Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...actaactgtgtcagtattctgacaatgttcttactgcaatattgcacaaataatgttttcatgcttgggagtaatagggtgcttgttcgtgatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAGGAACCCCACCAGATGTTGCTTGTGTTGTGTAGCGACAAGGTCTGATTAC

Basic information

species Physcomitrella patens
transcript PP1S100_61V6.1
intron # 5
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|67728148|gb|BJ978407.1|BJ978407
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
EST: gi|162267194|gb|FC442606.1|FC442606
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
EST: gi|162209502|gb|FC386135.1|FC386135
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
EST: gi|162261088|gb|FC436949.1|FC436949
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
EST: gi|67508592|gb|BJ941454.1|BJ941454
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
EST: gi|67578360|gb|BJ950527.1|BJ950527
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
EST: gi|18338320|gb|BJ170344.1|BJ170344
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
EST: gi|18362314|gb|BJ194384.1|BJ194384
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
EST: gi|67578398|gb|BJ950565.1|BJ950565
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
EST: gi|15262199|gb|BI437509.1|BI437509
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
EST: gi|67691811|gb|BJ952044.1|BJ952044
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
EST: gi|208376809|gb|DC918750.1|DC918750
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
EST: gi|37848504|gb|BJ606512.1|BJ606512
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
EST: gi|37850045|gb|BJ608053.1|BJ608053
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
EST: gi|67719884|gb|BJ970143.1|BJ970143
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
EST: gi|37853304|gb|BJ611312.1|BJ611312
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
EST: gi|67701294|gb|BJ961527.1|BJ961527
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
EST: gi|67691886|gb|BJ952119.1|BJ952119
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
EST: gi|18372924|gb|BJ204526.1|BJ204526
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
EST: gi|18359903|gb|BJ191964.1|BJ191964
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
EST: gi|208400671|gb|DC904857.1|DC904857
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
EST: gi|208390277|gb|DC949517.1|DC949517
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
EST: gi|67695988|gb|BJ956221.1|BJ956221
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
EST: gi|15261952|gb|BI437262.1|BI437262
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         GTAAAGGTGATAGGACCGGGTGGAAAGCCT
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCT
EST: gi|162209503|gb|FC386136.1|FC386136
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
EST: gi|37843440|gb|BJ601448.1|BJ601448
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
EST: gi|37851377|gb|BJ609385.1|BJ609385
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
EST: gi|162267193|gb|FC442605.1|FC442605
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
EST: gi|208365559|gb|DC935712.1|DC935712
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
EST: gi|67701245|gb|BJ961478.1|BJ961478
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
EST: gi|67727167|gb|BJ977426.1|BJ977426
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
EST: gi|37840814|gb|BJ598822.1|BJ598822
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
EST: gi|67572616|gb|BJ945440.1|BJ945440
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
EST: gi|67508661|gb|BJ941522.1|BJ941522
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
EST: gi|18371213|gb|BJ202815.1|BJ202815
EST:     TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAG                         TTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG
genomic: TGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAG

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: 31 (upstream exon), 34 (downstream exon)
Score: 7

AGGACGAGCATGATGTGACGTGGTTCACTTTGGAGAAGGGCCAAACGCACGAGTGCCCCGTGTGCACCCAGGTTTTTGAGgtaatttata ... gatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAGGAACCCCACCAGATGTTGCTTGTGTTGTGTAGCGACAAGGTCTGATTAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaaataatgttttcatgcttgggagtaatagggtgcttgttcgtgatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAGGAACCCCACCAGATGTTGCTTGTGTTGTGTAGCGACAAGGTCTGATTAC
     taatgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actaactgtgtcagtattctgacaatgttcttactgcaatattgcacaaataatgttttcatgcttgggagtaatagggtgcttgttcgtgatatggcagTTAAAGGTGATAGGACCGGGTGGAAAGCCTGGATCTGATGAACATCACTAGGAACCCCACCAGATGTTGCTTGTGTTGTGTAGCGACAAGGTCTGATTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - -tactgca
- - - - - - - - - - - - - - - - - - - - -ttgcaca