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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCTATTGCTGTAGAAGTTGGTGGTGTGGAAATGGGACAGGGTTTGTATACTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAGgtgggtgttaacatgacggtaaaatttgacattcgcttatgcacgtgagcattttttcagcaactgaaattaacaacaccgatgtcactcgtgagcgggctaatttgtcccctctctcgtggtgattgcag

Basic information

species Physcomitrella patens
transcript PP1S93_48V6.1
intron # 7
splice site 5'
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|162231673|gb|FC407642.1|FC407642
EST:     CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAG                         AATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
genomic: CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAGgtgggtgtta ... gtgattgcagAATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
EST: gi|162157103|gb|FC333673.1|FC333673
EST:     CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAG                         AATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
genomic: CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAGgtgggtgtta ... gtgattgcagAATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
EST: gi|162174886|gb|FC351678.1|FC351678
EST:     CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAG                         AATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
genomic: CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAGgtgggtgtta ... gtgattgcagAATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
EST: gi|162154018|gb|FC330253.1|FC330253
EST:     CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAG                         AATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
genomic: CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAGgtgggtgtta ... gtgattgcagAATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
EST: gi|162186249|gb|FC362181.1|FC362181
EST:     CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAG                         AATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
genomic: CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAGgtgggtgtta ... gtgattgcagAATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
EST: gi|162151233|gb|FC327193.1|FC327193
EST:     CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAG                         AATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
genomic: CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAGgtgggtgtta ... gtgattgcagAATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
EST: gi|7207166|gb|AW561169.1|AW561169
EST:     CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAG                         AATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
genomic: CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAGgtgggtgtta ... gtgattgcagAATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
EST: gi|162158928|gb|FC334801.1|FC334801
EST:     CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAG                         AATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
genomic: CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAGgtgggtgtta ... gtgattgcagAATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
EST: gi|100368665|gb|BY967116.1|BY967116
EST:     CTAAAGTGAG-CAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAG                         AATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
genomic: CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAGgtgggtgtta ... gtgattgcagAATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
EST: gi|162191113|gb|FC367375.1|FC367375
EST:     CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAG                         AATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
genomic: CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAGgtgggtgtta ... gtgattgcagAATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
EST: gi|162193300|gb|FC370918.1|FC370918
EST:     CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAG                         AATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
genomic: CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAGgtgggtgtta ... gtgattgcagAATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
EST: gi|162191400|gb|FC367143.1|FC367143
EST:     CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAG                         AATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
genomic: CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAGgtgggtgtta ... gtgattgcagAATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
EST: gi|162199013|gb|FC375783.1|FC375783
EST:     CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAG                         AATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
genomic: CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAGgtgggtgtta ... gtgattgcagAATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
EST: gi|162252728|gb|FC428765.1|FC428765
EST:     CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAG                         AATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
genomic: CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAGgtgggtgtta ... gtgattgcagAATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
EST: gi|162194330|gb|FC368513.1|FC368513
EST:     CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAG                         AATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
genomic: CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAGgtgggtgtta ... gtgattgcagAATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
EST: gi|162166947|gb|FC343332.1|FC343332
EST:     CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAG                         AATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
genomic: CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAGgtgggtgtta ... gtgattgcagAATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
EST: gi|100430081|gb|BY978237.1|BY978237
EST:     CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAG                         AATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
genomic: CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAGgtgggtgtta ... gtgattgcagAATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
EST: gi|7207158|gb|AW561161.1|AW561161
EST:     CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAG                         AATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
genomic: CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAGgtgggtgtta ... gtgattgcagAATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT
EST: gi|162161195|gb|FC337258.1|FC337258
EST:     CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAG                         AATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTNCCA-TCAGATTC
genomic: CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAGgtgggtgtta ... gtgattgcagAATAAGGACGTCGACATGATCCCAAATATCCGGGTTCT-CCAATCAGATTC
EST: gi|162186774|gb|FC362810.1|FC362810
EST:     CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAG                         AATAAGGACGTCGACATGATCCCAA-TATCCGGGTTCTC-AATCAGATTCT
genomic: CTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAGgtgggtgtta ... gtgattgcagAATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCT

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: 35 (upstream exon), 34 (downstream exon)
Score: 30

TTCTATTGCTGTAGAAGTTGGTGGTGTGGAAATGGGACAGGGTTTGTATACTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAGgtgggtgtta ... gtgattgcagAATAAGGACGTCGACATGATCCCAAATATCCGGGTTCTCCAATCAGATTCTCTCAGTTTACCGAACTCATTTTGTGATGGTGGGAGTACAACGTCTGAGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCTATTGCTGTAGAAGTTGGTGGTGTGGAAATGGGACAGGGTTTGTATACTAAAGTGAGGCAAACCGTGGCGTACTGTCTTAGTCCCCTATGGAAGAAGgtgggtgttaacatgacggtaaaatttgacattcgcttatgcacgtgagcattttttcagcaactgaaattaacaacaccgatgtcactcgtgagcgggctaatttgtcccctctctcgtggtgattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG