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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtagaattagaaggctggcgctggtatcgcgctttagatcgaaagttgtttcgattccaaatcccaaattgattcaattttgcgaatctcttcttgcagTCCAAACCTGCGCTGCCCGCCTTGGAGCGTCTCATCCATTCCAACGACGAAGAGGTTCTCACGGATGCGTGTTGGGCCCTTTCTTATTTGTCCGATGGCA

Basic information

species Physcomitrella patens
transcript PP1S43_141V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S43_141V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: LOC_Os05g06350.1 (Oryza sativa), 3'ss of exon 5
tgtagaattagaaggctggcgctggtatcgcgctttagatcgaaagttgtttcgattccaaatcccaaattgattcaattttgcgaatctcttcttgcagTCCAAACCTGCGCTGCCCGCCTTGGAGCGTCTCATCCATTCCAACGACGAAGAGGTTCTCACGGATGCGTGTTGGGCCCTTTCTTATTTGTCCGATGGCA
 ||  ||||    |       ||  | |   ||  |       ||||| ||   |||   |        ||||||   ||||| |      |||  ||||  |||||| |||||  | ||  || |||| |||||||||||  | ||||| ||||| || || ||||| || ||||| |||||||||||||| ||||| |
-gtttaattctgggctaccttctactttgatgcactgacct--aagtttttatcattaggatggttttgttgatt---ttttgtg------ttcgagcagGTCAAACCAGCGCTTTCTGCACTGCAGCGCCTCATCCATTCTCAGGACGAGGAGGTCCTGACTGATGCCTGCTGGGCTCTTTCTTATTTGTCTGATGGAA

upper sequence: PP1S43_141V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 5
tgtagaattagaaggctggcgctggtatcgcgctttagatcgaaagttgtttcgattccaaatcccaaattg--------attcaattttgcgaatctct---tcttgcagTCCAAACCTGCGCTGCCCGCCTTGGAGCGTCTCATCCATTCCAACGACGAAGAGGTTCTCACGGATGCGTGTTGGGCCCTTTCTTATTTGTCCGATGGCA
                               | |||| | | | | || |||  | | |   ||   || ||        |   ||   ||   |||| |   | ||  || | || ||||| ||||| ||  | |  || || ||||||||||||||||| || |||||||| ||||| || |||||||| || || || || || ||||
-------------------------------gttttaaa-caagacttcttttaactgcttttctgtaactgtggtaactaactaaacatgtttatctttggctgttatagACTAAGCCTGCTCTGCCAGCACTTGCACGACTTATCCATTCCAACGACGAGGAAGTTCTCACTGATGCATGCTGGGCCCTGTCATACTTATCTGACGGCA
















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: 9 (upstream exon), 33 (downstream exon)
Score: 2

TGCCCAGCTCACCGACAATACGAAACTCTCTATGCTCAGAAACGCCACGTGGACGCTCTCTAATTTTTGCCGGGGCAAGCCGCAGCCACCATTTGAGCAGgtgtgtattt ... cttcttgcagTCCAAACCTGCGCTGCCCGCCTTGGAGCGTCTCATCCATTCCAACGACGAAGAGGTTCTCACGGATGCGTGTTGGGCCCTTTCTTATTTGTCCGATGGCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgtttcgattccaaatcccaaattgattcaattttgcgaatctcttcttgcagTCCAAACCTGCGCTGCCCGCCTTGGAGCGTCTCATCCATTCCAACGACGAAGAGGTTCTCACGGATGCGTGTTGGGCCCTTTCTTATTTGTCCGATGGCA
                      aattgat  putative branch site (score: 2)
                                          tctcttcttgc  putative PPT
                     aaattgattcaatttt  TA-rich tract