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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catgcgacatgtcaggaacaattttggcgcgaatcatgattatagttgattcatattcttaaaccattttaatcatgagatttgtgagtgttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG

Basic information

species Physcomitrella patens
transcript PP1S99_59V6.3
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|208362407|gb|DC930968.1|DC930968
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAAGAGATACGCTGGATCANAAGCATGGACTGTGAAA
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|208388729|gb|DC941528.1|DC941528
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAANAGATACNCTGGATCANAANCATGGACTGTGAAG
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|208367480|gb|DC954940.1|DC954940
EST:     CCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAAGAGATACGCTGGATCAGAAAGCATGGACTGTGAAG
genomic: CCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAG-AAGCATGGACTGTGAAG
EST: gi|208355241|gb|DC929744.1|DC929744
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGANGAT                         ATAAAGAATAATAAGAGATACGCTGGATCA
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCA
EST: gi|208373717|gb|DC936544.1|DC936544
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAAGAGATACNCTGGATCAAAANCATGGACTGTGAA
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAA
EST: gi|208362869|gb|DC950819.1|DC950819
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|208372849|gb|DC956250.1|DC956250
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|208389559|gb|DC929456.1|DC929456
EST:     TCTATCCTCTGGATGCTGNTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAANAGATACGCTGGATCANAANCATGGACTGTGAAN
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|208354826|gb|DC934358.1|DC934358
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAAGAGATACNCTGGATCAAAANCATGGACTGTGAAN
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|208389923|gb|DC937754.1|DC937754
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAANAGATACNCTGGATCAAAANCATGGACTGTGAAG
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|208365068|gb|DC943377.1|DC943377
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAAGAGATACGCTGGATCANAAGCATGGACTGTGAAG
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|208380442|gb|DC914866.1|DC914866
EST:     CTATCCTCTGGATGCTGNTTTCCGACACTCCTGATGATGTCCCTGAGGAT                         ATAANGAATAATAAGAGATACNCTGGATCAGAANCATGGACTGTGAA
genomic: CTATCCTCTGGATGCTGTTTTC-GACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAA
EST: gi|208390204|gb|DC941983.1|DC941983
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAAGAGATACGCTGGATCAAAAGCATGGACTGTGAAN
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|208363068|gb|DC957995.1|DC957995
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|67719180|gb|BJ969439.1|BJ969439
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAAGAGATACGCTGGATCANAAGCATGGACTGTGAAG
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|162157331|gb|FC333459.1|FC333459
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|208390690|gb|DC937846.1|DC937846
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAAGAGATACGCTGGATCANAAGCATGGACTGTGAAN
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|208361941|gb|DC943233.1|DC943233
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAANAGATACNCTGGATCAAAANCATGGACTGTGAAN
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|208369171|gb|DC956046.1|DC956046
EST:     GCTG-TTTCGACA-TCCTGATGA-GTCCCTG-GGAT                         ATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGNAG
genomic: GCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|208390945|gb|DC945934.1|DC945934
EST:     TGATGATGTCCCTGAGGAT                         -TTAAGAATTATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
genomic: TGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|208362182|gb|DC935624.1|DC935624
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAA-GAATAATAANAGATACNCTGGATCA
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCA
EST: gi|208392588|gb|DC938553.1|DC938553
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAANANATACNCTGGATCANAANCATGGACTGTGAAN
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|208358028|gb|DC938871.1|DC938871
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAAGAGATACGCTGGATCAAAAGCATGGACTGTGAA
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAA
EST: gi|208363548|gb|DC939753.1|DC939753
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAAGAGATACGCTGGATCANAAGCATGGACTGTGAAG
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|208390983|gb|DC929302.1|DC929302
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAAGAGATACGCTGGATCANAANCATGGACTGTGAAG
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|208386618|gb|DC932680.1|DC932680
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAANAGATACNCTGGATCANAAGCATGGACTGTGAAN
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|208361752|gb|DC934992.1|DC934992
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAAGAGATACGCTGGATCANAAGCATGGACTGTGAAG
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|208360154|gb|DC939179.1|DC939179
EST:     TCTATCCTCTAGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAAGAGATACGCTGGA
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGA
EST: gi|208365560|gb|DC935713.1|DC935713
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAANAGATACNCTGGATCANAANCATGGACTGTGAAG
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|162280155|gb|FC455964.1|FC455964
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|208383608|gb|DC906999.1|DC906999
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAAGAGATACGCTGGATCAAAANCATGGACTGTGAAA
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|67727485|gb|BJ977744.1|BJ977744
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|208364518|gb|DC930908.1|DC930908
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATANTAANAGATACGCTGGATCANAANCATGGACTGTGAAG
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
EST: gi|208357946|gb|DC943058.1|DC943058
EST:     TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGAT                         ATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
genomic: TCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG

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: 33 (upstream exon), 35 (downstream exon)
Score: 10

ACTCCCCAACGGAGGGCTATTGGAGATAGCGAAAGTCTATCCTCTGGATGCTGTTTTCGACACTCCTGATGATGTCCCTGAGGATgtaagtgaac ... ttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgattcatattcttaaaccattttaatcatgagatttgtgagtgttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG
                     ttttaat  putative branch site (score: 10)
                                           tgttttctcc  putative PPT
       atattcttaaaccatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catgcgacatgtcaggaacaattttggcgcgaatcatgattatagttgattcatattcttaaaccattttaatcatgagatttgtgagtgttttctccagATAAAGAATAATAAGAGATACGCTGGATCAGAAGCATGGACTGTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA