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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttattatgcctggttttacttggtgggattccctaggttcgtgtgatcttttcatcgtacctatataaagtttaataactgtaggaattgcaaaatgcagGGGATGATTACAAGATAAAGGTATGGAACTACAAGATGCGGCGATGTCTGTTCACTTTGTTGGGTCACCTCGATTACATCCGGACGGTACAATTCCATCA

Basic information

species Physcomitrella patens
transcript PP1S135_34V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S135_34V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os03g50350.1 (Oryza sativa), 3'ss of exon 1
-ttattat--gcctggttttacttggtgggattccctaggttcgtgtgatcttttcatcgtacctatataaagtttaataactgtaggaattgcaaaatgcagGGGATGATTACAAGATAAAGGTATGGAACTACAAGATGCGGCGATGTCTGTTCACTTTGTTGGGTCACCTCGATTACATCCGGACGGTACAATTCCATCA
  |||| |  || |     |      |  ||||    |   || |   ||    ||     ||   |  |   ||  | |  | |  |   ||||   |||||| |||||||||||||| ||||||||||| |||||||  |  || || || |||||  |    || ||||| || ||||| || ||||| |||||||| ||
tgtattgttggcataacagtggcccatatgatttggaactgtcataaaataagatcgaacaactcctgaactcttcta-agttttccgtgatgcat--tgcagGTGATGATTACAAGATTAAGGTATGGAATTACAAGACACACCGTTGCCTCTTCACGCTTCATGGCCACCTTGACTACATTCGCACGGTGCAATTCCACCA

upper sequence: PP1S135_34V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os03g50340.1 (Oryza sativa), 3'ss of exon 1
--ttattatgcctggtt---ttacttggtgggattccctaggttcgtgtgatcttttcatcgtacctatataaagtttaataactgtaggaattgcaaaatgcagGGGATGATTACAAGATAAAGGTATGGAACTACAAGATGCGGCGATGTCTGTTCACTTTGTTGGGTCACCTCGATTACATCCGGACGGTACAATTCCATCA
  |  |  || | |||    || || |||||  |    || | | | |        |  | | || | |  |   ||  |  | |   |  ||     | |||||| |||||||||||||| ||||| ||||| |||||||  |  || || || |||||  |    || ||||| || || || || || || |||||||| ||
catactggtgtccggtcgtattgctcggtggactaa--tatgattgggatgcggaatggttgaacttctgaactattctaagatttctgtgat---gcattgcagGTGATGATTACAAGATTAAGGTGTGGAATTACAAGACACACCGCTGCCTCTTCACACTTCACGGGCACCTTGACTATATTCGCACCGTGCAATTCCACCA

upper sequence: PP1S135_34V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: LOC_Os09g04110.2 (Oryza sativa), 3'ss of exon 1
ttattatgcctggttttacttggtgggattccctaggttcgtgtgatcttttcatcgtacctat-----ataaagtttaataactgtaggaattgcaaaatgcagGGGATGATTACAAGATAAAGGTATGGAACTACAAGATGCGGCGATGTCTGTTCACTTTGTTGGGTCACCTCGATTACATCCGGACGGTACAATTCCATCA
 | ||  |||||||| || ||   ||    |  | || |  |  |||      || | |    |      || | | ||| |  | |  ||  ||||   |||||| |||||||||||||| ||||| ||||| |||||||  |  || || || |||||  |    || ||||| || ||||| || || || |||||||| ||
-tgttccgcctggttgtatttctgggatagctgtgggctaatacgattgggatatggaattgttgaatcgtagattctaagatttctgtga--tgcat--tgcagGTGATGATTACAAGATTAAGGTGTGGAATTACAAGACACACCGCTGCCTCTTCACACTTCATGGGCACCTTGACTACATTCGCACCGTGCAATTCCACCA

upper sequence: PP1S135_34V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA11G12080.1 (Glycine max), 3'ss of exon 1
-----ttattatgcctggttttacttggtgggattccctaggttcgtgtgatcttttcatcgtacctatataaagtttaataactgtagga-attgcaaaatgcagGGGATGATTACAAGATAAAGGTATGGAACTACAAGATGCGGCGATGTCTGTTCACTTTGTTGGGTCACCTCGATTACATCCGGACGGTACAATTCCATCA
     ||  |||     |||  | ||  ||   | |    ||   | | |  |||| | |  |||  || || || ||| | ||| ||     || |      ||||||||||||||||||| ||||| |||||||| |||||||   | ||  |||||||| |  | || ||||| ||||| ||||| || || ||||| |||||
gtacattggtataataagtt--atttattg---tccatgtggaaggggagggctttgctttataca-atttacagcttattgactatatattgtttcttgggacagGGGATGATTACAAGATTAAGGTTTGGAACTATAAGATGCATAGGTGCTTGTTCACTCTTCTAGGACACCTTGATTATATCCGTACCGTGCAATTTCATCA

upper sequence: PP1S135_34V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: GLYMA12G04290.2 (Glycine max), 3'ss of exon 1
ttattatgcctggttttacttggtgggattccctaggtt---cgtgtgatcttttcatcgtacctatataaagtttaataactgtagga-attgcaaaatgcagGGGATGATTACAAGATAAAGGTATGGAACTACAAGATGCGGCGATGTCTGTTCACTTTGTTGGGTCACCTCGATTACATCCGGACGGTACAATTCCATCA
    |      | ||||  |  |     | |   | ||     | | |   ||| | |  |||  || || || ||  | ||| ||     || |      ||||||||||||||||||| ||||| |||||||| |||||||   | ||| |||||||| |  | || ||||| ||||| ||||| || || ||||| |||||
--ggtggagaagattttgatgtgctatgtacatcatgtgaaaggggagggttttgctttataca-atttacagcttt-tgactatattttgtttcttgggacagGGGATGATTACAAGATTAAGGTTTGGAACTATAAGATGCATAGGTGTTTGTTCACTCTTCTAGGACACCTTGATTATATCCGTACTGTGCAATTTCATCA

upper sequence: PP1S135_34V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT2G21390.1 (Arabidopsis thaliana), 3'ss of exon 2
-----ttattatgcctggttttacttggtgggattccctaggttcgtgtgatcttttcatcgtacctatataaagtttaataactgtaggaattgcaaaatgcagGGGATGATTACAAGATAAAGGTATGGAACTACAAGATGCGGCGATGTCTGTTCACTTTGTTGGGTCACCTCGATTACATCCGGACGGTACAATTCCATCA
       | |      | || | ||| ||   | |    | | || |        ||  || ||  ||  | | |   | | | |  |    ||| |   ||||||||||||||||||||| || || ||||||||||| |  |   | ||||| |||||| |  | || || || ||||| ||||| || || ||||| || ||
aaatgcaaatggcttggattcttcttcgttacagttataatgctcttacagaacattactcatatgtagttgatggc-attgattaca----ttggatgttgcagGGGATGATTACAAGATTAAAGTTTGGAACTACAAAACTCACAGGTGTCTTTTCACTCTTCTCGGGCATCTTGATTATATCCGCACTGTCCAATTTCACCA

upper sequence: PP1S135_34V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: AT1G62020.1 (Arabidopsis thaliana), 3'ss of exon 2
----ttattatgcctggttttacttggtgggattccctaggttcgtgtga-tcttttcat-cgtacctatataaagtttaataactgtaggaattgcaaaatgcagGGGATGATTACAAGATAAAGGTATGGAACTACAAGATGCGGCGATGTCTGTTCACTTTGTTGGGTCACCTCGATTACATCCGGACGGTACAATTCCATCA
     ||| || |    |  |  || |||  ||    || | ||    || |   |  || | |   |   |  | |  ||| | ||| |   ||| | | ||||||||||||||||||||| || || ||||||||||| |  |   | || || |||||| |  | || || || ||||| ||||| ||||| || ||||||||
gtatatataattcggaatcattgttagtgaaatcgtataagctcaaaagaatggatctatacatgatttgttgcattacaatga-tgttgatcttg-atattgcagGGGATGATTACAAGATTAAAGTGTGGAACTACAAAAACCACAGGTGCCTTTTCACTCTTCTAGGGCATCTTGATTATATCCGCACGGTTCAGTTCCATCA

upper sequence: PP1S135_34V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ32142 (Selaginella moellendorffii), 3'ss of exon 1
-ttattatgcctggttttacttggtgggattccctaggttcgtgtgatcttttcatcgtacctatataaagtttaataactgtaggaattgcaaaatgc--agGGGATGATTACAAGATAAAGGTATGGAACTACAAGATGCGGCGATGTCTGTTCACTTTGTTGGGTCACCTCGATTACATCCGGACGGTACAATTCCATCA
 | |   | ||| | ||| ||    |      |     || ||  ||||     ||        | |   |  |     ||| | | ||  |    |    ||| ||||| |||||||| ||||| ||||||||||||| | || |||| ||||||||  || |||| ||  | |||||||||||||| || || ||||||||
gtaagatttccttgctttcctcaccgatcgatcgacattttgttcgatcgaccgatttctttgctttcctgagtcgctgctgaaaggatcccttctttttaagGTGATGACTACAAGATCAAGGTGTGGAACTACAAGACGAGGAGATGCCTGTTCACGCTGCTGGGCCATTTGGATTACATCCGGACAGTCCAGTTCCATCA

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: 34 (upstream exon), 35 (downstream exon)
Score: 9

GACTACCGAATGGGGACGCTCATTGACCGATTCGATGAGCATGATGGGCCAGTCAGGGGCGTCCATTTCCACAAGTCGCAGCCCCTGTTTGTATCTGGAGgtgagatttt ... caaaatgcagGGGATGATTACAAGATAAAGGTATGGAACTACAAGATGCGGCGATGTCTGTTCACTTTGTTGGGTCACCTCGATTACATCCGGACGGTACAATTCCATCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcttttcatcgtacctatataaagtttaataactgtaggaattgcaaaatgcagGGGATGATTACAAGATAAAGGTATGGAACTACAAGATGCGGCGATGTCTGTTCACTTTGTTGGGTCACCTCGATTACATCCGGACGGTACAATTCCATCA
                           taataac  putative branch site (score: 9)
                tatataaagtttaata  TA-rich tract