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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtacttcgtttagttctaagttcgggcgttcagcatgttgcctgccctgcggtaatcgagatggtttcaaaggccggaatttgctatctgattcttgcagATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGTACTAAAGTTGACCCGCGAACTGGCAGCTTTCTCACTTGGGAAAGCATGG

Basic information

species Physcomitrella patens
transcript PP1S199_33V6.1
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|208387706|gb|DC937271.1|DC937271
EST:     TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAG                         ATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
genomic: TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAGgtgaggggtg ... attcttgcagATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
EST: gi|67712571|gb|BJ966020.1|BJ966020
EST:     TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAG                         ATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
genomic: TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAGgtgaggggtg ... attcttgcagATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
EST: gi|100356789|gb|BY965281.1|BY965281
EST:     GAGATCGCTGTTTCCGTGAAGGAG                         ATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
genomic: GAGATCGCTGTTTCCGTGAAGGAGgtgaggggtg ... attcttgcagATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
EST: gi|100430358|gb|BY959829.1|BY959829
EST:     TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAG                         ATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
genomic: TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAGgtgaggggtg ... attcttgcagATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
EST: gi|100356940|gb|BY965355.1|BY965355
EST:     TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAG                         ATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
genomic: TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAGgtgaggggtg ... attcttgcagATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
EST: gi|162169490|gb|FC346054.1|FC346054
EST:     TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAG                         ATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
genomic: TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAGgtgaggggtg ... attcttgcagATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
EST: gi|18357165|gb|BJ189224.1|BJ189224
EST:     TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAG                         ATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
genomic: TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAGgtgaggggtg ... attcttgcagATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
EST: gi|208347370|gb|DC909733.1|DC909733
EST:     TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAG                         ATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
genomic: TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAGgtgaggggtg ... attcttgcagATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
EST: gi|100394804|gb|BY989933.1|BY989933
EST:     TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAG                         ATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
genomic: TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAGgtgaggggtg ... attcttgcagATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
EST: gi|162182687|gb|FC359434.1|FC359434
EST:     TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAG                         ATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
genomic: TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAGgtgaggggtg ... attcttgcagATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
EST: gi|208390159|gb|DC941966.1|DC941966
EST:     TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAG                         ATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
genomic: TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAGgtgaggggtg ... attcttgcagATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
EST: gi|67702639|gb|BJ962872.1|BJ962872
EST:     TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAG                         ATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
genomic: TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAGgtgaggggtg ... attcttgcagATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
EST: gi|100419133|gb|BY975861.1|BY975861
EST:     TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAG                         ATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
genomic: TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAGgtgaggggtg ... attcttgcagATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
EST: gi|67716618|gb|BJ966878.1|BJ966878
EST:     TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAG                         ATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
genomic: TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAGgtgaggggtg ... attcttgcagATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
EST: gi|18359809|gb|BJ191870.1|BJ191870
EST:     TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAG                         ATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
genomic: TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAGgtgaggggtg ... attcttgcagATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
EST: gi|67703570|gb|BJ963803.1|BJ963803
EST:     TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAG                         ATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
genomic: TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAGgtgaggggtg ... attcttgcagATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
EST: gi|18373838|gb|BJ205416.1|BJ205416
EST:     TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAG                         ATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
genomic: TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAGgtgaggggtg ... attcttgcagATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
EST: gi|162171538|gb|FC347840.1|FC347840
EST:     TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAG                         ATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
genomic: TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAGgtgaggggtg ... attcttgcagATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
EST: gi|18374858|gb|BJ206436.1|BJ206436
EST:     TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAG                         ATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
genomic: TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAGgtgaggggtg ... attcttgcagATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
EST: gi|18328079|gb|BJ160083.1|BJ160083
EST:     TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAG                         ATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
genomic: TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAGgtgaggggtg ... attcttgcagATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
EST: gi|208386342|gb|DC932838.1|DC932838
EST:     TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAG                         ATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
genomic: TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAGgtgaggggtg ... attcttgcagATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
EST: gi|100388374|gb|BY951976.1|BY951976
EST:     TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAG                         ATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
genomic: TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAGgtgaggggtg ... attcttgcagATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
EST: gi|67573305|gb|BJ946129.1|BJ946129
EST:     TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAG                         ATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
genomic: TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAGgtgaggggtg ... attcttgcagATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
EST: gi|18347014|gb|BJ179060.1|BJ179060
EST:     TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAG                         ATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
genomic: TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAGgtgaggggtg ... attcttgcagATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
EST: gi|67717729|gb|BJ967988.1|BJ967988
EST:     TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAG                         ATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT
genomic: TGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAGgtgaggggtg ... attcttgcagATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGT

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), 29 (downstream exon)
Score: 14

CCGATCGTTCTCTAGCGACAGCGAGGAGGAGAAGATCATCACGGCTACCTTGTTTCCGGGTGATGGCATTGGGCCCGAGATCGCTGTTTCCGTGAAGGAGgtgaggggtg ... attcttgcagATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGTACTAAAGTTGACCCGCGAACTGGCAGCTTTCTCACTTGGGAAAGCATGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctgcggtaatcgagatggtttcaaaggccggaatttgctatctgattcttgcagATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGTACTAAAGTTGACCCGCGAACTGGCAGCTTTCTCACTTGGGAAAGCATGG
                                        atctgat  putative branch site (score: 14)
                                              ttcttgc  CT-rich tract
                   tttcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttcgtttagttctaagttcgggcgttcagcatgttgcctgccctgcggtaatcgagatggtttcaaaggccggaatttgctatctgattcttgcagATTTTCGCTGCCGCGAAAGCCCCAATTGAATGGGATGAGCATTGGGTGGGTACTAAAGTTGACCCGCGAACTGGCAGCTTTCTCACTTGGGAAAGCATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT