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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctctgtccatctgggttggttcgttggaggcgcttcttggctcgtagccaagaagggaaatatgaactacgtactaatcttgtttgcatatgtgttgcagCGTCGGTACCGGCAGGGGAGCTGCTCACTCTCGAAGACGCACTGTAGGAGCCGCACCATCAGTCTCGTTTCGACAG

Basic information

species Physcomitrella patens
transcript PP1S41_288V6.1
intron # 4
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|162261873|gb|FC438397.1|FC438397
EST:     CCTGTTGCTGCTCCGAACATGACAGTGTCGGTCGTCAATAATGCGAGCAA                         CGTCGGTACCGGCAGGGGAGCTGCTCACTCTCGAAGACGCACTGTAGGAGC
genomic: CCTGTTGCTGCTCCGAACATGACAGTGTCGGTCGTCAATAATGCGAGCAAgtgagtggct ... tgtgttgcagCGTCGGTACCGGCAGGGGAGCTGCTCACTCTCGAAGACGCACTGTAGGAGC
EST: gi|162208338|gb|FC384650.1|FC384650
EST:     CCTGTTGCTGCTCCGAACATGACAGTGTCGGTCGTCAATAATGCGAGCAA                         CGTCGGTACCGGCAGGGGAGCTGCTCACTCTCGAAGACGCACTGTAGGAGC
genomic: CCTGTTGCTGCTCCGAACATGACAGTGTCGGTCGTCAATAATGCGAGCAAgtgagtggct ... tgtgttgcagCGTCGGTACCGGCAGGGGAGCTGCTCACTCTCGAAGACGCACTGTAGGAGC
EST: gi|208368231|gb|DC931457.1|DC931457
EST:     CCTGTTGCTGCTCN-AACATGACAGTGTCGGTCGTCAATA-TGCGAGCA-                         CGTCNGTACNGGCAGGG-ANCTGCTC
genomic: CCTGTTGCTGCTCCGAACATGACAGTGTCGGTCGTCAATAATGCGAGCAAgtgagtggct ... tgtgttgcagCGTCGGTACCGGCAGGGGAGCTGCTC
EST: gi|162262351|gb|FC437678.1|FC437678
EST:     CCTGTTGCTGCTCCGAACATGACAGTGTCGGTCGTCAATAATGCGAGCAA                         CGTCGGTACCGGCAGGGGAGCTGCTCACTCTCGAAGACGCACTGTAGGAGC
genomic: CCTGTTGCTGCTCCGAACATGACAGTGTCGGTCGTCAATAATGCGAGCAAgtgagtggct ... tgtgttgcagCGTCGGTACCGGCAGGGGAGCTGCTCACTCTCGAAGACGCACTGTAGGAGC
EST: gi|37848453|gb|BJ606461.1|BJ606461
EST:     CCTGTTGCTGCTCCGAACATGACAGTGTCGGTCGTCAATAATGCGAGCAA                         CGTCGGTACCGGCAGGGGAGCTGCTCACTCTCGAAGACGCACTGTAGGAGC
genomic: CCTGTTGCTGCTCCGAACATGACAGTGTCGGTCGTCAATAATGCGAGCAAgtgagtggct ... tgtgttgcagCGTCGGTACCGGCAGGGGAGCTGCTCACTCTCGAAGACGCACTGTAGGAGC
EST: gi|162208337|gb|FC384649.1|FC384649
EST:     CCTGTTGCTGCTCCGAACATGACAGTGTCGGTCGTCAATAATGCGAGCAA                         CGTCGGTACCGGCAGGGGAGCTGCTCACTCTCGAAGACGCACTGTAGGAGC
genomic: CCTGTTGCTGCTCCGAACATGACAGTGTCGGTCGTCAATAATGCGAGCAAgtgagtggct ... tgtgttgcagCGTCGGTACCGGCAGGGGAGCTGCTCACTCTCGAAGACGCACTGTAGGAGC
EST: gi|208385711|gb|DC952872.1|DC952872
EST:     CGTCAATAATGCGAGCAA                         CGTCGGTACCGGCA-GGGAGCTGCTCACTCTCGAAGACGCACTGTAGGAGC
genomic: CGTCAATAATGCGAGCAAgtgagtggct ... tgtgttgcagCGTCGGTACCGGCAGGGGAGCTGCTCACTCTCGAAGACGCACTGTAGGAGC
EST: gi|100447071|gb|CJ971370.1|CJ971370
EST:     CCTGTTGCTGCTCCGAACATGACAGTGTCGGTCGTCAATAATGCGAGCAA                         CGTCGGTACCGGCAGGGGAGCTGCTCACTCTCGAAGACGCACTGTAGGAGC
genomic: CCTGTTGCTGCTCCGAACATGACAGTGTCGGTCGTCAATAATGCGAGCAAgtgagtggct ... tgtgttgcagCGTCGGTACCGGCAGGGGAGCTGCTCACTCTCGAAGACGCACTGTAGGAGC
EST: gi|208389289|gb|DC933317.1|DC933317
EST:     CCTGTTGCTGCTCCGAACATGACAGTGTCGGTCGTCAATAATGCGAGCAN                         CGTCNGTACCGGCAGGGGAGCTGCTCACTCTCGAAG
genomic: CCTGTTGCTGCTCCGAACATGACAGTGTCGGTCGTCAATAATGCGAGCAAgtgagtggct ... tgtgttgcagCGTCGGTACCGGCAGGGGAGCTGCTCACTCTCGAAG
EST: gi|208391882|gb|DC945961.1|DC945961
EST:     CCTGTTGCTGCTCCGAACATGACAGTGTCGGTCGTCAATAATGCGAGCAA                         CGTCGGTACCGGCAGGGGAGCTGCTCACTCTCGAAGACGCACTGTAGGAGC
genomic: CCTGTTGCTGCTCCGAACATGACAGTGTCGGTCGTCAATAATGCGAGCAAgtgagtggct ... tgtgttgcagCGTCGGTACCGGCAGGGGAGCTGCTCACTCTCGAAGACGCACTGTAGGAGC
EST: gi|100447799|gb|CJ972098.1|CJ972098
EST:     CCTGTTGCTGCTCCGAACATGACAGTGTCGGTCGTCAATAATGCGAGCAA                         CGTCGGTACCGGCAGGGGAGCTGCTCACTCTCGAA
genomic: CCTGTTGCTGCTCCGAACATGACAGTGTCGGTCGTCAATAATGCGAGCAAgtgagtggct ... tgtgttgcagCGTCGGTACCGGCAGGGGAGCTGCTCACTCTCGAA
EST: gi|100416674|gb|BY993031.1|BY993031
EST:     CCTGTTGCTGCTCCGAACATGACAGTGTCGGTCGTCAATAATGCGAGCAA                         CGTCGGTACCGGCAGGGGAGCTG
genomic: CCTGTTGCTGCTCCGAACATGACAGTGTCGGTCGTCAATAATGCGAGCAAgtgagtggct ... tgtgttgcagCGTCGGTACCGGCAGGGGAGCTG
EST: gi|162261874|gb|FC438398.1|FC438398
EST:     CCTGTTGCTGCTCCGAACATGACAGTGTCGGTCGTCAATAATGCGAGCAA                         CGTCGGTACCGGCAGGGGAGCTGCTCACTCTCGAAGACGCACTGTAGGAGC
genomic: CCTGTTGCTGCTCCGAACATGACAGTGTCGGTCGTCAATAATGCGAGCAAgtgagtggct ... tgtgttgcagCGTCGGTACCGGCAGGGGAGCTGCTCACTCTCGAAGACGCACTGTAGGAGC
EST: gi|100383489|gb|BY950273.1|BY950273
EST:     CCTGT-GCTGCTCCGAACATGACAGTGTCGGTCGTCAATAATGCGAGCAA                         CGTCGGTACCGGCAGGGGAGCTGCTCAC
genomic: C-TGTTGCTGCTCCGAACATGACAGTGTCGGTCGTCAATAATGCGAGCAAgtgagtggct ... tgtgttgcagCGTCGGTACCGGCAGGGGAGCTGCTCAC
EST: gi|37844356|gb|BJ602364.1|BJ602364
EST:     CCTGTTGCTGCTCCGAACATGACAGTGTCGGTCGTCAATAATGCGAGCAA                         CGTCGGTACCGGCAGGGGAGCTGCTCACTCTCGAAGACGCACTGTAGGAGC
genomic: CCTGTTGCTGCTCCGAACATGACAGTGTCGGTCGTCAATAATGCGAGCAAgtgagtggct ... tgtgttgcagCGTCGGTACCGGCAGGGGAGCTGCTCACTCTCGAAGACGCACTGTAGGAGC

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: 15

GAACTGCATTTGGAAGGAAGCGTAATTTTCAGAGGGGTCCCAATACCTTCCCTGTTGCTGCTCCGAACATGACAGTGTCGGTCGTCAATAATGCGAGCAAgtgagtggct ... tgtgttgcagCGTCGGTACCGGCAGGGGAGCTGCTCACTCTCGAAGACGCACTGTAGGAGCCGCACCATCAGTCTCGTTTCGACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agccaagaagggaaatatgaactacgtactaatcttgtttgcatatgtgttgcagCGTCGGTACCGGCAGGGGAGCTGCTCACTCTCGAAGACGCACTGTAGGAGCCGCACCATCAGTCTCGTTTCGACAG
                          tactaat  putative branch site (score: 15)
            aaatatgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctctgtccatctgggttggttcgttggaggcgcttcttggctcgtagccaagaagggaaatatgaactacgtactaatcttgtttgcatatgtgttgcagCGTCGGTACCGGCAGGGGAGCTGCTCACTCTCGAAGACGCACTGTAGGAGCCGCACCATCAGTCTCGTTTCGACAG

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