattca--aaacttgtctggcagATGGATTACATCAACACATCACATCCTGCTTTTATAGGTGGAAGCAAGGCTGTGGAGATGGCTTTGAATCAGCAAAGGCATGCCAAGACGCTGGCTTCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttgaactaaagtattagtgatggtatcataatttcttgaatgtcgtttgcagATGGATTACATAAACACTTCACATCCAAATTTTATTGGTGGAACCAAGGCCGTGGAAGCTGCAATGCATCAAGTGAAGTCTTCGAGGATTCCCCATCCTG
      aactaaa  putative branch site (score: 2)
                          tatcataatttctt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgtataatgaattgaaaatcctacgttgagttgagtttctctattgtgtataaagagcccagactaatatgttggttgattagggaccttttttaatcttgagcagtgatttcctcgtttttgattgattagtttctttgaactaaagtattagtgatggtatcataatttcttgaatgtcgtttgcagATGGATTACATAAACACTTCACATCCAAATTTTATTGGTGGAACCAAGGCCGTGGAAGCTGCAATGCATCAAGTGAAGTCTTCGAGGATTCCCCATCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT