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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttctagcaattgtataacgcgcatctgcatttggtgcggcacttgtggacggttctgctagatgttctcctacatgtttgctgcatgaaacaatctcatctaacgctctttaaatcttattatttgtacagCCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCATCCTAAATTTAAAAGAAAAGGCGATGATTTGTTTGTGGAGCACAGTTTGA

Basic information

species Physcomitrella patens
transcript PP1S342_16V6.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S342_16V6.1 (Physcomitrella patens), 3'ss of exon 5
lower sequence: GRMZM2G118731_T01 (Zea mays), 3'ss of exon 6
gtatgttctagcaattgtataacgcgcatctgcatttggtgcggcacttgtggacggttctgctagatgttctcctacatgtttgctgcatgaaacaatctcatctaacgctctttaaatcttattatttgtacagCCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCATCCTAAATTTAAAAGAAAAGGCGATGATTTGTTTGTGGAGCACAGTTTGA
                                      ||| | | ||  |  || |||    || |  | |    |||| | |||  | |   |  |||| |||||| |   |||  || ||     || | |||||||| ||| | ||||| ||||| || |||||||||||| | ||||| ||||| |||||||| || |    |||||| || | ||| |||||||   |  
--------------------------------------gtgagtctctgtt--acagtt----tacacatgcatgcacatatctgcatcctatcagtatct-atctaatg---tttggattttcgctctttt-cagCCTGATACGGTTACAGGAGACATTGTTTTTGTCTTGCAACTTAAAGACCATCCAAAATTTAAGAGGATGTACGATGACTTATATGTTGAGCACACAATCT
















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|162279815|gb|FC455099.1|FC455099
EST:     GAATGGCGCATGGGCAGAAAATTACTTTCCAAGGCGAAGCTGATGAAGCG                         CCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
genomic: GAATGGCGCATGGGCAGAAAATTACTTTCCAAGGCGAAGCTGATGAAGCGgtatgttcta ... atttgtacagCCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
EST: gi|100401219|gb|BY990892.1|BY990892
EST:     GAATGGCGCATGGGCAGAAAATTACTTTCCAAGGCGAAGCTGATGAAGCG                         CCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
genomic: GAATGGCGCATGGGCAGAAAATTACTTTCCAAGGCGAAGCTGATGAAGCGgtatgttcta ... atttgtacagCCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
EST: gi|100414304|gb|BY992711.1|BY992711
EST:     GAATGGCGCATGGGCAGAAAATTACTTTCCAAGGCGAAGCTGATGAAGCG                         CCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
genomic: GAATGGCGCATGGGCAGAAAATTACTTTCCAAGGCGAAGCTGATGAAGCGgtatgttcta ... atttgtacagCCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
EST: gi|19778134|gb|BQ039262.1|BQ039262
EST:     GAATGGCGCATGGGCAGAAAATTACTTTCCAAGGCGAAGCTGATGAAGCG                         CCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
genomic: GAATGGCGCATGGGCAGAAAATTACTTTCCAAGGCGAAGCTGATGAAGCGgtatgttcta ... atttgtacagCCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
EST: gi|37840753|gb|BJ598761.1|BJ598761
EST:     GAATGGCGCATGGGCAGAAAATTACTTTCCAAGGCGAAGCTGATGAAGCG                         CCTGACACGATCCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCA
genomic: GAATGGCGCATGGGCAGAAAATTACTTTCCAAGGCGAAGCTGATGAAGCGgtatgttcta ... atttgtacagCCTGACACGAT-CACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCA
EST: gi|162219007|gb|FC395200.1|FC395200
EST:     GAATGACGCATGGGCAGAAGATTACTTTCCAAGGCGAAGCTGATGAAGCG                         CCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
genomic: GAATGGCGCATGGGCAGAAAATTACTTTCCAAGGCGAAGCTGATGAAGCGgtatgttcta ... atttgtacagCCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
EST: gi|162191909|gb|FC366914.1|FC366914
EST:     GAATGACGCATGGGCAGAAGATTACTTTCCAAGGCGAAGCTGATGAAGCG                         CCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
genomic: GAATGGCGCATGGGCAGAAAATTACTTTCCAAGGCGAAGCTGATGAAGCGgtatgttcta ... atttgtacagCCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
EST: gi|162152417|gb|FC327980.1|FC327980
EST:     CCAAGGCGAAGCTGATGAAGCG                         CCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
genomic: CCAAGGCGAAGCTGATGAAGCGgtatgttcta ... atttgtacagCCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
EST: gi|162189947|gb|FC365611.1|FC365611
EST:     GAATGACGCATGGGCAGAAGATTACTTTCCAAGGCGAAGCTGATGAAGCG                         CCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
genomic: GAATGGCGCATGGGCAGAAAATTACTTTCCAAGGCGAAGCTGATGAAGCGgtatgttcta ... atttgtacagCCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
EST: gi|162177365|gb|FC352898.1|FC352898
EST:     GAATGACGCATGGGCAGAAGATTACTTTCCAAGGCGAAGCTGATGAAGCG                         CCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
genomic: GAATGGCGCATGGGCAGAAAATTACTTTCCAAGGCGAAGCTGATGAAGCGgtatgttcta ... atttgtacagCCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
EST: gi|19790827|gb|BQ042076.1|BQ042076
EST:     GAATGGCGCATGGGCAGAAAATTACTTTCCAAGGCGAAGCTGATGAAGCG                         CCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
genomic: GAATGGCGCATGGGCAGAAAATTACTTTCCAAGGCGAAGCTGATGAAGCGgtatgttcta ... atttgtacagCCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
EST: gi|208381223|gb|DC919914.1|DC919914
EST:     AAGGCGAAGCTGATGAAGCG                         CCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
genomic: AAGGCGAAGCTGATGAAGCGgtatgttcta ... atttgtacagCCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
EST: gi|162152418|gb|FC327981.1|FC327981
EST:     GAATGACGCATGGGCAGAAGATTACTTTCCAAGGCGAAGCTGATGAAGCG                         CCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
genomic: GAATGGCGCATGGGCAGAAAATTACTTTCCAAGGCGAAGCTGATGAAGCGgtatgttcta ... atttgtacagCCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
EST: gi|7207505|gb|AW561505.1|AW561505
EST:     GAATGGCGCATGGGCAGAAAATTACTTTCCAAGGCGAAGCTGATGAAGCG                         CCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
genomic: GAATGGCGCATGGGCAGAAAATTACTTTCCAAGGCGAAGCTGATGAAGCGgtatgttcta ... atttgtacagCCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
EST: gi|162191908|gb|FC366913.1|FC366913
EST:     GAATGACGCATGGGCAGAAGATTACTTTCCAAGGCGAAGCTGATGAAGCG                         CCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
genomic: GAATGGCGCATGGGCAGAAAATTACTTTCCAAGGCGAAGCTGATGAAGCGgtatgttcta ... atttgtacagCCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
EST: gi|162195908|gb|FC375641.1|FC375641
EST:     GAATGACGCATGGGCAGAAGATTACTTTCCAAGGCGAAGCTGATGAAGCG                         CCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
genomic: GAATGGCGCATGGGCAGAAAATTACTTTCCAAGGCGAAGCTGATGAAGCGgtatgttcta ... atttgtacagCCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
EST: gi|162157608|gb|FC332930.1|FC332930
EST:     GAATGACGCATGGGCAGAAGATTACTTTCCAAGGCGAAGCTGATGAAGCG                         CCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
genomic: GAATGGCGCATGGGCAGAAAATTACTTTCCAAGGCGAAGCTGATGAAGCGgtatgttcta ... atttgtacagCCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
EST: gi|208382913|gb|DC928338.1|DC928338
EST:     GAATGGCGCATGGGCAGAAAATTACTTTCCAAGGCGAAGCTGATGAAGCG                         CCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
genomic: GAATGGCGCATGGGCAGAAAATTACTTTCCAAGGCGAAGCTGATGAAGCGgtatgttcta ... atttgtacagCCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
EST: gi|162185740|gb|FC362088.1|FC362088
EST:     GAATGACGCATGGGCAGAAGATTACTT-CCA-GGCGTAGCTGATGAAGCG                         CCTGACACGATCACAGGCGACATCGTC
genomic: GAATGGCGCATGGGCAGAAAATTACTTTCCAAGGCGAAGCTGATGAAGCGgtatgttcta ... atttgtacagCCTGACACGATCACAGGCGACATCGTC
EST: gi|208360138|gb|DC950167.1|DC950167
EST:     GCGAAGCTGATGAAGCG                         CCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
genomic: GCGAAGCTGATGAAGCGgtatgttcta ... atttgtacagCCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
EST: gi|162242593|gb|FC414984.1|FC414984
EST:     CGCATGGGCAGAAGATTACTTTCCAAGGCGAAGCTGATGAAGCG                         CCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
genomic: CGCATGGGCAGAAAATTACTTTCCAAGGCGAAGCTGATGAAGCGgtatgttcta ... atttgtacagCCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
EST: gi|208358989|gb|DC957737.1|DC957737
EST:     GAATGGCGCATGGGCAGAAAATTACTTTCCAAGGCGAAGCTGATGAAGCG                         CCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
genomic: GAATGGCGCATGGGCAGAAAATTACTTTCCAAGGCGAAGCTGATGAAGCGgtatgttcta ... atttgtacagCCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
EST: gi|162254102|gb|FC429626.1|FC429626
EST:     GAATGACGCATGGGCAGAAGATTACTTTCCAAGGCGAAGCTGATGAAGCG                         CCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
genomic: GAATGGCGCATGGGCAGAAAATTACTTTCCAAGGCGAAGCTGATGAAGCGgtatgttcta ... atttgtacagCCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
EST: gi|162162054|gb|FC338845.1|FC338845
EST:     GAATGACGCATGGGCAGAAGATTACTTTCCAAGGCGAAGCTGATGAAGCG                         CCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT
genomic: GAATGGCGCATGGGCAGAAAATTACTTTCCAAGGCGAAGCTGATGAAGCGgtatgttcta ... atttgtacagCCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCAT

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), 35 (downstream exon)
Score: 64

ACAAAAGGTTGTGCAGGATAAGAAATTGTTGGAAGTGCATGTCGAGAAAGGAATGGCGCATGGGCAGAAAATTACTTTCCAAGGCGAAGCTGATGAAGCGgtatgttcta ... atttgtacagCCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCATCCTAAATTTAAAAGAAAAGGCGATGATTTGTTTGTGGAGCACAGTTTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgctgcatgaaacaatctcatctaacgctctttaaatcttattatttgtacagCCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCATCCTAAATTTAAAAGAAAAGGCGATGATTTGTTTGTGGAGCACAGTTTGA
                     atctaac  putative branch site (score: 64)
                              tctttaaatcttatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttctagcaattgtataacgcgcatctgcatttggtgcggcacttgtggacggttctgctagatgttctcctacatgtttgctgcatgaaacaatctcatctaacgctctttaaatcttattatttgtacagCCTGACACGATCACAGGCGACATCGTCTTTGTCTTGCAATTGAAAGAGCATCCTAAATTTAAAAGAAAAGGCGATGATTTGTTTGTGGAGCACAGTTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA