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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgatttcatacgtatgtcttgtaagattaaccaatatgctgtgaacttgaaacggttttattatatattaacgtgtagtggatcatttgttcccgatgtcttgttaccatttaaacaataaccgtttattattctgcttggaacagCTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAG

Basic information

species Physcomitrella patens
transcript PP1S9_386V6.1
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|162275962|gb|FC452030.1|FC452030
EST:     CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAG                         CTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTG
genomic: CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAGgtatgatttc ... cttggaacagCTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTG
EST: gi|100399659|gb|BY972829.1|BY972829
EST:     CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAG                         CTGGTGTATACGTCAAAATGAAGAAGCCCGAATGCTGGAATTAGAGACGCT
genomic: CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAGgtatgatttc ... cttggaacagCTGGTGTATACGTTAAAATGAAGAAGCC-GAATGCTGCAATTAGAGACGCT
EST: gi|100427615|gb|BY977586.1|BY977586
EST:     CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAG                         CTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATT
genomic: CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAGgtatgatttc ... cttggaacagCTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATT
EST: gi|22492231|gb|BU052154.1|BU052154
EST:     CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAG                         CTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTG
genomic: CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAGgtatgatttc ... cttggaacagCTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTG
EST: gi|208347568|gb|DC912827.1|DC912827
EST:     CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAG                         CTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTG
genomic: CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAGgtatgatttc ... cttggaacagCTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTG
EST: gi|100417743|gb|BY975631.1|BY975631
EST:     CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAG                         CTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGNCA-TTAGAGACGCT
genomic: CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAGgtatgatttc ... cttggaacagCTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTG-CAATTAGAGACGCT
EST: gi|67717655|gb|BJ967914.1|BJ967914
EST:     CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAG                         CTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTANAGACGCTG
genomic: CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAGgtatgatttc ... cttggaacagCTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTG
EST: gi|100416732|gb|BY993060.1|BY993060
EST:     CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAG                         CTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTG
genomic: CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAGgtatgatttc ... cttggaacagCTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTG
EST: gi|18348196|gb|BJ180243.1|BJ180243
EST:     CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAG                         CTTGGTGTATACGTTAAA
genomic: CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAGgtatgatttc ... cttggaacagCT-GGTGTATACGTTAAA
EST: gi|100446593|gb|CJ970892.1|CJ970892
EST:     CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAG                         CTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTG
genomic: CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAGgtatgatttc ... cttggaacagCTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTG
EST: gi|162164761|gb|FC340483.1|FC340483
EST:     CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAG                         CTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTG
genomic: CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAGgtatgatttc ... cttggaacagCTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTG
EST: gi|208373792|gb|DC936577.1|DC936577
EST:     CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAG                         CTGGTGTTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCT
genomic: CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAGgtatgatttc ... cttggaacagCTGGTGT-ATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCT
EST: gi|208349326|gb|DC910385.1|DC910385
EST:     CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAG                         CTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTANAGACGCTG
genomic: CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAGgtatgatttc ... cttggaacagCTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTG
EST: gi|208344626|gb|DC912572.1|DC912572
EST:     CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAG                         CTGGTGTATACGTTAAAATGAANAAGCCGAATGCT
genomic: CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAGgtatgatttc ... cttggaacagCTGGTGTATACGTTAAAATGAAGAAGCCGAATGCT
EST: gi|67719577|gb|BJ969836.1|BJ969836
EST:     CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAG                         CTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTG
genomic: CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAGgtatgatttc ... cttggaacagCTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTG
EST: gi|67717904|gb|BJ968163.1|BJ968163
EST:     CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAG                         CTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTG
genomic: CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAGgtatgatttc ... cttggaacagCTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTG
EST: gi|100393447|gb|BY953403.1|BY953403
EST:     CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAG                         CTGGTGTATACGTTNAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTG
genomic: CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAGgtatgatttc ... cttggaacagCTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTG
EST: gi|162249194|gb|FC421537.1|FC421537
EST:     CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAG                         CTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTG
genomic: CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAGgtatgatttc ... cttggaacagCTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTG
EST: gi|208358732|gb|DC942926.1|DC942926
EST:     CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAG                         CTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTG
genomic: CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAGgtatgatttc ... cttggaacagCTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTG
EST: gi|100401417|gb|BY990992.1|BY990992
EST:     CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAG                         CTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTG
genomic: CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAGgtatgatttc ... cttggaacagCTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTG
EST: gi|162150303|gb|FC326388.1|FC326388
EST:     CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAG                         CTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTG
genomic: CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAGgtatgatttc ... cttggaacagCTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTG
EST: gi|208368260|gb|DC935643.1|DC935643
EST:     CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAG                         CTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTANAGACGCTG
genomic: CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAGgtatgatttc ... cttggaacagCTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTG
EST: gi|67704727|gb|BJ964960.1|BJ964960
EST:     CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAG                         CTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTANAGACGCTG
genomic: CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAGgtatgatttc ... cttggaacagCTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTG
EST: gi|67719148|gb|BJ969407.1|BJ969407
EST:     CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAG                         CTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTANAGACGCTG
genomic: CGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAGgtatgatttc ... cttggaacagCTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTG

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), 29 (downstream exon)
Score: 8

GGAAGTTGGAAGAAGCTCTTGAGTATTTTACCGAAGCTATAATCTGCAATCCACATTCAGCAATCCTATTCGCCAACCGAGgtatgatttc ... cttggaacagCTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccgatgtcttgttaccatttaaacaataaccgtttattattctgcttggaacagCTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAG
                        caataac  putative branch site (score: 8)
                                        ttctgctt  putative PPT
                 atttaaacaataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgatttcatacgtatgtcttgtaagattaaccaatatgctgtgaacttgaaacggttttattatatattaacgtgtagtggatcatttgttcccgatgtcttgttaccatttaaacaataaccgtttattattctgcttggaacagCTGGTGTATACGTTAAAATGAAGAAGCCGAATGCTGCAATTAGAGACGCTGATGCTGCTATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT