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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactactcctacatcctagtgtatgttgtttaaaattgaatcatcatgttatttcacttaatattttcacattttctccacccaatacatgaagtttttttggagtgtcttatgaatctgatgtccacaactacagGTGTGGGGCAAAATATGGGCAGTACTCTCGTTGCATTTTGTTGCGGCAGGGAGCCACGACGATGAAAAGATTGCAATGTACGCTATAGATTCTTTGAGGC

Basic information

species Physcomitrella patens
transcript PP1S122_29V6.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S122_29V6.1 (Physcomitrella patens), 3'ss of exon 6
lower sequence: AT3G43300.2 (Arabidopsis thaliana), 3'ss of exon 21
gtaactactcctacatcctagtgtatgttgtttaaaattgaa---tcatcatgttatttcacttaatattttcacat-tttctccacccaatacatga-agtttttttggagtgtcttatgaatctgatgtccacaactacagGTGTGGGGCAAAATATGGGCAGTACTCTCGTTGCATTTTGTTGCGGCAGGGAGCCACGACGATGAAAAGATTGCAATGTACGCTATAGATTCTTTGAGGC
                                 || ||||||    |   |  |||| |  ||||    ||  |  | ||||   ||  || || |   | ||| ||| | || | || ||    |||  |  ||     ||||| ||||  | ||||||| | || ||  |    ||||| ||  | || || |||||  | |||||||||||||||||||| || ||||||||| |||| |
---------------------------------aatattgaagggccgatagattatgtatctta-cgcttatatgtatttcaatacttaacacgtattactttattttgtgtttgttttg----tgacatatac-----cagGTCTGGGCAAGAATATGGTCTGTCCTTGCCGAACATTTCGTATCTGCTGGTAGCCATCATGATGAAAAGATTGCAATGTATGCCATAGATTCTCTGAGAC
















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: 14 (upstream exon), 22 (downstream exon)
Score: 2

TGAGGTATCTGCCAAAGAGCTGAACGAGGTGCCACCACGAGTTTTCAGTCTCACGAAAATGGTAGAAATTAGCTACTACAATATAACACGGATTCGTATGgtaactactc ... acaactacagGTGTGGGGCAAAATATGGGCAGTACTCTCGTTGCATTTTGTTGCGGCAGGGAGCCACGACGATGAAAAGATTGCAATGTACGCTATAGATTCTTTGAGGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccaatacatgaagtttttttggagtgtcttatgaatctgatgtccacaactacagGTGTGGGGCAAAATATGGGCAGTACTCTCGTTGCATTTTGTTGCGGCAGGGAGCCACGACGATGAAAAGATTGCAATGTACGCTATAGATTCTTTGAGGC
                                  atctgat  putative branch site (score: 2)
          aagttttttt  TA-rich tract