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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCGTGCTCTCAGTCCCTCTTTGCCACCTAACGCGGCAGCTTAGCTCTGCCGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAGgtgaggctatctcgttttgtggaggttttccaggctcgtgttgatttgctctattctggcacggccttgcttctagaagctcacacagttgcattgtgggttggtctttgtctttcag

Basic information

species Physcomitrella patens
transcript PP1S41_146V6.1
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|162217138|gb|FC392502.1|FC392502
EST:     CGCTTTGC-TGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAG                         TTCGTAGCTGACGGTG-TTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
genomic: CGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAGgtgaggctat ... tgtctttcagTTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
EST: gi|19788800|gb|BQ040933.1|BQ040933
EST:     CGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAG                         TTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
genomic: CGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAGgtgaggctat ... tgtctttcagTTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
EST: gi|19778407|gb|BQ039307.1|BQ039307
EST:     CGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAG                         TTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
genomic: CGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAGgtgaggctat ... tgtctttcagTTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
EST: gi|162259170|gb|FC435203.1|FC435203
EST:     TGAGCAAGAAGCGCAAG                         TTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
genomic: TGAGCAAGAAGCGCAAGgtgaggctat ... tgtctttcagTTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
EST: gi|67704473|gb|BJ964706.1|BJ964706
EST:     CGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAG                         TTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
genomic: CGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAGgtgaggctat ... tgtctttcagTTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
EST: gi|162230909|gb|FC406748.1|FC406748
EST:     CGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAG                         TTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
genomic: CGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAGgtgaggctat ... tgtctttcagTTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
EST: gi|67693697|gb|BJ953930.1|BJ953930
EST:     TCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAG                         TTCGTAGCTGACGGTGTTTT-TTCGCCGAGCTCAACGAGCTTCTCACCCGG
genomic: TCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAGgtgaggctat ... tgtctttcagTTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
EST: gi|162250244|gb|FC425495.1|FC425495
EST:     AACATGGCTACCCAAATGAGCAAGAAGCGCAAG                         TTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
genomic: AACATGGCTACCCAAATGAGCAAGAAGCGCAAGgtgaggctat ... tgtctttcagTTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
EST: gi|162250245|gb|FC425496.1|FC425496
EST:     CGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAG                         TTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
genomic: CGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAGgtgaggctat ... tgtctttcagTTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
EST: gi|162279949|gb|FC456135.1|FC456135
EST:     CGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAG                         TTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
genomic: CGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAGgtgaggctat ... tgtctttcagTTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
EST: gi|162217139|gb|FC392503.1|FC392503
EST:     CGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAG                         TTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
genomic: CGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAGgtgaggctat ... tgtctttcagTTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
EST: gi|162153703|gb|FC329106.1|FC329106
EST:     CGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAG                         TTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
genomic: CGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAGgtgaggctat ... tgtctttcagTTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
EST: gi|162246682|gb|FC425275.1|FC425275
EST:     CGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAG                         TTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
genomic: CGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAGgtgaggctat ... tgtctttcagTTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
EST: gi|67702691|gb|BJ962924.1|BJ962924
EST:     CGCTTTGCTTGTCTTCCAACATGGCTGCCCAAATGAGCAAGAAGCGCAAG                         TTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
genomic: CGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAGgtgaggctat ... tgtctttcagTTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
EST: gi|208379087|gb|DC911612.1|DC911612
EST:     CGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAG                         TTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
genomic: CGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAGgtgaggctat ... tgtctttcagTTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
EST: gi|208389218|gb|DC933246.1|DC933246
EST:     CGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAG                         TTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
genomic: CGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAGgtgaggctat ... tgtctttcagTTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
EST: gi|7147663|gb|AW509634.1|AW509634
EST:     GCTACCCAAATGAGCAAGAAGCGCAAG                         TTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
genomic: GCTACCCAAATGAGCAAGAAGCGCAAGgtgaggctat ... tgtctttcagTTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
EST: gi|18332170|gb|BJ164183.1|BJ164183
EST:     TTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCANGAAGCGCAAG                         TTCGTANCTGACGGTGTTTTCTTCGCCAAGCTCAACGAGCTTCTCACCCGG
genomic: TTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAGgtgaggctat ... tgtctttcagTTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
EST: gi|67575972|gb|BJ948796.1|BJ948796
EST:     CGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAG                         TTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
genomic: CGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAGgtgaggctat ... tgtctttcagTTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
EST: gi|162211611|gb|FC387691.1|FC387691
EST:     CGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAG                         TTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
genomic: CGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAGgtgaggctat ... tgtctttcagTTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
EST: gi|18344067|gb|BJ176106.1|BJ176106
EST:     CGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAG                         TTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
genomic: CGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAGgtgaggctat ... tgtctttcagTTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
EST: gi|67570422|gb|BJ943246.1|BJ943246
EST:     CGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAG                         TTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG
genomic: CGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAGgtgaggctat ... tgtctttcagTTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGG

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), 35 (downstream exon)
Score: 24

TTCGTGCTCTCAGTCCCTCTTTGCCACCTAACGCGGCAGCTTAGCTCTGCCGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAGgtgaggctat ... tgtctttcagTTCGTAGCTGACGGTGTTTTCTTCGCCGAGCTCAACGAGCTTCTCACCCGGGAACTTGCCGAGGATGGCTACTCCGGCGTTGAAGTGCGCGTGACCCCCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCGTGCTCTCAGTCCCTCTTTGCCACCTAACGCGGCAGCTTAGCTCTGCCGCTTTGCTTGTCTTCCAACATGGCTACCCAAATGAGCAAGAAGCGCAAGgtgaggctatctcgttttgtggaggttttccaggctcgtgttgatttgctctattctggcacggccttgcttctagaagctcacacagttgcattgtgggttggtctttgtctttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC