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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttttatctatttacttatttatttttgactcatttggggtatacccaatgcattagtgagttaaggtgtcctaagtttttgaagttgatcatactgcagATACGAACGCTCAGAGGACACACAAATGAGAAGAATTTTGTAGGATTGACTGTAAACAATGAGTATATTGCCTGCGGGAGTGAATCAAATGAGGTTTTCG

Basic information

species Physcomitrella patens
transcript PP1S154_52V6.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S154_52V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: LOC_Os02g53140.1 (Oryza sativa), 3'ss of exon 11
cttttatctatttacttatttatttttgactcatttggggtatacccaatgcattagtgagttaa--ggtgtcctaagtttttgaagttgat-catactgcagATACGAACGCTCAGAGGACACACAAATGAGAAGAATTTTGTAGGATTGACTGTAAACAATGAGTATATTGCCTGCGGGAGTGAATCAAATGAGGTTTTCG
   | |||||||    |   |   |||     | ||  |  || |        | ||  |    |  | || |||   | ||| || | | | | |  | ||| || | ||  ||||||| ||||  ||||| ||||| ||||| ||  || ||||||| || ||||| |||||||||||||||||| | ||||||||||| |
agctcatctattagtctggcttggtttagt--agttacgtcatgctaggcttctcagaaaacagattgttgaccttt-tgtttaaaatggttacctttttcagGTAAGGACATTCAGAGGGCACAAGAATGAAAAGAACTTTGTTGGGCTGTCTGTAAATAACGAGTACATTGCCTGCGGGAGTGAAACGAATGAGGTTTTTG

upper sequence: PP1S154_52V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GRMZM2G126795_T02 (Zea mays), 3'ss of exon 13
--cttttatctat-ttacttatttatttttgactcatttggggtatacccaatgcattagtgagttaaggtgtcctaagtttttgaagttgatcatactgcagATACGAACGCTCAGAGGACACACAAATGAGAAGAATTTTGTAGGATTGACTGTAAACAATGAGTATATTGCCTGCGGGAGTGAATCAAATGAGGTTTTCG
   ||   || || |||| |    | |||  | | ||   |     | |  |    || |       |  |||  |||     |     || |  |  | ||| |||| ||  ||||||| |||| |||||| ||||| || || |||||| |||| ||||||||||||||||| || || |||||| ||||||||||||| |
gatttggttcaatattacatgcccagtttgaaataatgcagcaatgaacatacattttggatgaccgatttgttataacaacattg---tggtttttttccagGTACGGACATTCAGAGGGCACAAAAATGAAAAGAACTTCGTTGGATTGTCTGTGAACAATGAGTATATTGCTTGTGGAAGTGAAACAAATGAGGTTTTTG

upper sequence: PP1S154_52V6.1 (Physcomitrella patens), 3'ss of exon 11
lower sequence: GRMZM2G104920_T02 (Zea mays), 3'ss of exon 9
cttttatctatttacttatttatttttgactcatttggggtatacccaatgcattagtgagttaaggtgtcctaagtttttgaagt----tgatcatactgcagATACGAACGCTCAGAGGACACACAAATGAGAAGAATTTTGTAGGATTGACTGTAAACAATGAGTATATTGCCTGCGGGAGTGAATCAAATGAGGTTTTCG
 | | || |  ||    |||      || |  |||||   ||   |   | |     | | ||  ||    | |  || ||  |      |  |  |  | ||| |||| ||  |||||||||||| |||||| ||||| ||||| || ||| |||| |||||||| |||||||| || || |||||  ||||||||||||| |
-tctgatttggttcaacatta---catgcccaatttgaaatagtgcagctacgaacataatttttggatgaccattttgttataacaacattgtgttttttcagGTACGGACATTCAGAGGACACAAAAATGAAAAGAACTTTGTTGGCTTGTCTGTGAACAATGAATATATTGCTTGTGGAAGTGAGACAAATGAGGTTTTTG

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: 30 (upstream exon), 35 (downstream exon)
Score: 16

GAAGGCTGTTTCTTACGTGAAGTTTATATCACCGACTGAGTTAGCTTCGGCATCTACAGATAGCACACTTCGACTTTGGGATGTTCAGCGAGACTGCTCGgtacgtcaat ... catactgcagATACGAACGCTCAGAGGACACACAAATGAGAAGAATTTTGTAGGATTGACTGTAAACAATGAGTATATTGCCTGCGGGAGTGAATCAAATGAGGTTTTCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaatgcattagtgagttaaggtgtcctaagtttttgaagttgatcatactgcagATACGAACGCTCAGAGGACACACAAATGAGAAGAATTTTGTAGGATTGACTGTAAACAATGAGTATATTGCCTGCGGGAGTGAATCAAATGAGGTTTTCG
                                      agttgat  putative branch site (score: 16)
                           taagttttt  TA-rich tract