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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgcttaagcgtaggtatgtgtgaactcgcgtgtgtgactgttggcttggtaaaaggtatggcagtttgccctgactaggtgatttctcttggtttgcagCTGGCTTGCTACTTTCATCATAGGTACAAATCAGGCAAGTCGAGCACATACAAGGAAGATGGTACGCAGCTTACCCTTTAGTTCAATTTCGCACAATTAG

Basic information

species Physcomitrella patens
transcript PP1S93_73V6.1
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|18367762|gb|BJ199845.1|BJ199845
EST:     ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCG                         CTGGCTTGCTACTTTCATCATA
genomic: ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCGgtgcgtttct ... tggtttgcagCTGGCTTGCTACTTTCATCATA
EST: gi|18368640|gb|BJ200725.1|BJ200725
EST:     ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCG                         CTGGCTTGCTATTTTCATCATAGGTACAAATCAGGCAAGTCGAGCACATAC
genomic: ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCGgtgcgtttct ... tggtttgcagCTGGCTTGCTACTTTCATCATAGGTACAAATCAGGCAAGTCGAGCACATAC
EST: gi|18367970|gb|BJ200054.1|BJ200054
EST:     ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCG                         CTGGCTTGCTACTTTCATCATAGGTACAAATCAGGCAAGTCGAGCACATAC
genomic: ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCGgtgcgtttct ... tggtttgcagCTGGCTTGCTACTTTCATCATAGGTACAAATCAGGCAAGTCGAGCACATAC
EST: gi|18327174|gb|BJ159176.1|BJ159176
EST:     ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCG                         CTGGCTTGCTACTTTCATCATAGGTACA
genomic: ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCGgtgcgtttct ... tggtttgcagCTGGCTTGCTACTTTCATCATAGGTACA
EST: gi|18366961|gb|BJ199041.1|BJ199041
EST:     ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCG                         CTGGCTTGCTACTTTCATCATAGGTACAAATCAGGCAAGTCGAGCACATAC
genomic: ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCGgtgcgtttct ... tggtttgcagCTGGCTTGCTACTTTCATCATAGGTACAAATCAGGCAAGTCGAGCACATAC
EST: gi|67702856|gb|BJ963089.1|BJ963089
EST:     ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCG                         CTGGCTTGCTACTTTCATCAT
genomic: ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCGgtgcgtttct ... tggtttgcagCTGGCTTGCTACTTTCATCAT
EST: gi|18345072|gb|BJ177113.1|BJ177113
EST:     ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCG                         CTGGCTTGCTACTTTCATCATAGGTACAAATCAGGCAAGTCGAGCACATAC
genomic: ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCGgtgcgtttct ... tggtttgcagCTGGCTTGCTACTTTCATCATAGGTACAAATCAGGCAAGTCGAGCACATAC
EST: gi|18346473|gb|BJ178516.1|BJ178516
EST:     ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCG                         CTGGCTTGCTACTTTCATCA
genomic: ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCGgtgcgtttct ... tggtttgcagCTGGCTTGCTACTTTCATCA
EST: gi|18363070|gb|BJ195142.1|BJ195142
EST:     ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCG                         CTGGCTTGCTACTTTCATCATAGGT
genomic: ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCGgtgcgtttct ... tggtttgcagCTGGCTTGCTACTTTCATCATAGGT
EST: gi|67709535|gb|BJ965351.1|BJ965351
EST:     ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCG                         CTGGCTTGCTACTTTCATCATAGGTACAAATCAGGCAAGTCGAGCACATAC
genomic: ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCGgtgcgtttct ... tggtttgcagCTGGCTTGCTACTTTCATCATAGGTACAAATCAGGCAAGTCGAGCACATAC
EST: gi|18355354|gb|BJ187413.1|BJ187413
EST:     ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCG                         CTGGCTTGCTACTTTCATCAT
genomic: ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCGgtgcgtttct ... tggtttgcagCTGGCTTGCTACTTTCATCAT
EST: gi|67704168|gb|BJ964401.1|BJ964401
EST:     ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCC                         CTGGCTTGCTACTTTC
genomic: ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCGgtgcgtttct ... tggtttgcagCTGGCTTGCTACTTTC
EST: gi|18369130|gb|BJ201215.1|BJ201215
EST:     ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCG                         CTGGCTTGCTACTTTCATCATAGGTACAAATCAGGCAAGTCGAGCACATAC
genomic: ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCGgtgcgtttct ... tggtttgcagCTGGCTTGCTACTTTCATCATAGGTACAAATCAGGCAAGTCGAGCACATAC
EST: gi|18330489|gb|BJ162495.1|BJ162495
EST:     ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCG                         CTGGCTTGCTACTTTCATCATAG
genomic: ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCGgtgcgtttct ... tggtttgcagCTGGCTTGCTACTTTCATCATAG
EST: gi|18373100|gb|BJ204702.1|BJ204702
EST:     ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCG                         CTGGCTTGCTACTTTCATCATAGGTACAAATCAGGCAAGTCGAGCACATAC
genomic: ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCGgtgcgtttct ... tggtttgcagCTGGCTTGCTACTTTCATCATAGGTACAAATCAGGCAAGTCGAGCACATAC
EST: gi|18372855|gb|BJ204457.1|BJ204457
EST:     ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCG                         CTGGCTTGCTACTTTCATCATAGGTACAAATCAGGCAAGTCGAGCACATAC
genomic: ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCGgtgcgtttct ... tggtttgcagCTGGCTTGCTACTTTCATCATAGGTACAAATCAGGCAAGTCGAGCACATAC
EST: gi|18372793|gb|BJ204395.1|BJ204395
EST:     ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCG                         CTGGCTTGCTACTTTCATCATAGGTACAAATCAGGCAAGTCGAGCACATAC
genomic: ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCGgtgcgtttct ... tggtttgcagCTGGCTTGCTACTTTCATCATAGGTACAAATCAGGCAAGTCGAGCACATAC
EST: gi|18368814|gb|BJ200899.1|BJ200899
EST:     ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCG                         CTGGCTTGCTACTTTCATCATAGGTACA
genomic: ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCGgtgcgtttct ... tggtttgcagCTGGCTTGCTACTTTCATCATAGGTACA
EST: gi|18352921|gb|BJ184976.1|BJ184976
EST:     ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCG                         CTGGCTTGCTACTTTCATCATAGGTACAAATCAGGCAAGTCGAGCACATAC
genomic: ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCGgtgcgtttct ... tggtttgcagCTGGCTTGCTACTTTCATCATAGGTACAAATCAGGCAAGTCGAGCACATAC
EST: gi|18353821|gb|BJ185876.1|BJ185876
EST:     ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCG                         CTGGCTTGCTACTTT
genomic: ACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCGgtgcgtttct ... tggtttgcagCTGGCTTGCTACTTT

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), 35 (downstream exon)
Score: 63

CGGAGAGATCGGAATAGGGTCGCCTCCCCAGCCCTTCGCTGTCATCTTCGACACCGGGAGCTCCAATCTCTGGGTCCCGTCTGCCAAGTGCTACTTGTCGgtgcgtttct ... tggtttgcagCTGGCTTGCTACTTTCATCATAGGTACAAATCAGGCAAGTCGAGCACATACAAGGAAGATGGTACGCAGCTTACCCTTTAGTTCAATTTCGCACAATTAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttggtaaaaggtatggcagtttgccctgactaggtgatttctcttggtttgcagCTGGCTTGCTACTTTCATCATAGGTACAAATCAGGCAAGTCGAGCACATACAAGGAAGATGGTACGCAGCTTACCCTTTAGTTCAATTTCGCACAATTAG
                        ccctgac  putative branch site (score: 63)
                                      tttctctt  putative PPT
     taaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcttaagcgtaggtatgtgtgaactcgcgtgtgtgactgttggcttggtaaaaggtatggcagtttgccctgactaggtgatttctcttggtttgcagCTGGCTTGCTACTTTCATCATAGGTACAAATCAGGCAAGTCGAGCACATACAAGGAAGATGGTACGCAGCTTACCCTTTAGTTCAATTTCGCACAATTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT