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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatgttttgtagagttgatttgctagagtgagaggaacctgtagttcgcttcccgatcagagatagtgctgtgtgtcatgccgcttttgtacgtgtgcagTTTGACTGTGGAATCCATCCTGGCTACTCTGGCATGGCAGCGCTGCCCTACTTCGATGAGATAGATCCTATCAGCATAGATGTTTTACTCGTGACGCA

Basic information

species Physcomitrella patens
transcript PP1S23_196V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S23_196V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os03g63590.1 (Oryza sativa), 3'ss of exon 1
----------aatgttttgtagagttgatttgctagagtgagaggaacctgtagttcgcttcccgatcagagatagtgctgtgtgtcatgccgc----------ttttgtacgtgtgcagTTTGACTGTGGAATCCATCCTGGCTACTCTGGCATGGCAGCGCTGCCCTACTTCGATGAGATAGATCCTATCAGCATAGATGTTTTACTCGTGACGCA
          |||       |   ||    | | |     ||      |||   |    ||   ||| |    |  |  ||| |||||||  |           ||   | | ||   |||| || || || ||||| || |  ||||| |||||||| ||||| ||||||||||||||||| |||||   || ||| |||||  | ||  | || ||
gtgagcatccaatccccc-cactctttccctccaaaccctagcttccactgctttcttttttatgataatttctgcttttgtttgtcatgtggtgtggtgtggtttggattcttggatagTTCGATTGCGGCATCCACCCGGCTTACTCCGGCATGGCGGCGCTCCCCTACTTCGATGAGATCGATCCCTCCACCATTGATGTCCTCCTAATCACCCA

upper sequence: PP1S23_196V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G083346_T01 (Zea mays), 3'ss of exon 1
aatgttttgtagagttgatttgctagagtgagaggaacctgtagttcgcttcccgatcagagatagtgctgtgtgtcatgccgcttttgtacgtgtgcagTTTGACTGTGGAATCCATCCTGGCTACTCTGGCATGGCAGCGCTGCCCTACTTCGATGAGATAGATCCTATCAGCATAGATGTTTTACTCGTGACGCA
      |    |  ||  |   |     | |      ||  |  | || ||| | |  |  |    ||  |  ||     |    | || | |     |||| ||||| || ||||| || |  ||| | |||||||| ||||||||||||||||| ||||| |||||   |  |||||| ||  | ||| | || ||
-----gtaagcgccttattcctcattcatcatcccctccccttctccgattcgccactactgcagctgacgaatgctcctctctctgtg-atgccgctagTTCGACTGCGGCATCCACCCGGCGTACACCGGCATGGCGGCGCTGCCCTACTTCGACGAGATCGATCCGTCCGCCATAGACGTCCTCCTCATCACCCA

upper sequence: PP1S23_196V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GRMZM2G422649_T01 (Zea mays), 3'ss of exon 1
------------------aatgttttgtagagttgatttgctagagtgagaggaacctgtag---ttcgcttcccgatcagagatagtgctgtgtgtcatgccgcttttgt---acgtgtgcagTTTGACTGTGGAATCCATCCTGGCTACTCTGGCATGGCAGCGCTGCCCTACTTCGATGAGATAGATCCTATCAGCATAGATGTTTTACTCGTGACGCA
                  | | |         |       ||    |   |    |||  |    | || ||| | | ||  |    || ||  ||     ||   | | |   | | |   |||| ||||| || ||||| || |  ||||| |||||||| ||||||||||||||||| ||||| || ||   |  |||||| ||  | ||| | || ||
gtaagcacctcattccccattctcaacccccctcctcccactccccttgcaaacccctacatgtttccgattcgccaccaccgcagctgatgaatgctcccccctctctctgtaatgcggctagTTCGACTGCGGCATCCACCCCGCGTACTCCGGCATGGCGGCGCTGCCCTACTTCGACGAGATCGACCCGTCCGCCATAGACGTCCTCCTCATCACCCA

upper sequence: PP1S23_196V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT1G61010.1 (Arabidopsis thaliana), 3'ss of exon 1
aatgttttgtagagttgatttgctagagtgagaggaacctgtagttcgcttcccgatcagagatagtgctgtgtgtcatgccgcttttgtacgtgtgcagTTTGACTGTGGAATCCATCCTGGCTACTCTGGCATGGCAGCGCTGCCCTACTTCGATGAGATAGATCCTATCAGCATAGATGTTTTACTCGTGACGCA
     |  |       | |||| |  | | |    ||  |||  ||   ||     |  | |   ||  | |   | ||   | || |||   |||||||||||| ||||| || |||||||  ||||| |||||||| ||| |||| |||||||||||||| ||||||     ||| |||||  |  |  | || ||
----gtcagcttctccgttttgttctaatcaagcaaatgtgtt-ttgattttgttgttggggcatgtcttatagttgattttggttgtgt---tgtgcagTTTGATTGTGGGATTCATCCTGCGTACTCGGGCATGGCTGCGTTGCCTTACTTCGATGAGATTGATCCTTCTTCCATTGATGTCCTCTTGATTACTCA

upper sequence: PP1S23_196V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv12s0035g00030.t01 (Vitis vinifera), 3'ss of exon 1
----aatgttttgtagagttgatttgctagagtgagaggaacctgtagttcgcttcccga-----tcagagatagtgc-tgtgtgtcatgccgcttttgtacgtgtgcagTTTGACTGTGGAATCCATCCTGGCTACTCTGGCATGGCAGCGCTGCCCTACTTCGATGAGATAGATCCTATCAGCATAGATGTTTTACTCGTGACGCA
    |   |  || |   ||  |||  |   ||     |    | || || | || |        | | |  | ||   | | | |  ||   || || |  |     |||||||||||||||| ||||| |  ||||| |||||||| ||  |||| ||||| |||||||| ||||||   | ||| |||||  |  | ||||| ||
gtataccataatgcattattcgtttattttggttgctagtttttatactttgttttcgatattttttataatttgtttgtttctattttgttcctgttctgtgatgatagTTTGACTGTGGAATTCATCCCGCATACTCAGGCATGGCTGCTTTGCCATACTTTGATGAGATTGATCCTTCAACCATTGATGTCCTTTTGGTGACACA

upper sequence: PP1S23_196V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: Vv12s0035g00190.t01 (Vitis vinifera), 3'ss of exon 1
---------aatgttttgtagagttgatttgctag--agtgagaggaacctgtagttcgcttcccgatcagagatagtgctgtgtgtcatgccgcttttgtacgtgtgcagTTTGACTGTGGAATCCATCCTGGCTACTCTGGCATGGCAGCGCTGCCCTACTTCGATGAGATAGATCCTATCAGCATAGATGTTTTACTCGTGACGCA
         ||||   | |    ||  |||| | |  |||      |   |    ||  | |     |   |  |  |  | | | |  ||   |  || || |     |||||||||||||||| ||||| |  ||||| |||||||| ||  |||| ||||| |||||||| ||||||   | ||| |||||  |  | ||||| ||
gtagaccataatgcactatgcttttactttggttgctagtttttatactttcattttgacatttttttttaatttgtttgtttctattttgttcccgttctatgatgatagTTTGACTGTGGAATTCATCCCGCATACTCGGGCATGGCTGCTTTGCCATACTTTGATGAGATTGATCCTTCGACCATTGATGTCCTTTTGGTGACACA

upper sequence: PP1S23_196V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ04498 (Selaginella moellendorffii), 3'ss of exon 1
aatgttttgtagagttgatttgctagagtgagaggaacctgtagttcgcttcccgatcagagatagtgctgtgtgtcatgccgcttttgtacgtgtgcagTTTGACTGTGGAATCCATCCTGGCTACTCTGGCATGGCAGCGCTGCCCTACTTCGATGAGATAGATCCTATCAGCATAGATGTTTTACTCGTGACGCA
                           ||||| |||    |   ||   |||    ||    |  |   ||||     ||     |||   | ||  ||||| ||||||||||||||||| |||||| |||| ||||| ||| |||| || ||||||||||| |||||    |  || || ||  |  | || || ||
---------------------------gtgagtggatttcgagatttctttctt--tcgagcaaggaaatgtgaaatgtgagtgcttt---cctgcccagTTCGACTGTGGAATCCATCCCGGCTACACTGGAATGGCCGCGTTGCCGTATTTCGATGAGATTGATCCGTCGACAATCGACGTGCTGTTAGTAACTCA

upper sequence: PP1S23_196V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ12712 (Selaginella moellendorffii), 3'ss of exon 3
aatgttttgtagagttgatttgctagagtgagaggaacctgtagttcgcttcccgatcagagatagtgctgtgtgtcatgccgcttttgtacgtgtgcagTTTGACTGTGGAATCCATCCTGGCTACTCTGGCATGGCAGCGCTGCCCTACTTCGATGAGATAGATCCTATCAGCATAGATGTTTTACTCGTGACGCA
                           ||||| |||    |   ||   |||    |  |||  |  |   ||||  |||    |  | ||| ||  ||||| ||||||||||||||||| || ||| |||| ||||| ||| |||| || ||||||||||| |||||    |  || || ||  |  | || || ||
---------------------------gtgagtggatttcgagatttctttct---ttcgag-caaggaaatgtgaaatgtgagtgct-tacctgcccagTTCGACTGTGGAATCCATCCCGGGTACACTGGAATGGCCGCGTTGCCGTATTTCGATGAGATTGATCCGTCGACAATCGACGTGCTGTTAGTAACTCA

upper sequence: PP1S23_196V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ13866 (Selaginella moellendorffii), 3'ss of exon 1
aatgttttgtagagttgatttgctagagtgagaggaacctgtagttcgcttcccgatcagagatagtgctgtgtgtcatgccgcttttgtacgtgtgcagTTTGACTGTGGAATCCATCCTGGCTACTCTGGCATGGCAGCGCTGCCCTACTTCGATGAGATAGATCCTATCAGCATAGATGTTTTACTCGTGACGCA
                           ||||| |||    |   ||   |||    ||    |  |   ||||     ||     |||   | ||  ||||| ||||||||||||||||| || ||| |||| ||||| ||| |||| || ||||||||||| |||||    |  || || ||  |  | || || ||
---------------------------gtgagtggatttcgagatttctttctt--tcgagcaaggaaatgtgaaatgtgagtgcttt---cctgcccagTTCGACTGTGGAATCCATCCCGGGTACACTGGAATGGCCGCGTTGCCGTATTTCGATGAGATTGATCCGTCGACAATCGACGTGCTGTTAGTAACTCA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 33 (upstream exon), 25 (downstream exon)
Score: 3

GTCACGGGAAGGGGACAAGCTGGAGGTCACCCCACTCGGTGCTGGAAATGAAGTCGGGCGTTCGTGTGTTTATATGACCTACAAGGGCAAGACTGTGATGgtacgcactc ... acgtgtgcagTTTGACTGTGGAATCCATCCTGGCTACTCTGGCATGGCAGCGCTGCCCTACTTCGATGAGATAGATCCTATCAGCATAGATGTTTTACTCGTGACGCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgcttcccgatcagagatagtgctgtgtgtcatgccgcttttgtacgtgtgcagTTTGACTGTGGAATCCATCCTGGCTACTCTGGCATGGCAGCGCTGCCCTACTTCGATGAGATAGATCCTATCAGCATAGATGTTTTACTCGTGACGCA
                                       ttttgta  TA-rich tract