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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGTTCCGAGCTGTGGAAGTGCGGATCCAATCAATGCCCGTGCGCAAGTCCCTGCAGGTCGTCGCCATGGCGCCACCCAAGCCCGGGAAGGCGAAGAAAGgtattcgagtgttttcttaagtgtggaagctcttttttttaatgggattgggtgtggtattctaggtcgtgaaggaattgaattcatgaatggtttctggtagttcaatttttgcggtctcgtacgctagcgtttgaaagaagttgggatgggtgcggaggaatgcag

Basic information

species Physcomitrella patens
transcript PP1S46_69V6.1
intron # 1
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|100410606|gb|BY992182.1|BY992182
EST:     CCTGCAGGTCGTCGCCATGGCGCCACCCAAGCCCGGGAAGGCGAAGAAAG                         TGGTTGGTCTTGTGAAGCTCGCCTTGGAGGCTGGAAAGGCCACCCCCGCGC
genomic: CCTGCAGGTCGTCGCCATGGCGCCACCCAAGCCCGGGAAGGCGAAGAAAGgtattcgagt ... aggaatgcagTGGTTGGTCTTGTGAAGCTCGCCTTGGAGGCTGGAAAGGCCACCCCCGCGC
EST: gi|162277905|gb|FC453828.1|FC453828
EST:     CCTGCAGGTCGTCGCCATGGCGCCACCCAAGCCCGGGAAGGCGAAGAAAG                         TGGTTGGTCTTGTGAAGCTCGCCTTGGAGGCTGGAAAGGCCACCCCCGCGC
genomic: CCTGCAGGTCGTCGCCATGGCGCCACCCAAGCCCGGGAAGGCGAAGAAAGgtattcgagt ... aggaatgcagTGGTTGGTCTTGTGAAGCTCGCCTTGGAGGCTGGAAAGGCCACCCCCGCGC
EST: gi|100411876|gb|BY992384.1|BY992384
EST:     CCTGCAGGTCGTCGCCATGGCGCCACCCAAGCCCGGGAAGGCGAAGAAAG                         TGGTTGGTCTTGTGAAGCTCGCCTTGGAGGCTGGAAAGGCCACCCCCGCGC
genomic: CCTGCAGGTCGTCGCCATGGCGCCACCCAAGCCCGGGAAGGCGAAGAAAGgtattcgagt ... aggaatgcagTGGTTGGTCTTGTGAAGCTCGCCTTGGAGGCTGGAAAGGCCACCCCCGCGC
EST: gi|162234054|gb|FC410320.1|FC410320
EST:     CCTGCAGGTCGTCGCCATGGCGCCACCCAAGCCCGGGAAGGCGAAGAAAG                         TGGTTGGTCTTGTGAAGCTCGCCTTGGAGGCTGGAAAGGCCACCCCCGCGC
genomic: CCTGCAGGTCGTCGCCATGGCGCCACCCAAGCCCGGGAAGGCGAAGAAAGgtattcgagt ... aggaatgcagTGGTTGGTCTTGTGAAGCTCGCCTTGGAGGCTGGAAAGGCCACCCCCGCGC
EST: gi|7147874|gb|AW509796.1|AW509796
EST:     CCTGCAGGTCGTCGCCATGGCGCCACCCAAGCCCGGGAAGGCGAAGAAAG                         TGGTTGGTCTTGTGAAGCTCGCCTTGGAGGCTGGAAAGGCCACCCCCGCGC
genomic: CCTGCAGGTCGTCGCCATGGCGCCACCCAAGCCCGGGAAGGCGAAGAAAGgtattcgagt ... aggaatgcagTGGTTGGTCTTGTGAAGCTCGCCTTGGAGGCTGGAAAGGCCACCCCCGCGC
EST: gi|19776753|gb|BQ039104.1|BQ039104
EST:     CCTGCAGGTCGTCGCCATGGCGCCACCCAAGCCCGGGAAGGCGAAGAAAG                         TGGTTGGTCTTGTGAAGCTCGCCTTGGAGGCTGGAAAGGCCACCCCCGCGC
genomic: CCTGCAGGTCGTCGCCATGGCGCCACCCAAGCCCGGGAAGGCGAAGAAAGgtattcgagt ... aggaatgcagTGGTTGGTCTTGTGAAGCTCGCCTTGGAGGCTGGAAAGGCCACCCCCGCGC
EST: gi|208356326|gb|DC957360.1|DC957360
EST:     CCTGCAGGTCGTCGCCATGGCGCCACCCAAGCCCGGGAAGGCGAAGAAAG                         TGGTTGGTCTTGTGAAGCTCGCCTTGGAGGCTGGAAAGGCCACCCCCGCGC
genomic: CCTGCAGGTCGTCGCCATGGCGCCACCCAAGCCCGGGAAGGCGAAGAAAGgtattcgagt ... aggaatgcagTGGTTGGTCTTGTGAAGCTCGCCTTGGAGGCTGGAAAGGCCACCCCCGCGC
EST: gi|162260841|gb|FC438197.1|FC438197
EST:     CCTGCAGGTCGTCGCCATGGCGCCACCCAAGCCCGGGAAGGCGAAGAAAG                         TGGTTGGTCTTGTGAAGCTCGCCTTGGAGGCTGGAAAGGCCACCCCCGCGC
genomic: CCTGCAGGTCGTCGCCATGGCGCCACCCAAGCCCGGGAAGGCGAAGAAAGgtattcgagt ... aggaatgcagTGGTTGGTCTTGTGAAGCTCGCCTTGGAGGCTGGAAAGGCCACCCCCGCGC
EST: gi|162234055|gb|FC410321.1|FC410321
EST:     CCTGCAGGTCGTCGCCATGGCGCCACCCAAGCCCGGGAAGGCGAAGAAAG                         TGGTTGGTCTTGTGAAGCTCGCCTTGGAGGCTGGAAAGGCCACCCCCGCGC
genomic: CCTGCAGGTCGTCGCCATGGCGCCACCCAAGCCCGGGAAGGCGAAGAAAGgtattcgagt ... aggaatgcagTGGTTGGTCTTGTGAAGCTCGCCTTGGAGGCTGGAAAGGCCACCCCCGCGC
EST: gi|208386417|gb|DC937084.1|DC937084
EST:     CCTGCAGGTCGTCGCCATGGCGCCACCCAAGCCCGGGAAGGCGAAGAAAG                         TGGTTGGTCTTGTGAAGCTCGCCTTGGAGGCTGGAAAGGCCACCCCCGCGC
genomic: CCTGCAGGTCGTCGCCATGGCGCCACCCAAGCCCGGGAAGGCGAAGAAAGgtattcgagt ... aggaatgcagTGGTTGGTCTTGTGAAGCTCGCCTTGGAGGCTGGAAAGGCCACCCCCGCGC
EST: gi|19782770|gb|BQ039911.1|BQ039911
EST:     CCTGCAGGTCGTCGCCATGGCGCCACCCAAGCCCGGGAAGGCGAAGAAAG                         TGGTTGGTCTTGTGAAGCTCGCCTTGGAGGCTGGAAAGGCCACCCCCGCGC
genomic: CCTGCAGGTCGTCGCCATGGCGCCACCCAAGCCCGGGAAGGCGAAGAAAGgtattcgagt ... aggaatgcagTGGTTGGTCTTGTGAAGCTCGCCTTGGAGGCTGGAAAGGCCACCCCCGCGC
EST: gi|19788061|gb|BQ040708.1|BQ040708
EST:     CCTGCAGGTCGTCGCCATGGCGCCACCCAAGCCCGGGAAGGCGAAGAAAG                         TGGTTGGTCTTGTGAAGCTCGCCTTGGAGGCTGGAAAGGCCACCCCCGCGC
genomic: CCTGCAGGTCGTCGCCATGGCGCCACCCAAGCCCGGGAAGGCGAAGAAAGgtattcgagt ... aggaatgcagTGGTTGGTCTTGTGAAGCTCGCCTTGGAGGCTGGAAAGGCCACCCCCGCGC

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), 31 (downstream exon)
Score: 10

GCGTTCCGAGCTGTGGAAGTGCGGATCCAATCAATGCCCGTGCGCAAGTCCCTGCAGGTCGTCGCCATGGCGCCACCCAAGCCCGGGAAGGCGAAGAAAGgtattcgagt ... aggaatgcagTGGTTGGTCTTGTGAAGCTCGCCTTGGAGGCTGGAAAGGCCACCCCCGCGCCACCCGTAGGTCCAGCTCTTGGTTCCAAGGGTGTCAACATTATGGCTTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGTTCCGAGCTGTGGAAGTGCGGATCCAATCAATGCCCGTGCGCAAGTCCCTGCAGGTCGTCGCCATGGCGCCACCCAAGCCCGGGAAGGCGAAGAAAGgtattcgagtgttttcttaagtgtggaagctcttttttttaatgggattgggtgtggtattctaggtcgtgaaggaattgaattcatgaatggtttctggtagttcaatttttgcggtctcgtacgctagcgtttgaaagaagttgggatgggtgcggaggaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA