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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcctcattcaccaattgaagttttttgttgaatgcccgttatgttatttgggcttcgtgagagttgacgtgtatggattgctttcccccttcgattactcgaggtgagaagtttgtggttttcttagcttcgtttattacagATGTCTATGAAAGATTGGTGGTGAAAGGGAGGAGACCCGGTTTCCGGCAGCTCCTCGCCACACAAGTCGTGAGCGCCATCTGGCAT

Basic information

species Physcomitrella patens
transcript PP1S61_93V6.2
intron # 4
splice site 3'
intron type U12 (go to U12 genes for details)

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|19788935|gb|BQ041007.1|BQ041007
EST:     AGAGATTCCCAAGTATTGGAACATTCATGTGAGCGTGTGGCTGCGTCATT                         ATGTCTATGAAAGATTGGTGGTGAAAGGGAGGAGACCCGGTTTCCGGCAGC
genomic: AGAGATTCCCAAGTATTGGAACATTCATGTGAGCGTGTGGCTGCGTCATTgtatcctcat ... tttattacagATGTCTATGAAAGATTGGTGGTGAAAGGGAGGAGACCCGGTTTCCGGCAGC
EST: gi|67728055|gb|BJ978314.1|BJ978314
EST:     AGAGATTCCCAAGTATTGGAACATTCATGTGAGCGTGTGGCTGCGTCATT                         ATGTCTATGAAAGATTGGTGGTGAAAGGGAGGAGACCCGGTTTCCGGCAGC
genomic: AGAGATTCCCAAGTATTGGAACATTCATGTGAGCGTGTGGCTGCGTCATTgtatcctcat ... tttattacagATGTCTATGAAAGATTGGTGGTGAAAGGGAGGAGACCCGGTTTCCGGCAGC

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-Seq library.


Block sizes: 33 (upstream exon), 33 (downstream exon)
Score: 6

AGAGCACAGAATGTTGATATTCTCAACGTAGAGCTGGCTACAAGTGCAGCAGAGATTCCCAAGTATTGGAACATTCATGTGAGCGTGTGGCTGCGTCATTgtatcctcat ... tttattacagATGTCTATGAAAGATTGGTGGTGAAAGGGAGGAGACCCGGTTTCCGGCAGCTCCTCGCCACACAAGTCGTGAGCGCCATCTGGCAT































 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttcgattactcgaggtgagaagtttgtggttttcttagcttcgtttattacagATGTCTATGAAAGATTGGTGGTGAAAGGGAGGAGACCCGGTTTCCGGCAGCTCCTCGCCACACAAGTCGTGAGCGCCATCTGGCAT
 tttcttagc  putative branch site 
                                        cttcgttt  putative PPT
                                             tttattaca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcctcattcaccaattgaagttttttgttgaatgcccgttatgttatttgggcttcgtgagagttgacgtgtatggattgctttcccccttcgattactcgaggtgagaagtttgtggttttcttagcttcgtttattacagATGTCTATGAAAGATTGGTGGTGAAAGGGAGGAGACCCGGTTTCCGGCAGCTCCTCGCCACACAAGTCGTGAGCGCCATCTGGCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC