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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggctatcataccaatacttgaatcctcgatgctccagctgcttttttaaaaattcttcagggatcacacttgaaatttgattcgtatttatgtatgtgttttaaaacagTCTCTGCAAGCTCTCAAAAAGATATCTCAGGAGCACCCAACTGCCTGTTTGCGAGCTGGTGCTCTTATGGCTGTGCTCTCGTATCTGGATTTCTTCTCCA

Basic information

species Arabidopsis thaliana
transcript AT4G38600.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G38600.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G374574_T02 (Zea mays), 3'ss of exon 2
----------------------------------------------gttggctatcat-accaatacttga--atcctcgatgctccagctgcttttttaaaaattcttcagggatcacacttgaaatttgatt-cgtatttatgtatgtgttttaaaacagTCTCTGCAAGCTCTCAAAAAGATATCTCAGGAGCACCCAACTGCCTGTTTGCGAGCTGGTGCTCTTATGGCTGTGCTCTCGTATCTGGATTTCTTCTCCA
                                               | |   ||| | || |  |  | |  ||     ||| ||   |  | | |  |   || |     |   |  ||        || |  |  |||||  | |           |||||||| ||||| || || ||||| |||| ||||||||||||||||||||||||||||||||| || |||||||| || |||||||| || ||||||||||
gtggtgccttccctttgtcttcttcttcctcgttttatcctgtatcatcgctcatcctcactatcatctaaaaatgaaatatgatcagtcatcctctgcatgcatgcccttagccccttaccaaggtgctgctaacacatttactt-tactcgcctgctcagTCTCTACAAGCCCTTAAGAAGATCTCTCTGGAGCACCCAACTGCCTGTTTGCGAGCTGGTGCCCTAATGGCTGTTCTATCGTATCTCGACTTCTTCTCCA

upper sequence: AT4G38600.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GRMZM2G049141_T02 (Zea mays), 3'ss of exon 1
gttggctat-cataccaatacttgaatcctcgatgctccagctgcttttttaaaaattcttcagggatcacacttgaaatttgattcgtatttatg-tatgtgttttaaaacagTCTCTGCAAGCTCTCAAAAAGATATCTCAGGAGCACCCAACTGCCTGTTTGCGAGCTGGTGCTCTTATGGCTGTGCTCTCGTATCTGGATTTCTTCTCCA
      ||| |||||  ||| | ||  | |   ||  ||| ||   ||| ||     | |  | | ||  | |||||   | |  |   || |||| || || |||| |   ||||  |||||||||| ||||| ||||| | |||||| |||||||| || |||||||||||||| || ||||| || || || || || || || |||||||
------tatgcatacagataatagacgcatacgtgtaccatct--ctttgta-----tttgtatgcat-gctcttgatggtggcctaacatatatgctacgtttttttatttagTCATTGCAAGCTCTTAAAAAAATATCCCTGGAGCATCCAACTGCGTGCTTGCGAGCTGGTGCACTAATGGCAGTCCTATCATACCTTGACTTTTTCTCCA

upper sequence: AT4G38600.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G00600.2 (Glycine max), 3'ss of exon 1
gttggctatcataccaatacttgaa-tcctcgatgc-tccagctgcttt---tttaaaaattcttcagggatcacacttgaaatttgattcgtatttatgtatgtgtt--ttaaaacagTCTCTGCAAGCTCTCAAAAAGATATCTCAGGAGCACCCAACTGCCTGTTTGCGAGCTGGTGCTCTTATGGCTGTGCTCTCGTATCTGGATTTCTTCTCCA
        | ||      |||  |  || |  |||| |  || |  | |   | |  || |  ||   | ||      | |  ||  ||||  ||  ||||   ||||  |   | |||||||| ||||| || || ||||| |||||||||||||||||||||||| | |||||||| ||||| |||||||| || || ||  |||| |||||||| |
-------gttattttctcactcaatctcttttatgcctttagttattatgtatctggaattctttttagaattttgtcttactttgaattctgatagatgtgattgttgatgtgagcagTCTCTTCAAGCACTAAAGAAGATTTCTCAGGAGCACCCAACTGCCTGTCTTCGAGCTGGAGCTCTGATGGCTGTTCTTTCTTACTTGGACTTCTTCTCGA

upper sequence: AT4G38600.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA12G03640.1 (Glycine max), 3'ss of exon 1
gttggctatcataccaatacttgaatcctcgatgctccagctgcttttttaaaaattcttcagggatcacacttgaaatttgattcgtatttatgtatgtgttttaaaacagTCTCTGCAAGCTCTCAAAAAGATATCTCAGGAGCACCCAACTGCCTGTTTGCGAGCTGGTGCTCTTATGGCTGTGCTCTCGTATCTGGATTTCTTCTCCA
     |  |  ||  || | ||    | |   |  |  | ||     ||  |  ||| |  |      |  | |  | |||||||  | | | ||   |  |     ||||||| || |||||||| || ||||||||||||||||| || ||||||||  | ||||| |||||||||||||| ||||| || ||| |||| ||||| || |
-----cagttgtag-aagaattatgccttttttttttaatctaagactt--agcattttgaaaatgaaattcatatagtttgattactgtatttgatggcat----gaacagTCCCTTCAAGCTCTGAAGAAGATATCTCAGGAGCATCCCACTGCCTGCCTACGAGCAGGTGCTCTTATGGCCGTGCTTTCCTATTTGGACTTCTTTTCAA

upper sequence: AT4G38600.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA04G00530.1 (Glycine max), 3'ss of exon 1
-------------------------------------------------------------------------------------gttggctatcataccaatacttgaatcctcgatgctccagctgcttttttaaaaattcttcagggatcacacttgaaatttgattcgtatttatgtatgtgttttaaaacagTCTCTGCAAGCTCTCAAAAAGATATCTCAGGAGCACCCAACTGCCTGTTTGCGAGCTGGTGCTCTTATGGCTGTGCTCTCGTATCTGGATTTCTTCTCCA
                                                                                      || | | |   |      |||   || |  | |       |    ||| | | |   | | |   ||    ||||| | ||||    | || ||  |||   |   |||||||||| ||||| || || ||||| |||||||||||||||||||||||| |  ||||||| ||||| |||||||| || || ||  |||| |||||||| |
gttattttctcagtcaatctcttttgtgcctttacttattatgtatctgtgtcttacgatgtatgagcttcctaagtccttaacccttagttgttgaaaatgggcttccgtcttaaacgaggttcttatcatttgacacaccttacggttttctactttgaattctgat----agttgtgattgttgatgtgaacagTCTCTTCAAGCACTAAAGAAGATTTCTCAGGAGCACCCAACTGCCTGTCTTAGAGCTGGAGCTCTGATGGCTGTTCTTTCTTACTTGGACTTCTTCTCAA

upper sequence: AT4G38600.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA11G11490.2 (Glycine max), 3'ss of exon 1
--------------------------------------------------------------gttgg--ctatcataccaatacttgaatcctcg-atgctccagctgcttttttaaaaattcttcagggatcacactt----gaaatttgattcgta----tttatgtatgtgtttta------aaacagTCTCTGCAAGCTCTCAAAAAGATATCTCAGGAGCACCCAACTGCCTGTTTGCGAGCTGGTGCTCTTATGGCTGTGCTCTCGTATCTGGATTTCTTCTCCA
                                                                |||  ||  |  |    |  || || |   | ||  | ||     | |      | || |  | | ||||  | |     ||||   |||| ||    || ||   ||||||| |       ||||||| || |||||| | || ||||| |||| |||||| || ||||||||  | ||||| |||||||||||||| ||||| || ||| |||| ||||| || |
gttgttctttaatgggaatggtgttagaagaaacttatgaaatataaatatttgtcttgaactctggtgctgcctaattgttttttaaaactatgtatattgcaatgtttctgggttcagttgtagaagaatcatgcattttgaaaatgaaattcttatagtttgattactgtgtttgatggcatgaacagTCCCTTCAAGCTTTGAAGAAGATCTCTCTGGAGCATCCCACTGCCTGCCTACGAGCAGGTGCTCTTATGGCCGTGCTTTCTTATTTGGACTTCTTTTCAA

upper sequence: AT4G38600.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv03s0038g02340.t01 (Vitis vinifera), 3'ss of exon 1
gttggctatcataccaatacttgaatcctcgatgctccagctgcttttttaaaaattcttcagggatcac--acttgaaatttgattcgtatttatgtatgtgttttaaaacagTCTCTGCAAGCTCTCAAAAAGATATCTCAGGAGCACCCAACTGCCTGTTTGCGAGCTGGTGCTCTTATGGCTGTGCTCTCGTATCTGGATTTCTTCTCCA
      |    | ||||   ||    ||   ||| |     ||  ||    ||||||   ||  |    |   |||  | | |   | || ||| || |||       ||||||||| |||||||||| || |||||||||||||| |||||||||||||| ||||||||||| || || ||||| ||||| || |||||||||||||||||||
-----ttcctttgccaaattttattgccataatgatgtcaatg--ttacagaaaatttcccattgcctgcctgcttatagtatttatggtttttgtg-atg------gaaacagTCTTTGCAAGCTCTTAAGAAGATATCTCAGGAACACCCAACTGCCTGCTTGCGAGCTGGAGCACTCATGGCAGTGCTTTCATATCTGGATTTCTTCTCCA

upper sequence: AT4G38600.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv04s0023g03830.t01 (Vitis vinifera), 3'ss of exon 1
gttggctatcataccaatacttgaatcctcgatgctccagctgcttttttaaaaattcttcagggatcacacttgaaat-ttgattcgtatttatgtatgtgtt--ttaaaacagTCTCTGCAAGCTCTCAAAAAGATATCTCAGGAGCACCCAACTGCCTGTTTGCGAGCTGGTGCTCTTATGGCTGTGCTCTCGTATCTGGATTTCTTCTCCA
                |||   |  || | | |  ||  | ||  |     ||| |||||  |   |  |   | |||   |    | |  || ||| ||||    | |   |||||| |||||||||| || |||||||| |||||||| || ||||||||||||||||| |||||||| ||||| ||||| || | ||| || |||||| | |
--------------tgataaagggctctttg-ttttctggttgggtgaaataaatttctttggctgtagctgataaaaggctcgccctttgttttgtttgtgacaataagtgcagTCTTTGCAAGCTCTGAAGAAGATATCCCAGGAGCAGCCTACTGCCTGTTTGCGAGCAGGTGCTCTAATGGCAGTGCTTTCTTTTCTTGACTTCTTCCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcagggatcacacttgaaatttgattcgtatttatgtatgtgttttaaaacagTCTCTGCAAGCTCTCAAAAAGATATCTCAGGAGCACCCAACTGCCTGTTTGCGAGCTGGTGCTCTTATGGCTGTGCTCTCGTATCTGGATTTCTTCTCCA
                    atttgat  putative branch site (score: 5)
                              tatttatgtatgtgtt  TA-rich tract