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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagctcagttacttatttttgtttgcttttcctttttctttttctttaaaaaaaaaaatcatagtaatgtatccgtgtgtggggataatcagctttattgtattataaatgattgactaatggtattattgttccatcagGCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACAT

Basic information

species Physcomitrella patens
transcript PP1S215_25V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S215_25V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GLYMA06G13720.1 (Glycine max), 3'ss of exon 5
gtgagctcagttacttatttttgtttgcttttcctttttctttttctttaaaaaaaaaaatcatagtaatgtatccgtgtgtggggataatcagctttattgtattataaatgattgactaatggtattattgttccatcagGCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACAT
                          |   |  | || | || |||||   |||  |  || ||    |  | | |  |||     ||| | |  || ||   || ||  ||  ||  || ||               |||||| |||||||| ||||| ||| |||||||||| ||||| || |  || || |||||||||||||||||
--------------------------gtactgtcattatattcttctt---aaatgattataatgcacaaattttctagtgactttatattaactttcatctcatcatgtat--ttatctgatt--------------tcagGCCATCATGGCTGAAGGTAAACAGCATGCTCTTGCTATTGGCTTTACAAAAATGTCTGCAAAAGACAT
















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|208376363|gb|DC932273.1|DC932273
EST:     CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTG                         GCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
genomic: CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTGgtgagctcag ... gttccatcagGCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
EST: gi|18356615|gb|BJ188674.1|BJ188674
EST:     CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTG                         GCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
genomic: CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTGgtgagctcag ... gttccatcagGCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
EST: gi|208345629|gb|DC909299.1|DC909299
EST:     CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTG                         GCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
genomic: CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTGgtgagctcag ... gttccatcagGCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
EST: gi|162259779|gb|FC436759.1|FC436759
EST:     CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTG                         GCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
genomic: CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTGgtgagctcag ... gttccatcagGCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
EST: gi|208363408|gb|DC947006.1|DC947006
EST:     AGTGCCTGCAGATTCACCTGTG                         GCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
genomic: AGTGCCTGCAGATTCACCTGTGgtgagctcag ... gttccatcagGCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
EST: gi|18343486|gb|BJ175524.1|BJ175524
EST:     CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTG                         GCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
genomic: CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTGgtgagctcag ... gttccatcagGCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
EST: gi|22132705|gb|BQ827296.1|BQ827296
EST:     CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTG                         GCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
genomic: CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTGgtgagctcag ... gttccatcagGCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
EST: gi|18357148|gb|BJ189207.1|BJ189207
EST:     CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTG                         GCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATA
genomic: CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTGgtgagctcag ... gttccatcagGCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATA
EST: gi|208371667|gb|DC932496.1|DC932496
EST:     CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTG                         GCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
genomic: CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTGgtgagctcag ... gttccatcagGCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
EST: gi|162259765|gb|FC436758.1|FC436758
EST:     CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTG                         GCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
genomic: CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTGgtgagctcag ... gttccatcagGCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
EST: gi|162221749|gb|FC397081.1|FC397081
EST:     CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTG                         GCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
genomic: CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTGgtgagctcag ... gttccatcagGCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
EST: gi|67578005|gb|BJ950172.1|BJ950172
EST:     CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTG                         GCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
genomic: CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTGgtgagctcag ... gttccatcagGCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
EST: gi|37822681|gb|BJ580747.1|BJ580747
EST:     CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTG                         GCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
genomic: CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTGgtgagctcag ... gttccatcagGCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
EST: gi|208365150|gb|DC946779.1|DC946779
EST:     CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTG                         GCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
genomic: CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTGgtgagctcag ... gttccatcagGCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
EST: gi|22492644|gb|BU052567.1|BU052567
EST:     CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTG                         GCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
genomic: CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTGgtgagctcag ... gttccatcagGCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
EST: gi|208354986|gb|DC914250.1|DC914250
EST:     CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTG                         GCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
genomic: CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTGgtgagctcag ... gttccatcagGCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
EST: gi|162228094|gb|FC404649.1|FC404649
EST:     CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTG                         GCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
genomic: CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTGgtgagctcag ... gttccatcagGCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
EST: gi|208382460|gb|DC927994.1|DC927994
EST:     CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTG                         GCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
genomic: CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTGgtgagctcag ... gttccatcagGCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
EST: gi|7584206|gb|AW700103.1|AW700103
EST:     GCAGATTCACCTGTG                         GCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
genomic: GCAGATTCACCTGTGgtgagctcag ... gttccatcagGCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
EST: gi|208395953|gb|DC915713.1|DC915713
EST:     CATCTGCTGGTGGTNATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTG                         GCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
genomic: CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTGgtgagctcag ... gttccatcagGCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
EST: gi|18350245|gb|BJ182296.1|BJ182296
EST:     CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTG                         GCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
genomic: CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTGgtgagctcag ... gttccatcagGCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
EST: gi|67693833|gb|BJ954066.1|BJ954066
EST:     CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTG                         GCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
genomic: CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTGgtgagctcag ... gttccatcagGCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
EST: gi|208382492|gb|DC923162.1|DC923162
EST:     CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTG                         GCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
genomic: CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTGgtgagctcag ... gttccatcagGCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
EST: gi|18332428|gb|BJ164441.1|BJ164441
EST:     CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTG                         GCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
genomic: CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTGgtgagctcag ... gttccatcagGCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
EST: gi|162221748|gb|FC397080.1|FC397080
EST:     CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTG                         GCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG
genomic: CATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTGgtgagctcag ... gttccatcagGCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAG

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: 26 (upstream exon), 33 (downstream exon)
Score: 10

AGCTATCAAATTTGTGCTGGCGGGTGCCAATATCATGTGCCCGGGACTGACATCTGCTGGTGGTAATCTCGATGAAGAAGTGCCTGCAGATTCACCTGTGgtgagctcag ... gttccatcagGCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatcagctttattgtattataaatgattgactaatggtattattgttccatcagGCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACAT
                             gactaat  putative branch site (score: 10)
                                           ttgttcc  putative PPT
        tttattgtattataaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagctcagttacttatttttgtttgcttttcctttttctttttctttaaaaaaaaaaatcatagtaatgtatccgtgtgtggggataatcagctttattgtattataaatgattgactaatggtattattgttccatcagGCAATCATGGCAGAAGGCAAAGAGCATGCTCTGGCTATAGGATACACCAAGATGTCTGCAAAAGACAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG