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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgaagaggaacttcattatctgggagataaattcttagaagtgatgtaatgtaaggtggagtaattccggttatttatttatttttttcctctgtgcagGTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAG

Basic information

species Physcomitrella patens
transcript PP1S168_70V6.1
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|208391163|gb|DC942075.1|DC942075
EST:     ACTCTGGTTTTGCCTATCTTCGTTTCACAGCACCCGCGACGTCGTGCAAG                         GTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGAT
genomic: ACTCTGGTTTTGCCTATCTTCGTTTCACAGCACCCGCGACGTCGTGCAAGgttgtaatat ... ctctgtgcagGTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGAT
EST: gi|18360636|gb|BJ192699.1|BJ192699
EST:     ACTCTGGTTTTGCCTATCTTCGTTTCACAGCACCCGCGACGTCGTGCAAG                         GTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGAT
genomic: ACTCTGGTTTTGCCTATCTTCGTTTCACAGCACCCGCGACGTCGTGCAAGgttgtaatat ... ctctgtgcagGTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGAT
EST: gi|100386703|gb|BY970244.1|BY970244
EST:     ACTCTGGTTTTGCCTATCTTCGTTTCACAGCACCCGCGACGTCGTGCAAG                         GTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGAT
genomic: ACTCTGGTTTTGCCTATCTTCGTTTCACAGCACCCGCGACGTCGTGCAAGgttgtaatat ... ctctgtgcagGTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGAT
EST: gi|18345963|gb|BJ178006.1|BJ178006
EST:     ACTCTGGTTTTGCCTATCTTCGTTTCACAGCACCCGCGACGTCGTGCAAG                         GTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGAT
genomic: ACTCTGGTTTTGCCTATCTTCGTTTCACAGCACCCGCGACGTCGTGCAAGgttgtaatat ... ctctgtgcagGTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGAT
EST: gi|18359483|gb|BJ191544.1|BJ191544
EST:     ACTCTGGTTTTGCCTATCTTCGTTTCACAGCACCCGCGACGTCGTGCAAG                         GTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGAT
genomic: ACTCTGGTTTTGCCTATCTTCGTTTCACAGCACCCGCGACGTCGTGCAAGgttgtaatat ... ctctgtgcagGTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGAT
EST: gi|18365419|gb|BJ197494.1|BJ197494
EST:     ACTCTGGTTTTGCCTATCTTCGTTTCACAGCACCCGCGACGTCGTGCAAG                         GTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGAT
genomic: ACTCTGGTTTTGCCTATCTTCGTTTCACAGCACCCGCGACGTCGTGCAAGgttgtaatat ... ctctgtgcagGTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGAT
EST: gi|162181557|gb|FC358171.1|FC358171
EST:     ACTCTGGTTTTGCCTATCTTCGTTTCACAGCA-CCGCGACGTCGTGCAAG                         GTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGAT
genomic: ACTCTGGTTTTGCCTATCTTCGTTTCACAGCACCCGCGACGTCGTGCAAGgttgtaatat ... ctctgtgcagGTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGAT
EST: gi|18346813|gb|BJ178858.1|BJ178858
EST:     ACTCTGGTTTTGCCTATCTTCGTTTCACAGCACCCGCGACGTCGTGCAAG                         GTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGAT
genomic: ACTCTGGTTTTGCCTATCTTCGTTTCACAGCACCCGCGACGTCGTGCAAGgttgtaatat ... ctctgtgcagGTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGAT
EST: gi|18369304|gb|BJ201390.1|BJ201390
EST:     ACTCTGGTTTTGCCTATCTTCGTTTCACAGCACCCGCGACGTCGTGCAAG                         GTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGAT
genomic: ACTCTGGTTTTGCCTATCTTCGTTTCACAGCACCCGCGACGTCGTGCAAGgttgtaatat ... ctctgtgcagGTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGAT
EST: gi|18367821|gb|BJ199904.1|BJ199904
EST:     ACTCTGGTTTTGCCTATCTTCGTTTCACAGCACCCGCGACGTCGTGCAAG                         GTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGAT
genomic: ACTCTGGTTTTGCCTATCTTCGTTTCACAGCACCCGCGACGTCGTGCAAGgttgtaatat ... ctctgtgcagGTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGAT
EST: gi|18366141|gb|BJ198219.1|BJ198219
EST:     ACTCTGGTTTTGCCTATCTTCGTTTCACAGCACCCGCGACGTCGTGCAAG                         GTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGAT
genomic: ACTCTGGTTTTGCCTATCTTCGTTTCACAGCACCCGCGACGTCGTGCAAGgttgtaatat ... ctctgtgcagGTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGAT
EST: gi|18371368|gb|BJ202970.1|BJ202970
EST:     ACTCTGGTTTTGCCTATCTTCGTTTCACAGCACCCGCGACGTCGTGCAAG                         GTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGAT
genomic: ACTCTGGTTTTGCCTATCTTCGTTTCACAGCACCCGCGACGTCGTGCAAGgttgtaatat ... ctctgtgcagGTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGAT
EST: gi|100368990|gb|BY984972.1|BY984972
EST:     ATCTTCGTTTCACAGCACCCGCGACGTCGTGCAAG                         GTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGAT
genomic: ATCTTCGTTTCACAGCACCCGCGACGTCGTGCAAGgttgtaatat ... ctctgtgcagGTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGAT
EST: gi|67575939|gb|BJ948763.1|BJ948763
EST:     ACTCTGGTTTTGCCTATCTTCGTTTCACAGCACCCGCGACGTCGTGCAAG                         GTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGAT
genomic: ACTCTGGTTTTGCCTATCTTCGTTTCACAGCACCCGCGACGTCGTGCAAGgttgtaatat ... ctctgtgcagGTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGAT
EST: gi|18360603|gb|BJ192666.1|BJ192666
EST:     ACTCTGGTTTTGCCTATCTTCGTTTCACAGCACCCGCGACGTCGTGCAAG                         GTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGAT
genomic: ACTCTGGTTTTGCCTATCTTCGTTTCACAGCACCCGCGACGTCGTGCAAGgttgtaatat ... ctctgtgcagGTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGAT

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), 33 (downstream exon)
Score: 13

TTTTGTAACTCCTTGTCACCGGTGGATTGTAAAGTACTCTGCTCGCGCGCACTCTGGTTTTGCCTATCTTCGTTTCACAGCACCCGCGACGTCGTGCAAGgttgtaatat ... ctctgtgcagGTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaatgtaaggtggagtaattccggttatttatttatttttttcctctgtgcagGTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAG
                          ttatttatttattttt  CT-rich tract
                 taattccggttattta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaagaggaacttcattatctgggagataaattcttagaagtgatgtaatgtaaggtggagtaattccggttatttatttatttttttcctctgtgcagGTCTTGTAAGATGGGTCTTTTTAAGGTGGTGGAGCAGGAAACTAAGCCGATCGATGGCCAGAAGCCTGGCACATCTGGTCTGCGCAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG