Skip to another splice site:
1  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcgtcgagatgggaatgcggcggtcgcgatgttcctgaaattgggtcgattccggccccttacgacggcagctgacgcttggccatgaatgtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGCTCAAGGCCAACCCCGGCATCTGCACGTACATGGAGCCCTCCCTGAACGT

Basic information

species Physcomitrella patens
transcript PP1S463_8V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S463_13V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ34147 (Selaginella moellendorffii), 3'ss of exon 1
-----gcgtcgagatgggaatgcggcggtcgcgatgttcctga---aattgggtcgattccggccccttacgacggcagctgacgctt-----------ggccatgaatgtcgat----------gcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGCTCAAGGCCAACCCCGGCATCTGCACGTACATGGAGCCCTCCCTGAACGT
      | || |     | ||||  ||||| ||   ||||      |  | |    ||  ||   | |     |      |  |||||           | || || || ||| |          |||||||||| ||| || ||    ||| | ||  | | |||    |||||| | |||||||||||||| || || ||||||||||||||| | || ||| ||||
gtaagtcctccaccctcggatgcc-cggtcccggcattccccgctcacgtagaaaaatctcgtttcttcgtagcaaagcttctcgcttctgatcacgtcgtccctggatttcgtttctgcgcattgcagGTGACAGGTCAGGCATAAAAAAGAGACATTTTTACCTGGACGAGGAGATCCTCAAGGCCAACCCGGGGATGTGCACGTACATGGAGGCGTCGCTGGACGT
















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|18358677|gb|BJ190736.1|BJ190736
EST:     CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCT                         GTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCAC
genomic: CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCAC
EST: gi|208374526|gb|DC940743.1|DC940743
EST:     CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCT                         GTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
genomic: CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
EST: gi|100448466|gb|CJ972765.1|CJ972765
EST:     CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCT                         GTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
genomic: CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
EST: gi|100354483|gb|BY983441.1|BY983441
EST:     CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCT                         GTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
genomic: CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
EST: gi|208392531|gb|DC938524.1|DC938524
EST:     CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCT                         GTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
genomic: CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
EST: gi|100372540|gb|BY985648.1|BY985648
EST:     CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCT                         GTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
genomic: CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
EST: gi|100442420|gb|BY963114.1|BY963114
EST:     ACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAAATTCA-GCGCATCT                         GTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
genomic: ACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAA-TTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
EST: gi|100449581|gb|CJ973831.1|CJ973831
EST:     CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCT                         GTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
genomic: CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
EST: gi|100392555|gb|BY971768.1|BY971768
EST:     CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCT                         GTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
genomic: CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
EST: gi|18345192|gb|BJ177233.1|BJ177233
EST:     CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCT                         GTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCA
genomic: CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCA
EST: gi|100353119|gb|BY945615.1|BY945615
EST:     CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCT                         GTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
genomic: CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
EST: gi|100396679|gb|BY953773.1|BY953773
EST:     CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCT                         GTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
genomic: CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
EST: gi|67572532|gb|BJ945356.1|BJ945356
EST:     CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCT                         GTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
genomic: CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
EST: gi|208376076|gb|DC906763.1|DC906763
EST:     CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCT                         GTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
genomic: CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
EST: gi|100361037|gb|BY946882.1|BY946882
EST:     CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCT                         GTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
genomic: CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
EST: gi|100417833|gb|BY975676.1|BY975676
EST:     CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCT                         GTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
genomic: CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
EST: gi|208359234|gb|DC939057.1|DC939057
EST:     CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCT                         GTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
genomic: CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
EST: gi|100407765|gb|BY955767.1|BY955767
EST:     CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCT                         GTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
genomic: CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
EST: gi|100430823|gb|BY978415.1|BY978415
EST:     CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCT                         GTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAAGTGC
genomic: CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
EST: gi|100401342|gb|BY990954.1|BY990954
EST:     CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCT                         GTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
genomic: CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
EST: gi|208371018|gb|DC931520.1|DC931520
EST:     CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCT                         GTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
genomic: CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
EST: gi|208361778|gb|DC935018.1|DC935018
EST:     CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCT                         GTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
genomic: CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
EST: gi|100445631|gb|CJ969930.1|CJ969930
EST:     CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCT                         GTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
genomic: CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
EST: gi|100441949|gb|BY981172.1|BY981172
EST:     ACCAACTGCGGCGAGAAGGACGCCCCTGGAGGCCAAATTCAAGCGCATCT                         GTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
genomic: ACCAACTGCGGCGAGAAGGACGCCC-TGAAGGCCAAATTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
EST: gi|208353969|gb|DC930109.1|DC930109
EST:     CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCTAAATTCAAGCGCATCT                         GTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
genomic: CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
EST: gi|100440710|gb|BY980530.1|BY980530
EST:     CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCT                         GTGACAAGTCGGGGATCGGCAAGCGCCACATGTTCCTCACGGAGGAGGT
genomic: CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGT
EST: gi|100427391|gb|BY959124.1|BY959124
EST:     CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCT                         GTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
genomic: CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
EST: gi|208377214|gb|DC932364.1|DC932364
EST:     CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCT                         GTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
genomic: CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
EST: gi|18361347|gb|BJ193413.1|BJ193413
EST:     CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCT                         GTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCAC
genomic: CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCAC
EST: gi|18368514|gb|BJ200599.1|BJ200599
EST:     CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCT                         GTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGG
genomic: CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGG
EST: gi|100384238|gb|BY969369.1|BY969369
EST:     CCAAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAAATTCA-GCGCATCT                         GTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
genomic: CCAA-CTGCGGCGAGAAGGACGCCCTGAAGGCCAAA-TTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
EST: gi|208373390|gb|DC941029.1|DC941029
EST:     CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCT                         GTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
genomic: CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
EST: gi|100397256|gb|BY972408.1|BY972408
EST:     CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCT                         GTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC
genomic: CACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGC

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-Seq library.


Block sizes: 35 (upstream exon), 30 (downstream exon)
Score: 26

CCTCCCGCGGAGTTCCTGCAGAGCGAGTACCCCGACTTCTTCTTCAACATCACCAACTGCGGCGAGAAGGACGCCCTGAAGGCCAAATTCAAGCGCATCTgtaagtccac ... gtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGCTCAAGGCCAACCCCGGCATCTGCACGTACATGGAGCCCTCCCTGAACGT































 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcgattccggccccttacgacggcagctgacgcttggccatgaatgtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGCTCAAGGCCAACCCCGGCATCTGCACGTACATGGAGCCCTCCCTGAACGT
                        agctgac  putative branch site (score: 26)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcgtcgagatgggaatgcggcggtcgcgatgttcctgaaattgggtcgattccggccccttacgacggcagctgacgcttggccatgaatgtcgatgcagGTGACAAGTCGGGGATCCGCAAGCGCCACATGTTCCTCACGGAGGAGGTGCTCAAGGCCAACCCCGGCATCTGCACGTACATGGAGCCCTCCCTGAACGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA