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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAGgtgaggagtgagcgaagttgttggtgaggatgagagttgaagcttgcgtggtggtggggcggcacggatgtgtagtgttctgatggggaggtgggtgcag

Basic information

species Physcomitrella patens
transcript PP1S6_313V6.1
intron # 3
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|208398261|gb|DC916428.1|DC916428
EST:     GACTTCGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: GACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|208353105|gb|DC921849.1|DC921849
EST:     GCCCGAGGACTTNGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTNGGTGCCGC
genomic: GCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|208350739|gb|DC918199.1|DC918199
EST:     AGCCCGAGGANTTCGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: AGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|208396788|gb|DC920412.1|DC920412
EST:     GAAGAAGCCCGAGGANTTCGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: GAAGAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|208364400|gb|DC950701.1|DC950701
EST:     TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|208373312|gb|DC948586.1|DC948586
EST:     ACGACCC-TTC-GNTTGTCGNAGAAGCCCGAGGANTTCGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: ACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|208363096|gb|DC958009.1|DC958009
EST:     TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|162177735|gb|FC354569.1|FC354569
EST:     ACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: ACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|208387587|gb|DC953329.1|DC953329
EST:     TAT-GGTACGACCCTTTCGG-TTGTCGNAGAAGCCCGAGGACTTCGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|208346173|gb|DC917126.1|DC917126
EST:     GTCGAAGAAGCCCGAGGANTTCGACAG                         GTACCCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCG
genomic: GTCGAAGAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTA-CCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCG
EST: gi|162267721|gb|FC443711.1|FC443711
EST:     TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|162189777|gb|FC365311.1|FC365311
EST:     TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|208359540|gb|DC954093.1|DC954093
EST:     TAT-GGTACGACCCTTTCGG-TTGTCGAAGAAGCCCGAGGACTTCGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|208374900|gb|DC956173.1|DC956173
EST:     AAGAAGCCCGAGGACTTCGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTNGGTGCCGC
genomic: AAGAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|208377519|gb|DC922622.1|DC922622
EST:     AGCCCGAGGACTTCGACAG                         GTACCAAGCGTACGAG-TGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: AGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|162272756|gb|FC448772.1|FC448772
EST:     CCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: CCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|162246281|gb|FC423639.1|FC423639
EST:     TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|208359085|gb|DC957833.1|DC957833
EST:     TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG                         GTACCAAGCGTACGAGTTGATNCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|162232039|gb|FC409113.1|FC409113
EST:     TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|162271665|gb|FC448590.1|FC448590
EST:     TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|162263794|gb|FC439659.1|FC439659
EST:     TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|162170792|gb|FC347406.1|FC347406
EST:     TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|208350525|gb|DC926230.1|DC926230
EST:     TTCGG-TTGTCGNAGAAGCCCGAGGANTTCGACA-                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTTGGGTGCCG
genomic: TTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATG-TTGGGTGCCG
EST: gi|208382499|gb|DC923169.1|DC923169
EST:     TATGGGTACGACCCTTTCGGTTTGTNGAAGAAGCCCGAGGANTTCGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|208347850|gb|DC921149.1|DC921149
EST:     AGCCCGAGGANTTCGACAG                         GTACCCAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: AGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|208396742|gb|DC920394.1|DC920394
EST:     AGCCCGAGGACTTCGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: AGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|208376856|gb|DC918769.1|DC918769
EST:     AAGCCCGAGGACTTCGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: AAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|162231613|gb|FC408232.1|FC408232
EST:     TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|208381665|gb|DC915531.1|DC915531
EST:     TACGACCCTTTCGG-TTGTCGAAGAAGCCCGAGGACTTCGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: TACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|208370222|gb|DC952044.1|DC952044
EST:     AGCCCGAGGACTTCGACAG                         GTACCAAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCG
genomic: AGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACC-AAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCG
EST: gi|162157170|gb|FC333740.1|FC333740
EST:     TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|162233003|gb|FC408410.1|FC408410
EST:     TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|208357339|gb|DC953719.1|DC953719
EST:     TATGGGTACGACCNTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|208400530|gb|DC925280.1|DC925280
EST:     GAAGAAGCCCGAGGANTTCGACAG                         GTACCAAGCGTACGAGNTGATCCACGCGANGTGGGCCATGTTGGGTGCCGC
genomic: GAAGAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|208346104|gb|DC917057.1|DC917057
EST:     TATGGGTACGACCCTTTCGG-TTGTCGAAGNAGCCCGAGGACTTCGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|208366912|gb|DC951399.1|DC951399
EST:     TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCTGAGGACTTCGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|208399681|gb|DC920899.1|DC920899
EST:     GTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: GTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|162234779|gb|FC409265.1|FC409265
EST:     GAAGCCCGAGGACTTCGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: GAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|162194119|gb|FC369462.1|FC369462
EST:     TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|162271664|gb|FC448589.1|FC448589
EST:     AGGACTTCGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: AGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|208380204|gb|DC927483.1|DC927483
EST:     TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAG                         GTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: TATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
EST: gi|208355034|gb|DC926699.1|DC926699
EST:     AGAAG-CCGAGGA-TTNGACAG                         GTACCCAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC
genomic: AGAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGC

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: 526

CTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAGgtgaggagtg ... gtgggtgcagGTACCAAGCGTACGAGTTGATCCACGCGAGGTGGGCCATGTTGGGTGCCGCTGGGTTCGTTCTTCCCGAGGCATTCAACAAGTTCGGCGCTGTGTGCGGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTATGGGTACGACCCTTTCGGTTTGTCGAAGAAGCCCGAGGACTTCGACAGgtgaggagtgagcgaagttgttggtgaggatgagagttgaagcttgcgtggtggtggggcggcacggatgtgtagtgttctgatggggaggtgggtgcag

- - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - -  AGAAGC