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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTGgtacgtcgctttcttggacacattgcattaaatttatgaagcgggttttaaacttcagaacatgtgagccgacttgtaagcaacattatgtttttaaaaa...

Basic information

species Physcomitrella patens
transcript PP1S269_30V6.2
intron # 12
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|162255598|gb|FC431596.1|FC431596
EST:     AGGAGCAGTTCTGTTCTG                         GGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
genomic: AGGAGCAGTTCTGTTCTGgtacgtcgct ... ttctgtgcagGGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
EST: gi|162279090|gb|FC455429.1|FC455429
EST:     CTAGGAGCAGTTCTGTTCTG                         GGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
genomic: CTAGGAGCAGTTCTGTTCTGgtacgtcgct ... ttctgtgcagGGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
EST: gi|208348107|gb|DC916917.1|DC916917
EST:     CTCNTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG                         GGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
genomic: CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTGgtacgtcgct ... ttctgtgcagGGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
EST: gi|67696733|gb|BJ956966.1|BJ956966
EST:     CTCTTGCCA-TTTGGACTCTTCTAGGAGCAGTTCTGTTCTG                         GGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
genomic: CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTGgtacgtcgct ... ttctgtgcagGGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
EST: gi|208376570|gb|DC922601.1|DC922601
EST:     CTCNTGCCATTTTGGACTCNTCTAGGAGCAGTTCTGTTCTG                         GGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
genomic: CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTGgtacgtcgct ... ttctgtgcagGGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
EST: gi|162183659|gb|FC359900.1|FC359900
EST:     AGGAGCAGTTCTGTTCTG                         GGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
genomic: AGGAGCAGTTCTGTTCTGgtacgtcgct ... ttctgtgcagGGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
EST: gi|208381414|gb|DC927850.1|DC927850
EST:     CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG                         GGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
genomic: CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTGgtacgtcgct ... ttctgtgcagGGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
EST: gi|208344725|gb|DC905174.1|DC905174
EST:     CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG                         GGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
genomic: CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTGgtacgtcgct ... ttctgtgcagGGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
EST: gi|208394434|gb|DC928486.1|DC928486
EST:     CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG                         GGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
genomic: CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTGgtacgtcgct ... ttctgtgcagGGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
EST: gi|208354437|gb|DC926614.1|DC926614
EST:     CCATTTTGGACTTTTCTAGGAGCAGTTCTGTTCTG                         GGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
genomic: CCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTGgtacgtcgct ... ttctgtgcagGGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
EST: gi|208397506|gb|DC916390.1|DC916390
EST:     CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG                         GGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
genomic: CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTGgtacgtcgct ... ttctgtgcagGGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
EST: gi|208347298|gb|DC925322.1|DC925322
EST:     CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG                         GGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
genomic: CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTGgtacgtcgct ... ttctgtgcagGGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
EST: gi|208356794|gb|DC926805.1|DC926805
EST:     CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG                         GGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
genomic: CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTGgtacgtcgct ... ttctgtgcagGGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
EST: gi|208363842|gb|DC943299.1|DC943299
EST:     CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG                         GGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
genomic: CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTGgtacgtcgct ... ttctgtgcagGGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
EST: gi|208395040|gb|DC924175.1|DC924175
EST:     CTAGGAGCAGTTCTGTTCT-                         GGGGNGGACATCACCTTCTGATATCNTAAGGTTTCAACCACATTTGGTCAT
genomic: CTAGGAGCAGTTCTGTTCTGgtacgtcgct ... ttctgtgcagGGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
EST: gi|208380224|gb|DC919060.1|DC919060
EST:     CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG                         GGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
genomic: CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTGgtacgtcgct ... ttctgtgcagGGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
EST: gi|208355907|gb|DC926668.1|DC926668
EST:     CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG                         GGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
genomic: CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTGgtacgtcgct ... ttctgtgcagGGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
EST: gi|100395052|gb|BY953582.1|BY953582
EST:     CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG                         GGGGTGGACATCACCTTCTGATATCTTAAGGTTTCA-CCACATTTGGTCAT
genomic: CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTGgtacgtcgct ... ttctgtgcagGGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
EST: gi|208354673|gb|DC918699.1|DC918699
EST:     CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTG                         GGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT
genomic: CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTGgtacgtcgct ... ttctgtgcagGGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCAT

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), 23 (downstream exon)
Score: 4

CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTGgtacgtcgct ... ttctgtgcagGGGGTGGACATCACCTTCTGATATCTTAAGGTTTCAACCACATTTGGTCATGATGGGAGCTGGATTCGCCTTCGCTTACCTAGTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCTTGCCATTTTGGACTCTTCTAGGAGCAGTTCTGTTCTGgtacgtcgctttcttggacacattgcattaaatttatgaagcgggttttaaacttcagaacatgtgagccgacttgtaagcaacattatgtttttaaaaa

- - - - - - - - - - - - GGAGCA
- - - - - - - - - - - -  GAGCAG