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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGCTCTGTGAACAGCACTTTTGTGGTGGTGGGAGTTGGCGCAAGGCCACTTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAGgttcgtttcattctcctccataaactatgaggtccatgaacccggacgatatatacctgcaaactcacctcctcgtgtgttcgttaacttgaaatcctga...

Basic information

species Physcomitrella patens
transcript PP1S90_28V6.4
intron # 9
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|162158959|gb|FC334819.1|FC334819
EST:     TTCTGGCTCCTCTGAAGGGTNTGATAGAAGAAGAGAAGGGTGGTTTCAAG                         GTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
genomic: TTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAGgttcgtttca ... ttgttggcagGTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
EST: gi|162166733|gb|FC342702.1|FC342702
EST:     GAAGGGTNTGATAGAAGAAGAGAAGGGTGGTTTCAAG                         GTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
genomic: GAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAGgttcgtttca ... ttgttggcagGTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
EST: gi|162178357|gb|FC355179.1|FC355179
EST:     TTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAG                         GTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
genomic: TTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAGgttcgtttca ... ttgttggcagGTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
EST: gi|37828254|gb|BJ586266.1|BJ586266
EST:     TGATAGAAGAAGAGAAGGGTGGTTTCAAG                         GTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
genomic: TGATAGAAGAAGAGAAGGGTGGTTTCAAGgttcgtttca ... ttgttggcagGTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
EST: gi|162278698|gb|FC454808.1|FC454808
EST:     TTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAG                         GTTGATGCTTCATTC
genomic: TTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAGgttcgtttca ... ttgttggcagGTTGATGCTTCATTC
EST: gi|67696822|gb|BJ957055.1|BJ957055
EST:     TCTGGCTCCTCNTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAG                         GTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
genomic: TCTGGCTCCTC-TGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAGgttcgtttca ... ttgttggcagGTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
EST: gi|162225063|gb|FC401687.1|FC401687
EST:     GAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAG                         GTTGATGCTTCATTCAAAACAAGCAACCNCAATGTGTACGCCGTAGGTGAC
genomic: GAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAGgttcgtttca ... ttgttggcagGTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
EST: gi|37838802|gb|BJ596810.1|BJ596810
EST:     TTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAG                         GTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
genomic: TTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAGgttcgtttca ... ttgttggcagGTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
EST: gi|37852518|gb|BJ610526.1|BJ610526
EST:     TTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAG                         GTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
genomic: TTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAGgttcgtttca ... ttgttggcagGTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
EST: gi|18341461|gb|BJ173496.1|BJ173496
EST:     AAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAG                         GTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
genomic: AAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAGgttcgtttca ... ttgttggcagGTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
EST: gi|37836214|gb|BJ594222.1|BJ594222
EST:     TTTGATAGAAGAAGAGAAGGGTGGTTTCAAG                         GTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
genomic: TTTGATAGAAGAAGAGAAGGGTGGTTTCAAGgttcgtttca ... ttgttggcagGTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
EST: gi|162181159|gb|FC357604.1|FC357604
EST:     TTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAG                         GTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
genomic: TTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAGgttcgtttca ... ttgttggcagGTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
EST: gi|208373118|gb|DC948883.1|DC948883
EST:     TTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAG                         GTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
genomic: TTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAGgttcgtttca ... ttgttggcagGTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
EST: gi|162221160|gb|FC397801.1|FC397801
EST:     TTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAG                         GTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
genomic: TTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAGgttcgtttca ... ttgttggcagGTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
EST: gi|162225064|gb|FC401688.1|FC401688
EST:     TCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTTCA-G                         GTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACG
genomic: TCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTT-CAAGgttcgtttca ... ttgttggcagGTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACG
EST: gi|208387453|gb|DC949238.1|DC949238
EST:     TTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAG                         GTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
genomic: TTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAGgttcgtttca ... ttgttggcagGTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
EST: gi|208392192|gb|DC957271.1|DC957271
EST:     TTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAG                         GTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
genomic: TTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAGgttcgtttca ... ttgttggcagGTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
EST: gi|162278697|gb|FC454807.1|FC454807
EST:     TCTGAAGGGTNTGATAGAAGAAGAGAAGGGTGGTTTCAAG                         GTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
genomic: TCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAGgttcgtttca ... ttgttggcagGTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
EST: gi|37850756|gb|BJ608764.1|BJ608764
EST:     TCTGGCTCCTTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAG                         GTTGATGCTTCATTCAAAACAAGCAACCCCCAATGTGTACGCCGTAGGTGA
genomic: TCTGGCTCC-TCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAGgttcgtttca ... ttgttggcagGTTGATGCTTCATTCAAAACAAGCAA-CCCCAATGTGTACGCCGTAGGTGA
EST: gi|162178358|gb|FC355180.1|FC355180
EST:     TTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAG                         GTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
genomic: TTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAGgttcgtttca ... ttgttggcagGTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
EST: gi|37842364|gb|BJ600372.1|BJ600372
EST:     TTCTGGCTCNTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAG                         GTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
genomic: TTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAGgttcgtttca ... ttgttggcagGTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
EST: gi|18340059|gb|BJ172087.1|BJ172087
EST:     AAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAG                         GTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
genomic: AAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAGgttcgtttca ... ttgttggcagGTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
EST: gi|162237032|gb|FC413191.1|FC413191
EST:     GAAGGGTNTGATAGAAGAAGAGAAGGGTGGTTTCAAG                         GTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
genomic: GAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAGgttcgtttca ... ttgttggcagGTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
EST: gi|162181158|gb|FC357603.1|FC357603
EST:     GGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAG                         GTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
genomic: GGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAGgttcgtttca ... ttgttggcagGTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
EST: gi|37841480|gb|BJ599488.1|BJ599488
EST:     TTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAG                         GTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
genomic: TTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAGgttcgtttca ... ttgttggcagGTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
EST: gi|208378994|gb|DC922840.1|DC922840
EST:     TTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAG                         GTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
genomic: TTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAGgttcgtttca ... ttgttggcagGTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
EST: gi|162221161|gb|FC397802.1|FC397802
EST:     TTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAG                         GTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
genomic: TTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAGgttcgtttca ... ttgttggcagGTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
EST: gi|37824881|gb|BJ582947.1|BJ582947
EST:     TTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAG                         GTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
genomic: TTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAGgttcgtttca ... ttgttggcagGTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
EST: gi|208395391|gb|DC919967.1|DC919967
EST:     TTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAG                         GTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC
genomic: TTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAGgttcgtttca ... ttgttggcagGTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGAC

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: 34 (upstream exon), 34 (downstream exon)
Score: 60

AAGCTCTGTGAACAGCACTTTTGTGGTGGTGGGAGTTGGCGCAAGGCCACTTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAGgttcgtttca ... ttgttggcagGTTGATGCTTCATTCAAAACAAGCAACCCCAATGTGTACGCCGTAGGTGACATTGCAACATTCCCAATGAAGATGTATGGTGATAGCCGGCGAGTGGAGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGCTCTGTGAACAGCACTTTTGTGGTGGTGGGAGTTGGCGCAAGGCCACTTCTGGCTCCTCTGAAGGGTTTGATAGAAGAAGAGAAGGGTGGTTTCAAGgttcgtttcattctcctccataaactatgaggtccatgaacccggacgatatatacctgcaaactcacctcctcgtgtgttcgttaacttgaaatcctga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA