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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACAGCCGTGGCGATTGCGAGGGAGTTGGGAATCGAGAGGCCATGCGTGCACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtttgcctggtgcacgagcatgcgtgggggctgcgggggaagtttgacctggggagggaacgcgagcgccggggtgggattggattgcgtaatgggggaagcagaggcgagtgatgaggacgcttggtgaacaagcatgctgacgctgaggtttgtgggatgcag

Basic information

species Physcomitrella patens
transcript PP1S83_69V6.1
intron # 4
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|162275157|gb|FC451744.1|FC451744
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162152469|gb|FC328032.1|FC328032
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162180046|gb|FC355896.1|FC355896
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162267246|gb|FC442658.1|FC442658
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162154573|gb|FC330783.1|FC330783
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162266238|gb|FC442170.1|FC442170
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162192499|gb|FC369129.1|FC369129
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162198739|gb|FC374222.1|FC374222
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162205789|gb|FC381027.1|FC381027
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162263866|gb|FC439174.1|FC439174
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162263638|gb|FC440122.1|FC440122
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|67572499|gb|BJ945323.1|BJ945323
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162235274|gb|FC412241.1|FC412241
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162208862|gb|FC384998.1|FC384998
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162151846|gb|FC328092.1|FC328092
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162276530|gb|FC452910.1|FC452910
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162205788|gb|FC381026.1|FC381026
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162188683|gb|FC364593.1|FC364593
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|22132295|gb|BQ827083.1|BQ827083
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162173031|gb|FC348656.1|FC348656
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162180399|gb|FC355820.1|FC355820
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162264369|gb|FC440535.1|FC440535
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162189736|gb|FC366790.1|FC366790
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162218370|gb|FC394752.1|FC394752
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|22131683|gb|BQ826742.1|BQ826742
EST:     GAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: GAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162246406|gb|FC419942.1|FC419942
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162153131|gb|FC329537.1|FC329537
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162275156|gb|FC451743.1|FC451743
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162273416|gb|FC449865.1|FC449865
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
EST: gi|162276531|gb|FC452911.1|FC452911
EST:     ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAG                         GCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA
genomic: ACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCA

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: 200

CACAGCCGTGGCGATTGCGAGGGAGTTGGGAATCGAGAGGCCATGCGTGCACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtt ... tgggatgcagGCGGCAGGGACGTCGGTGGCCATGGTGGGGGACGGCATCAACGATTCGCCAGCGTTGGTCGCAGCGGACGTGGGGATGGCGATAGGAGCGGGGACGGACA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACAGCCGTGGCGATTGCGAGGGAGTTGGGAATCGAGAGGCCATGCGTGCACGCAGAGTCGTTGCCAGAAGACAAGGCCAGGATCGTGGAAGAAATGCAGgttcgtggtttgcctggtgcacgagcatgcgtgggggctgcgggggaagtttgacctggggagggaacgcgagcgccggggtgggattggattgcgtaatgggggaagcagaggcgagtgatgaggacgcttggtgaacaagcatgctgacgctgaggtttgtgggatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA