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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCTGTGGAAGAGGAATTGTTGCAGAGGTTTCCCACGATGGCCATGGCTCCCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGGgtatgtccctcttcgagctctctttctttgcgcttcacttgttagcttagatttcttctcttgtagttttgtagttttccggttaactcgttgaaaattg...

Basic information

species Physcomitrella patens
transcript PP1S132_95V6.1
intron # 2
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|67718471|gb|BJ968730.1|BJ968730
EST:     CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGG                         GTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
genomic: CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGGgtatgtccct ... cttgtcatagGTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
EST: gi|100356048|gb|BY946170.1|BY946170
EST:     CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGG                         GTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
genomic: CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGGgtatgtccct ... cttgtcatagGTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
EST: gi|100380016|gb|BY968804.1|BY968804
EST:     CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGG                         GTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
genomic: CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGGgtatgtccct ... cttgtcatagGTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
EST: gi|18351892|gb|BJ183944.1|BJ183944
EST:     CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGG                         GTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
genomic: CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGGgtatgtccct ... cttgtcatagGTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
EST: gi|100446010|gb|CJ970309.1|CJ970309
EST:     CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGG                         GTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
genomic: CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGGgtatgtccct ... cttgtcatagGTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
EST: gi|100390341|gb|BY952749.1|BY952749
EST:     CCTCTGTGTTTGAGCACGTTCAGCAAGTACCCGAGGATCCCATTTTGGGG                         GTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
genomic: CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGGgtatgtccct ... cttgtcatagGTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
EST: gi|100448896|gb|CJ973195.1|CJ973195
EST:     CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGG                         GTAACAGTGGCTTACAACAAGGACCCAAGTCCATTGAAGGTGAACCTTGGA
genomic: CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGGgtatgtccct ... cttgtcatagGTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
EST: gi|100355096|gb|BY965000.1|BY965000
EST:     CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGG                         GTAACAGTGGCTTNANNCAACAAGGATCCAAGNTCCAT
genomic: CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGGgtatgtccct ... cttgtcatagGTAACAGTGGCTT-A--CAACAAGGATCCAAG-TCCAT
EST: gi|162267156|gb|FC443387.1|FC443387
EST:     CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGG                         GTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
genomic: CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGGgtatgtccct ... cttgtcatagGTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
EST: gi|100417339|gb|BY957283.1|BY957283
EST:     CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGG                         GTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
genomic: CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGGgtatgtccct ... cttgtcatagGTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
EST: gi|18365276|gb|BJ197350.1|BJ197350
EST:     CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGG                         GTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
genomic: CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGGgtatgtccct ... cttgtcatagGTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
EST: gi|208344839|gb|DC912673.1|DC912673
EST:     CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGG                         GTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
genomic: CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGGgtatgtccct ... cttgtcatagGTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
EST: gi|208397779|gb|DC912002.1|DC912002
EST:     CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGG                         GTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
genomic: CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGGgtatgtccct ... cttgtcatagGTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
EST: gi|208352476|gb|DC910190.1|DC910190
EST:     CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGG                         GTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
genomic: CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGGgtatgtccct ... cttgtcatagGTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
EST: gi|18361573|gb|BJ193639.1|BJ193639
EST:     CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGG                         GTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
genomic: CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGGgtatgtccct ... cttgtcatagGTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
EST: gi|208384190|gb|DC911298.1|DC911298
EST:     CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGG                         GTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
genomic: CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGGgtatgtccct ... cttgtcatagGTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
EST: gi|18371678|gb|BJ203280.1|BJ203280
EST:     CCTCTGTGTTTGANCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGG                         GTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
genomic: CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGGgtatgtccct ... cttgtcatagGTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
EST: gi|18332250|gb|BJ164263.1|BJ164263
EST:     CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGG                         GTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
genomic: CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGGgtatgtccct ... cttgtcatagGTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
EST: gi|162263809|gb|FC438428.1|FC438428
EST:     CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGG                         GTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA
genomic: CCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGGgtatgtccct ... cttgtcatagGTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGA

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: 26 (upstream exon), 34 (downstream exon)
Score: 16

AGCTGTGGAAGAGGAATTGTTGCAGAGGTTTCCCACGATGGCCATGGCTCCCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGGgtatgtccct ... cttgtcatagGTAACAGTGGCTTACAACAAGGATCCAAGTCCATTGAAGGTGAACCTTGGAGTCGGAGCCTACCGAACAGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCTGTGGAAGAGGAATTGTTGCAGAGGTTTCCCACGATGGCCATGGCTCCCTCTGTGTTTGAGCACGTTCAGCAAGCACCCGAGGATCCCATTTTGGGGgtatgtccctcttcgagctctctttctttgcgcttcacttgttagcttagatttcttctcttgtagttttgtagttttccggttaactcgttgaaaattg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT