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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cctgctttggaagaaaagaacttgaataggacccatttctgttcaatttggtatacactacttgctgaggtgaatatatgcttgaatgtgattgaaacagAGGATTTTGGGGTGGATACGTGAAGGAGTACATTGAAGCAACCAAACCAGCATTTGCTATAGGAGAATACTGGGACAGTCTGGCATATGAGGGTGGTCAA

Basic information

species Physcomitrella patens
transcript PP1S100_191V6.1
intron # 9
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|19780303|gb|BQ039545.1|BQ039545
EST:     TGGCTTCGTAGTGACTTCGGTTTCGATGGATGGCGGCTCGACTTTGTCAG                         AGGATTTTGGGGTGGATACGTGAAGGAGTACATTGAAGCAACCAAACCAGC
genomic: TGGCTTCGTAGTGACTTCGGTTTCGATGGATGGCGGCTCGACTTTGTCAGgtcgagtaat ... attgaaacagAGGATTTTGGGGTGGATACGTGAAGGAGTACATTGAAGCAACCAAACCAGC
EST: gi|162245205|gb|FC422134.1|FC422134
EST:     TTTCGATGGAGGGCGGCTCGACTTTGTCAG                         AGGATTTTGGGGTGGATACGTGAAGGAGTACATTGAAGCAACCAAACCAGC
genomic: TTTCGATGGATGGCGGCTCGACTTTGTCAGgtcgagtaat ... attgaaacagAGGATTTTGGGGTGGATACGTGAAGGAGTACATTGAAGCAACCAAACCAGC
EST: gi|162164680|gb|FC340727.1|FC340727
EST:     TGGCTTCGTAGTGACTTCGGTTTCGATGGATGGCGGCTCGACTTTGTCAG                         AGGATTTTGGGGTGGATACGTGAAGGAGTACATTGAAGCAACCAAACCAGC
genomic: TGGCTTCGTAGTGACTTCGGTTTCGATGGATGGCGGCTCGACTTTGTCAGgtcgagtaat ... attgaaacagAGGATTTTGGGGTGGATACGTGAAGGAGTACATTGAAGCAACCAAACCAGC
EST: gi|162245206|gb|FC422135.1|FC422135
EST:     TGGCTTCGTAGTGACTTCGGTTTCGATGGATGGCGGCTCGACTTTGTCAG                         AGGATTTTGGGGTGGATACGTGAAGGAGTACATTGAAGCAAC-AAACCAGC
genomic: TGGCTTCGTAGTGACTTCGGTTTCGATGGATGGCGGCTCGACTTTGTCAGgtcgagtaat ... attgaaacagAGGATTTTGGGGTGGATACGTGAAGGAGTACATTGAAGCAACCAAACCAGC
EST: gi|162150065|gb|FC326596.1|FC326596
EST:     TGGCTTCGTAGTGACTTCGGTTTCGATGGATGGCGGCTCGACTTTGTCAG                         AGGATTTTGGGGTGGATACGTGAAGGAGTACATTGAAGCAACCAAACCAGC
genomic: TGGCTTCGTAGTGACTTCGGTTTCGATGGATGGCGGCTCGACTTTGTCAGgtcgagtaat ... attgaaacagAGGATTTTGGGGTGGATACGTGAAGGAGTACATTGAAGCAACCAAACCAGC
EST: gi|162248531|gb|FC425307.1|FC425307
EST:     TGGCTTCGTAGTGACTTCGGTTTCGATGGATGGCGGCTCGACTTTGTCAG                         AGGATTTTGGGGTGGATACGTGAAGGAGTACATTG
genomic: TGGCTTCGTAGTGACTTCGGTTTCGATGGATGGCGGCTCGACTTTGTCAGgtcgagtaat ... attgaaacagAGGATTTTGGGGTGGATACGTGAAGGAGTACATTG
EST: gi|162171741|gb|FC348202.1|FC348202
EST:     TGGCTTCGTAGTGACTTCGGTTTCGATGGATGGCGGCTCGACTTTGTCAG                         AGGATTTTGGGGTGGATACGTGAAGGAGTACATTGAAGCAACCAAACCAGC
genomic: TGGCTTCGTAGTGACTTCGGTTTCGATGGATGGCGGCTCGACTTTGTCAGgtcgagtaat ... attgaaacagAGGATTTTGGGGTGGATACGTGAAGGAGTACATTGAAGCAACCAAACCAGC
EST: gi|162167713|gb|FC344027.1|FC344027
EST:     TGGCTTCGTAGTGACTTCGGTTTCGATGGATGGCGGCTCGACTTTGTCAG                         AGGATTTTGGGGTGGATACGTGAAGGAGTACATTGAAGCAACCAAACCAGC
genomic: TGGCTTCGTAGTGACTTCGGTTTCGATGGATGGCGGCTCGACTTTGTCAGgtcgagtaat ... attgaaacagAGGATTTTGGGGTGGATACGTGAAGGAGTACATTGAAGCAACCAAACCAGC
EST: gi|162191939|gb|FC366944.1|FC366944
EST:     TGGCTTCGTAGTGACTTCGGTTTCGATGGATGGCGGCTCGACTTTGTCAG                         AGGATTTTGGGGTGGATACGTGAAGGAGTACATTGAAGCAACCAAACCAGC
genomic: TGGCTTCGTAGTGACTTCGGTTTCGATGGATGGCGGCTCGACTTTGTCAGgtcgagtaat ... attgaaacagAGGATTTTGGGGTGGATACGTGAAGGAGTACATTGAAGCAACCAAACCAGC

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: 25 (upstream exon), 28 (downstream exon)
Score: 3

TCGATCATTCCCAGGACTTCGTTAGGAGAGATATTATAGAGTGGATGAAATGGCTTCGTAGTGACTTCGGTTTCGATGGATGGCGGCTCGACTTTGTCAGgtcgagtaat ... attgaaacagAGGATTTTGGGGTGGATACGTGAAGGAGTACATTGAAGCAACCAAACCAGCATTTGCTATAGGAGAATACTGGGACAGTCTGGCATATGAGGGTGGTCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttggtatacactacttgctgaggtgaatatatgcttgaatgtgattgaaacagAGGATTTTGGGGTGGATACGTGAAGGAGTACATTGAAGCAACCAAACCAGCATTTGCTATAGGAGAATACTGGGACAGTCTGGCATATGAGGGTGGTCAA
                         tgaatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cctgctttggaagaaaagaacttgaataggacccatttctgttcaatttggtatacactacttgctgaggtgaatatatgcttgaatgtgattgaaacagAGGATTTTGGGGTGGATACGTGAAGGAGTACATTGAAGCAACCAAACCAGCATTTGCTATAGGAGAATACTGGGACAGTCTGGCATATGAGGGTGGTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA