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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAGgtacttaatgtttactctgtcttttcctttggttcatgtgtttatctgcatgttacatggcacgtcagcaacgtagagatggttaaattgcctatttacatgattttgagcgcaactagcaactttttaagggagtcctggtggtcgcag

Basic information

species Physcomitrella patens
transcript PP1S47_175V6.1
intron # 6
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|100446572|gb|CJ970871.1|CJ970871
EST:     TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAG                         GCTAGTGCNTATGTTTCAAGAGTCAGCC-CACAGCGACCAGGC
genomic: TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAGgtacttaatg ... gtggtcgcagGCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGC
EST: gi|208400386|gb|DC925024.1|DC925024
EST:     TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAG                         GCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGT
genomic: TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAGgtacttaatg ... gtggtcgcagGCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGT
EST: gi|100375388|gb|BY948854.1|BY948854
EST:     TGC-TCTGANTC-ACTGATTTTTCACAAGGGCAGCGAGCAAAGCTCCA-G                         GCTAGTGCCTATGTTTCCAGAGTCAGCCACACAGCGACCAGGCGAAAAAG
genomic: -GCCTCTGA-TCCACTGATTTTTCACAAGGGCAGCGAGCAA-GCTCCAAGgtacttaatg ... gtggtcgcagGCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAG
EST: gi|208353342|gb|DC946290.1|DC946290
EST:     TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAG                         GCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGT
genomic: TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAGgtacttaatg ... gtggtcgcagGCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGT
EST: gi|208363065|gb|DC946934.1|DC946934
EST:     TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAG                         GCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGT
genomic: TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAGgtacttaatg ... gtggtcgcagGCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGT
EST: gi|100379831|gb|BY949966.1|BY949966
EST:     TTGCCTCTGATCCACTGATTTTTTCACA-GGGCAGCGAGCAAGCTCCNAG                         GCTAGTGCCTATGTTTTCA-GAGTCAGCCACACAGCGACCAGGCGAAAAAG
genomic: TTGCCTCTGATCCACTGATTTTT-CACAAGGGCAGCGAGCAAGCTCCAAGgtacttaatg ... gtggtcgcagGCTAGTGCCTATGTTT-CAAGAGTCAGCCACACAGCGACCAGGCGAAAAAG
EST: gi|67724008|gb|BJ974267.1|BJ974267
EST:     TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAG                         GCTAGTGCCTATGTTTCAAGAGTTAGCCACACAGCGACCAGGCGAAAAAGT
genomic: TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAGgtacttaatg ... gtggtcgcagGCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGT
EST: gi|208355833|gb|DC930196.1|DC930196
EST:     TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAG                         GCTAGTGCNTATGTTTCAAGANTCANCCACACAGCGACCAGG
genomic: TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAGgtacttaatg ... gtggtcgcagGCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGG
EST: gi|67569178|gb|BJ942002.1|BJ942002
EST:     TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAG                         GCTAGTGCCTATGTTTCAGGAGTCAGCCACACAGCGACCAGGCGAA
genomic: TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAGgtacttaatg ... gtggtcgcagGCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAA
EST: gi|208384047|gb|DC911225.1|DC911225
EST:     TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAG                         GCTAGTGCCTATGTTTCAAGANTCAGCCACACAGCGACCAGGCGAAAA
genomic: TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAGgtacttaatg ... gtggtcgcagGCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAA
EST: gi|208366345|gb|DC943863.1|DC943863
EST:     TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAG                         GCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGT
genomic: TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAGgtacttaatg ... gtggtcgcagGCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGT
EST: gi|208370373|gb|DC931785.1|DC931785
EST:     TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAG                         GCTAGTGCCTATGTT-CAAGAGTCAGCN-CACAGCGACCAG
genomic: TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAGgtacttaatg ... gtggtcgcagGCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAG
EST: gi|208394403|gb|DC942563.1|DC942563
EST:     TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAG                         GCTAGTGCCTATGTTTCANA-AGTCANCCACACAGCGACNAGGC
genomic: TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAGgtacttaatg ... gtggtcgcagGCTAGTGCCTATGTTTCA-AGAGTCAGCCACACAGCGACCAGGC
EST: gi|67692423|gb|BJ952656.1|BJ952656
EST:     TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAG                         GCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGT
genomic: TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAGgtacttaatg ... gtggtcgcagGCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGT
EST: gi|208389723|gb|DC938299.1|DC938299
EST:     TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAG                         NCTANTGCCTATGTTTCAAGAGTCA
genomic: TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAGgtacttaatg ... gtggtcgcagGCTAGTGCCTATGTTTCAAGAGTCA
EST: gi|208391012|gb|DC929331.1|DC929331
EST:     TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAG                         GCTAGTGCCTATGTTNCAAGAGTCAGCCACACAGCGAC-AGGCGAAAA-GT
genomic: TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAGgtacttaatg ... gtggtcgcagGCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGT
EST: gi|100364611|gb|BY947820.1|BY947820
EST:     TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCNAG                         GCTAGTGCCTATGTNNTCA-GAGTCAGCCACACAGCGACCAGGCGAAAAAG
genomic: TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAGgtacttaatg ... gtggtcgcagGCTAGTGCCTATGTT-TCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAG
EST: gi|208385596|gb|DC937141.1|DC937141
EST:     TTTGCCTCTGATCCACTGATTTTTCACAGGGGCAGCGAGCAAGCTCCAAG                         GCTAGTGCCTATGTTNCA-GAGTCAGCC-CACAGCGACCAGGCGAAAA-GT
genomic: TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAGgtacttaatg ... gtggtcgcagGCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGT
EST: gi|208373997|gb|DC944730.1|DC944730
EST:     TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAG                         GCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGT
genomic: TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAGgtacttaatg ... gtggtcgcagGCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGT
EST: gi|208354200|gb|DC957420.1|DC957420
EST:     TTTGCCTCTGATCCACTGATTTTTCACAGGGGCAGCGAGCAAGCTCCAAG                         GCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGT
genomic: TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAGgtacttaatg ... gtggtcgcagGCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGT
EST: gi|7286494|gb|AW598981.1|AW598981
EST:     GATTTTTCACAAGGGCAGCGAGCAAGCTCCAAG                         GCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGT
genomic: GATTTTTCACAAGGGCAGCGAGCAAGCTCCAAGgtacttaatg ... gtggtcgcagGCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGT
EST: gi|67725438|gb|BJ975697.1|BJ975697
EST:     TTTGCCACTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAG                         GCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGT
genomic: TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAGgtacttaatg ... gtggtcgcagGCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGT
EST: gi|208389767|gb|DC933641.1|DC933641
EST:     TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCA-GCTCCAAG                         GCTAGTGCCTATGTTNCA-GAGTCAGCC-CACAGCGACCAGGCG
genomic: TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAGgtacttaatg ... gtggtcgcagGCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCG
EST: gi|208361102|gb|DC957553.1|DC957553
EST:     TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAG                         GCTAGTGCCTATGTTTCAAGAGTCAGCCACACAACGACCAGGCGAAAAAGT
genomic: TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAGgtacttaatg ... gtggtcgcagGCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGT
EST: gi|162272918|gb|FC448854.1|FC448854
EST:     TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAG                         GCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGT
genomic: TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAGgtacttaatg ... gtggtcgcagGCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGT
EST: gi|208368388|gb|DC955557.1|DC955557
EST:     TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAG                         GCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGT
genomic: TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAGgtacttaatg ... gtggtcgcagGCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGT
EST: gi|162275152|gb|FC451739.1|FC451739
EST:     TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAG                         GCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGT
genomic: TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAGgtacttaatg ... gtggtcgcagGCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGT
EST: gi|162272917|gb|FC448853.1|FC448853
EST:     TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAG                         GCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGT
genomic: TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAGgtacttaatg ... gtggtcgcagGCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGT
EST: gi|208368823|gb|DC951347.1|DC951347
EST:     TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAG                         GCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGT
genomic: TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAGgtacttaatg ... gtggtcgcagGCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGT
EST: gi|208387707|gb|DC937272.1|DC937272
EST:     TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCANGCTCCA-G                         GCTAGTGCCTATGTTTCAAGAGTCAGCC-CACAACGACCAGGCG
genomic: TTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAGgtacttaatg ... gtggtcgcagGCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCG

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), 34 (downstream exon)
Score: 10

CCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAGgtacttaatg ... gtggtcgcagGCTAGTGCCTATGTTTCAAGAGTCAGCCACACAGCGACCAGGCGAAAAAGTTACTGAAGAGGAGGGGACAAAGGAAAAGACTTTTTGGCAGAAATAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAGAGGACTGGACCTTTGCCTCTGATCCACTGATTTTTCACAAGGGCAGCGAGCAAGCTCCAAGgtacttaatgtttactctgtcttttcctttggttcatgtgtttatctgcatgttacatggcacgtcagcaacgtagagatggttaaattgcctatttacatgattttgagcgcaactagcaactttttaagggagtcctggtggtcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT