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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatttatttgaccatttcacaactttcatgatcttcttttctgtgtatgttgcgtttctctagttacgtcaatctgctgtcatatagagtaagcggccgcgaatgtaatatgttatccagGTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACCATGGAGGACATTCTTGTGGAGCTCAAGAAACAGATGGCTAATCCGGCTA

Basic information

species Physcomitrella patens
transcript PP1S60_129V6.1
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|162211928|gb|FC387800.1|FC387800
EST:     GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTG                         GTTGATCCGAGATACTTCCCCTTGCTGGCAAATTGGCGTCGTAATCACACC
genomic: GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTGgtaagattta ... tgttatccagGTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
EST: gi|7584254|gb|AW700150.1|AW700150
EST:     GATTCCACTCCCGAATCAATATGACTGATGTGAACTCAGAGACAGGATTG                         GTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
genomic: GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTGgtaagattta ... tgttatccagGTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
EST: gi|162271334|gb|FC447219.1|FC447219
EST:     GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTG                         GTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
genomic: GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTGgtaagattta ... tgttatccagGTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
EST: gi|22132526|gb|BQ827212.1|BQ827212
EST:     GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTG                         GTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
genomic: GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTGgtaagattta ... tgttatccagGTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
EST: gi|22132462|gb|BQ827175.1|BQ827175
EST:     GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTG                         GTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
genomic: GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTGgtaagattta ... tgttatccagGTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
EST: gi|162271333|gb|FC447218.1|FC447218
EST:     GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTG                         GTTGATCCGAGATACTTCCCCTTACTGGCAAATGGGCGTCGTAATCACACC
genomic: GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTGgtaagattta ... tgttatccagGTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
EST: gi|162240765|gb|FC417475.1|FC417475
EST:     GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTG                         GTTGATCCGAGATACTTCCCCTTGCTGGCAAATTGGCGTCGTAATCACACC
genomic: GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTGgtaagattta ... tgttatccagGTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
EST: gi|67574644|gb|BJ947468.1|BJ947468
EST:     GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTG                         GTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
genomic: GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTGgtaagattta ... tgttatccagGTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
EST: gi|15729419|gb|BI741306.1|BI741306
EST:     GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTG                         GTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
genomic: GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTGgtaagattta ... tgttatccagGTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
EST: gi|162224222|gb|FC399494.1|FC399494
EST:     GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTG                         GTTGATCCGAGATACTTCCCCTTGCTGGCAAATTGGCGTCGTAATCACACC
genomic: GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTGgtaagattta ... tgttatccagGTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
EST: gi|67571600|gb|BJ944424.1|BJ944424
EST:     GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTG                         GTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
genomic: GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTGgtaagattta ... tgttatccagGTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
EST: gi|67694950|gb|BJ955183.1|BJ955183
EST:     GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTG                         GTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
genomic: GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTGgtaagattta ... tgttatccagGTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
EST: gi|22492518|gb|BU052441.1|BU052441
EST:     GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTG                         GTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
genomic: GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTGgtaagattta ... tgttatccagGTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
EST: gi|7584264|gb|AW700160.1|AW700160
EST:     GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTG                         GTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
genomic: GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTGgtaagattta ... tgttatccagGTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
EST: gi|162227636|gb|FC402629.1|FC402629
EST:     GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTG                         GTTGATCCGAGATACTTCCCCTTGCTGGCAAATTGGCGTCGTAATCACACC
genomic: GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTGgtaagattta ... tgttatccagGTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
EST: gi|67698060|gb|BJ958293.1|BJ958293
EST:     GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTG                         GTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
genomic: GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTGgtaagattta ... tgttatccagGTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
EST: gi|18371364|gb|BJ202966.1|BJ202966
EST:     GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTG                         GTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
genomic: GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTGgtaagattta ... tgttatccagGTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
EST: gi|162227635|gb|FC402628.1|FC402628
EST:     GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTG                         GTTGATCCGAGATACTTCCCCTTGCTGGCAAATTGGCGTTGTAATCACACC
genomic: GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTGgtaagattta ... tgttatccagGTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
EST: gi|22492562|gb|BU052478.1|BU052478
EST:     GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTG                         GTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
genomic: GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTGgtaagattta ... tgttatccagGTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
EST: gi|18329558|gb|BJ161564.1|BJ161564
EST:     GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTG                         GTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
genomic: GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTGgtaagattta ... tgttatccagGTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
EST: gi|18346800|gb|BJ178845.1|BJ178845
EST:     GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTG                         GTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
genomic: GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTGgtaagattta ... tgttatccagGTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
EST: gi|37851532|gb|BJ609540.1|BJ609540
EST:     GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTG                         GTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC
genomic: GATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTGgtaagattta ... tgttatccagGTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACC

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: 24

ATTGAAGTTATTTTGCGACAAGGACTATCCCGACAAGCCTCCAACTGTTAGATTCCACTCCCGAATCAATATGACTCATGTGAACTCAGAGACAGGATTGgtaagattta ... tgttatccagGTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACCATGGAGGACATTCTTGTGGAGCTCAAGAAACAGATGGCTAATCCGGCTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acgtcaatctgctgtcatatagagtaagcggccgcgaatgtaatatgttatccagGTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACCATGGAGGACATTCTTGTGGAGCTCAAGAAACAGATGGCTAATCCGGCTA
                                    aatgtaatatgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatttatttgaccatttcacaactttcatgatcttcttttctgtgtatgttgcgtttctctagttacgtcaatctgctgtcatatagagtaagcggccgcgaatgtaatatgttatccagGTTGATCCGAGATACTTCCCCTTACTGGCAAATTGGCGTCGTAATCACACCATGGAGGACATTCTTGTGGAGCTCAAGAAACAGATGGCTAATCCGGCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG