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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgttctgtgctcttacggagtaacatatcgtttctttgtttaagataatactaatattggtgtggtttttacatgatgcagTATGTACATTACCTTCAGCGCAAGTACTCGCTTAACTCATTCAACCTATTGGGACATACCGCTCCAGCCCAAGCCGCAACATTACTGGTAGTTGGCCCGT

Basic information

species Arabidopsis thaliana
transcript AT1G34020.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G34020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os05g12490.1 (Oryza sativa), 3'ss of exon 4
------------gtaagtgttctgtgctcttacggagtaacat-atcgtttctttgtttaaga-taatactaatattggtgtggtttttacatgatgcagTATGTACATTACCTTCAGCGCAAGTACTCGCTTAACTCATTCAACCTATTGGGACATACCGCTCCAGCCCAAGCCGCAACATTACTGGTAGTTGGCCCGT
             ||   ||  ||| |  || |   | |   | || |    |||  |||| | || ||||  | ||| |    |  ||   || |||||||||| ||| |||||||  | ||||||||||||  |||||||||||| ||||| ||||| |||||||| || || ||| | ||||| ||| | || || |
gtttgtctgctaatagaagtcttgtcccttttctacgcactttcatggcaaattttcttaacactattacttgttttgtttctttgcttctgtgctgcagTATGTTCATCACCTTCAAAGGAAGTACTCGCTTGGCTCATTCAACCTCTTGGGTCATACTGCTCCAGCTCAGGCAGCATCTTTACTAGTACTGGGGCCTT

upper sequence: AT1G34020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os02g40090.4 (Oryza sativa), 3'ss of exon 4
-gtaagtgttctgtgct---cttacggagtaacatatcgtttctttgtttaagataat----actaatattggtgtggtt------tttacatgatgcagTATGTACATTACCTTCAGCGCAAGTACTCGCTTAACTCATTCAACCTATTGGGACATACCGCTCCAGCCCAAGCCGCAACATTACTGGTAGTTGGCCCGT
   |    || ||| |    ||   |   | || | |  |      ||||  ||||||    |||  | ||  |   |||       || |||| ||||||| || ||| |||||||    ||||||||||||  |||||||||||||||||| ||||| |||||||| || || ||| |  |  |  || | || || |
aacagaaattttgtccctcgctgctgttttcacttttaatggtgaggttttggataattagcacttgttttattccagttatttttctttcatgctgcagTACGTTCATCACCTTCAAAAGAAGTACTCGCTTGGCTCATTCAACCTATTGGGTCATACTGCTCCAGCTCAGGCAGCATCCCTGTTAATACTGGGGCCTT

upper sequence: AT1G34020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os12g05830.1 (Oryza sativa), 3'ss of exon 4
---gtaagtgttctgtgctcttacggagtaac------atatcgtttctttgttta-------agataatactaatattggtgtggtttttacatgatgcagTATGTACATTACCTTCAGCGCAAGTACTCGCTTAACTCATTCAACCTATTGGGACATACCGCTCCAGCCCAAGCCGCAACATTACTGGTAGTTGGCCCGT
   || | | |  |  | | |  |  | || |      || || |||| ||   |        ||| ||||| | | |   | |  | ||| | |  |||||||||| ||||  || || || |||||||| || ||||||||||||||  |||| || || |||||||||||||| | | |  | ||| |||| || || |
tttgtcatt-tcttaagttatagccaaatagcaccttaatttcttttccttacctggacgcatagacaatacaattttaactcttctattttcctt-tgcagTATGTTCATTTTCTCCAACGAAAGTACTCTCTGAACTCATTCAACCTCCTGGGTCACACTGCTCCAGCCCAAGCAGGATCCCTTCTGCTAGTGGGGCCCT

upper sequence: AT1G34020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os12g05780.3 (Oryza sativa), 3'ss of exon 4
gtaagtgttctgtgctc------ttacggagtaacatatcgtttctttgttta-agataa------tactaatattggtgtggtttttacatga--tgcagTATGTACATTACCTTCAGCGCAAGTACTCGCTTAACTCATTCAACCTATTGGGACATACCGCTCCAGCCCAAGCCGCAACATTACTGGTAGTTGGCCCGT
 | | |  |  |  |||      | |     |    | ||  ||||||  ||| ||| ||       | || | |   |    ||| ||  |    |||||||||| ||||  || ||  | |||||||| || ||||||||||||||  |||| || || |||||||||||||| | | |  | ||| ||||||| || |
-tgaataattggcactccctaaatcatttgtttgtttgtcacttctttaattatagacaaattactcattagtttcctttccttttctattttccttgcagTATGTTCATTTTCTCCAAAGGAAGTACTCTCTGAACTCATTCAACCTCCTGGGCCACACTGCTCCAGCCCAAGCGGGATCTCTTCTGCTAGTTGGGCCCT

upper sequence: AT1G34020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G147446_T02 (Zea mays), 3'ss of exon 2
-----gtaagtgttctgtgctcttacggagtaacatatcgtttctttgtttaagataatactaata--ttggtgtggttttta--------catgatgcagTATGTACATTACCTTCAGCGCAAGTACTCGCTTAACTCATTCAACCTATTGGGACATACCGCTCCAGCCCAAGCCGCAACATTACTGGTAGTTGGCCCGT
      ||||||     |  || |  ||| |        ||   | ||   || |||||    | |  || |  |   |||||        | |  |||||||||| ||||  || || ||||||||||| || ||||||||||||||  |||| || || |||||||||||||| |   || | ||| |||| || || |
actatttaagtgccactttttcatttggacttcggccctgtca-tgtgcccaatataatgggcacaatttagactcacttttatttctgctccttctgcagTATGTCCATTTTCTCCAACGCAAGTACTCCCTGAACTCATTCAACCTCCTGGGCCACACAGCTCCAGCCCAAGCTGGGTCACTGCTGCTAGTGGGACCAT

upper sequence: AT1G34020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G089630_T03 (Zea mays), 3'ss of exon 3
-----------gtaagtgttctgtgctcttacggagtaacatatcgtttctttgtttaagataatactaatattggtgtggttt----ttacatgatgcagTATGTACATTACCTTCAGCGCAAGTACTCGCTTAACTCATTCAACCTATTGGGACATACCGCTCCAGCCCAAGCCGCAACATTACTGGTAGTTGGCCCGT
            |    |   ||  |||   |     |  |||||  || || |   |   ||  |||    |   | ||||||     |   || |||||||||| ||  |||||||  | ||||||||||||  |||||||||||| || || ||||| ||||||||||| || ||| | ||  | ||| | || || |
tagtgttgggcctgttggccgtgccctcccccctgccatgatatc-cttattagggcatattatcactgtgttctatttggtttactcctctttgctgcagTATGTTCACCACCTTCAATGGAAGTACTCGCTTGGCTCATTCAACCTCTTAGGCCATACTGCTCCAGCCCAGGCAGCATCGTTGTTAGTATTGGGTCCTT

upper sequence: AT1G34020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G071378_T02 (Zea mays), 3'ss of exon 4
---gtaagtgttctgtgctcttacgga-gtaacatatcgtttctttgtttaagataatactaatattggtg--tggtttttacatga--------tgcagTATGTACATTACCTTCAGCGCAAGTACTCGCTTAACTCATTCAACCTATTGGGACATACCGCTCCAGCCCAAGCCGCAACATTACTGGTAGTTGGCCCGT
    |   |   |   | | | |   | | | | |  |  |||  |||      ||| |  |  |  | |   |  ||||||  ||         |||||||||| || |  || || ||||||||||| || ||||||||||||||  |||| || || |||||||||||||| |   || | ||| |||| || || |
gctcttgctaccccacgttttcagaaatggaccgttgcccttccatgtagccagtaaaagcagcacagtttactcatttttatttgtgttccttctgcagTATGTCCACTTTCTCCAACGCAAGTACTCTCTGAACTCATTCAACCTGCTGGGCCACACTGCTCCAGCCCAAGCTGGGTCACTCCTGCTAGTGGGACCAT

upper sequence: AT1G34020.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv18s0072g00080.t01 (Vitis vinifera), 3'ss of exon 3
----------------gtaagtgttctgtgctcttacggagtaacatatc-gtttctttgtttaagataatactaatattggtgtggtttttacatgatgcagTATGTACATTACCTTCAGCGCAAGTACTCGCTTAACTCATTCAACCTATTGGGACATACCGCTCCAGCCCAAGCCGCAACATTACTGGTAGTTGGCCCGT
                 | | |||||     |   |     | |||  || ||| || |   |    ||   ||  ||||| | | ||| ||  || ||||||||||| |||| |||||| || ||||| || ||||  || |||||||||||||||||||| || |||||||| || | | |  | ||  || | ||||| |
ttgtttagatcaattactgaatgttccaaattacaaaattctcacaagtctgttgctctaaatgtcttatctct--tattgttcttgttcttgtat-atgcagTATGTGCATTTCCTTCAACGGAAGTATTCACTTAGTTCTTTCAACCTATTGGGACATACTGCCCCAGCCCAGGCTGGATCGCTGCTTTTATTAGGCCCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcgtttctttgtttaagataatactaatattggtgtggtttttacatgatgcagTATGTACATTACCTTCAGCGCAAGTACTCGCTTAACTCATTCAACCTATTGGGACATACCGCTCCAGCCCAAGCCGCAACATTACTGGTAGTTGGCCCGT
                      tactaat  putative branch site (score: 1)
                                       tttttac  putative PPT
     ttctttgtttaagata  TA-rich tract