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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcctttctgatcggccgattctctttggaactgatttgtagtttcattgtctgggactggcgcatgctagggtttgggtgattagagtgggatggggtgttaatgatgagctcgtggaggtttcacagTGCGAGATAATGTCAAGGCTGCAAGGAGGGAGTTCGATAAGACGGAGGATGACCTGAAGGCTCTGCAGAGCGTGGGTCAAATCATCGGGGAAGTGTTGAG

Basic information

species Physcomitrella patens
transcript PP1S13_419V6.1
intron # 1
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|100430442|gb|BY959871.1|BY959871
EST:     CAGGCGCAAGCTTCTGCAGCACAAGGAGATTGATTCGAGGCTAAGGAGTT                         TGCGAGATAATGTCAAGGCTGCAAGGAGGGAGTTCGATAAGACGGAGGATG
genomic: CAGGCGCAAGCTTCTGCAGCACAAGGAGATTGATTCGAGGCTAAGGAGTTgtaagccttt ... ggtttcacagTGCGAGATAATGTCAAGGCTGCAAGGAGGGAGTTCGATAAGACGGAGGATG
EST: gi|18368384|gb|BJ200469.1|BJ200469
EST:     CAGGCGCAAGCTTCTGCAGCACAAGGAGATTGATTCGAGGCTAAGGAGTT                         TGCGAGATAATGTCAAGGCTGCAAGGAGGGAGTTCGATAAGACGGAGGATG
genomic: CAGGCGCAAGCTTCTGCAGCACAAGGAGATTGATTCGAGGCTAAGGAGTTgtaagccttt ... ggtttcacagTGCGAGATAATGTCAAGGCTGCAAGGAGGGAGTTCGATAAGACGGAGGATG
EST: gi|18327039|gb|BJ159040.1|BJ159040
EST:     CAGGCGCAAGCTTCTGCAGCACAAGGAGATTGATTCGAGGCTAAGGAGTT                         TGCGAGATAATGTCAAGGCTGCAAGGAGGGAGTTCGATAAGACGGAGGATG
genomic: CAGGCGCAAGCTTCTGCAGCACAAGGAGATTGATTCGAGGCTAAGGAGTTgtaagccttt ... ggtttcacagTGCGAGATAATGTCAAGGCTGCAAGGAGGGAGTTCGATAAGACGGAGGATG
EST: gi|18360089|gb|BJ192151.1|BJ192151
EST:     CAGGCGCAAGCTTCTGCAGCACAAGGAGATTGATTCGAGGCTAAGGAGTT                         TGCGAGATAATGTCAAGGCTGCAAGGAGGGAGTTCGATAAGACGGAGGATG
genomic: CAGGCGCAAGCTTCTGCAGCACAAGGAGATTGATTCGAGGCTAAGGAGTTgtaagccttt ... ggtttcacagTGCGAGATAATGTCAAGGCTGCAAGGAGGGAGTTCGATAAGACGGAGGATG
EST: gi|67507697|gb|BJ940577.1|BJ940577
EST:     CAGGCGCAAGCTTCTGCAGCACAAGGAGATTGATTCGAGGCTAAGGAGTT                         TGCGAGATAATGTCAAGGCTGCAAGGAGGGAGTTCGATAAGACGGAGGATG
genomic: CAGGCGCAAGCTTCTGCAGCACAAGGAGATTGATTCGAGGCTAAGGAGTTgtaagccttt ... ggtttcacagTGCGAGATAATGTCAAGGCTGCAAGGAGGGAGTTCGATAAGACGGAGGATG
EST: gi|18373133|gb|BJ204735.1|BJ204735
EST:     CAGGCGCAAGCTTCTGCAGCACAAGGAGATTGATTCGAGGCTAAGGAGTN                         TGCGAGATAATGTCAAGGCTGCANGGAGGGAG
genomic: CAGGCGCAAGCTTCTGCAGCACAAGGAGATTGATTCGAGGCTAAGGAGTTgtaagccttt ... ggtttcacagTGCGAGATAATGTCAAGGCTGCAAGGAGGGAG
EST: gi|18346638|gb|BJ178683.1|BJ178683
EST:     CAGGCGCAAGCTTCTGCAGCACAAGGAGATTGATTCNAGGCTAAGGAGTT                         TGCGAGATAATGTCAAGGCTGCAAGGAGGGAGTTCGATAAGACGGAGGATG
genomic: CAGGCGCAAGCTTCTGCAGCACAAGGAGATTGATTCGAGGCTAAGGAGTTgtaagccttt ... ggtttcacagTGCGAGATAATGTCAAGGCTGCAAGGAGGGAGTTCGATAAGACGGAGGATG
EST: gi|67702864|gb|BJ963097.1|BJ963097
EST:     CAGGCGCAAGCTTCTGCAGCACAAGGAGATTGATTCGAGGCTAAGGAGTT                         TGCGAGATAATGTCAAGGCTGCAAGGAGGGAGTTCGATA
genomic: CAGGCGCAAGCTTCTGCAGCACAAGGAGATTGATTCGAGGCTAAGGAGTTgtaagccttt ... ggtttcacagTGCGAGATAATGTCAAGGCTGCAAGGAGGGAGTTCGATA
EST: gi|208391808|gb|DC942342.1|DC942342
EST:     CAGGCGCAAGCTTCTGCAGCACAAGGAGATTGATTCGAGGCTAAGGAGTT                         TGCGAGATAATGTCAAGGCTGCAAGGAGGGAGTTCGATAAGACGGAGGATG
genomic: CAGGCGCAAGCTTCTGCAGCACAAGGAGATTGATTCGAGGCTAAGGAGTTgtaagccttt ... ggtttcacagTGCGAGATAATGTCAAGGCTGCAAGGAGGGAGTTCGATAAGACGGAGGATG
EST: gi|100383943|gb|BY987200.1|BY987200
EST:     CAGGCGCAAGCTTCTGCAGCACAAGGAGATTGATTCGAGGCTAAGGAGTT                         TGCGAGATAATGTCAAGGCTGCAAGGAGGGAGTTCGATAAGACGGAGGATG
genomic: CAGGCGCAAGCTTCTGCAGCACAAGGAGATTGATTCGAGGCTAAGGAGTTgtaagccttt ... ggtttcacagTGCGAGATAATGTCAAGGCTGCAAGGAGGGAGTTCGATAAGACGGAGGATG

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), 31 (downstream exon)
Score: 9

TGCGCTTGTCTGTCCGCCATGGCGGATCCCGAAGCGGTGCGCGTTGAATACAGGCGCAAGCTTCTGCAGCACAAGGAGATTGATTCGAGGCTAAGGAGTTgtaagccttt ... ggtttcacagTGCGAGATAATGTCAAGGCTGCAAGGAGGGAGTTCGATAAGACGGAGGATGACCTGAAGGCTCTGCAGAGCGTGGGTCAAATCATCGGGGAAGTGTTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgggtgattagagtgggatggggtgttaatgatgagctcgtggaggtttcacagTGCGAGATAATGTCAAGGCTGCAAGGAGGGAGTTCGATAAGACGGAGGATGACCTGAAGGCTCTGCAGAGCGTGGGTCAAATCATCGGGGAAGTGTTGAG
                        tgttaat  putative branch site (score: 9)
                          ttaatgat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcctttctgatcggccgattctctttggaactgatttgtagtttcattgtctgggactggcgcatgctagggtttgggtgattagagtgggatggggtgttaatgatgagctcgtggaggtttcacagTGCGAGATAATGTCAAGGCTGCAAGGAGGGAGTTCGATAAGACGGAGGATGACCTGAAGGCTCTGCAGAGCGTGGGTCAAATCATCGGGGAAGTGTTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG