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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttcattagctttatgtgtgagaagttggagattgagttttcttgataaacgaaattcttttgatcgcttgttttggtttcttttaatgatctctgcagATTCATACTTCTAGAATGACTATGGCTGATGATGTAAACCTAGAGGAGTTTGTGATGACCAAAGATGAGTTTTCTGGTGCTGACATTAAAGCTATCTGTA

Basic information

species Physcomitrella patens
transcript PP1S109_234V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 3'ss of exon 4
tcttcattagctttatgtgtgagaagttggagattgagttttcttgataaacgaaattcttttgatcgcttgttttggtttcttttaatgatctctgcagATTCATACTTCTAGAATGACTATGGCTGATGATGTAAACCTAGAGGAGTTTGTGATGACCAAAGATGAGTTTTCTGGTGCTGACATTAAAGCTATCTGTA
           |   | | |   | |||  |  ||  || || |||  || |    |  || | |||  | ||||| |  |               |||||| || || ||||  |||||  |||| |||||||| |||||||| ||||||||||||||||| ||||||||||||||||||||||| ||||| || ||||
----------gtgcttttctacaatgtttcaagttctgtcttattggaaacctgcttcgttcttatcaatagtttttgggt---------------gcagATACACACATCTAAGATGACATTGGCAGATGATGTTAACCTAGAAGAGTTTGTGATGACCAAGGATGAGTTTTCTGGTGCTGACATCAAAGCAATATGTA

upper sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: LOC_Os07g49150.1 (Oryza sativa), 3'ss of exon 3
-----tcttcattagctttatgtgtgagaagttggagattgagttttcttgataaacgaaattcttttgatcgcttgttttggtttcttttaatgatctctgcagATTCATACTTCTAGAATGACTATGGCTGATGATGTAAACCTAGAGGAGTTTGTGATGACCAAAGATGAGTTTTCTGGTGCTGACATTAAAGCTATCTGTA
     | | ||||||   ||| | | |||| ||    ||  |   |   |||||| |  | ||| |||| |  ||  |    |||        |||    ||||||| || || ||||  |||||  |||| |||||||| ||||| || |||||||| |||||||| ||||||||||| |||||||| || ||||| || ||||
gtaaatatccattag---tatcttttagaacttcagaatgcatgataactgataagc--agttcctttggtt-ctcatgaatgtt-------gtgaatcgtgcagATACACACATCTAAGATGACATTGGCAGATGATGTGAACCTGGAAGAGTTTGTCATGACCAAGGATGAGTTTTCCGGTGCTGATATCAAAGCAATATGTA

upper sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G104373_T01 (Zea mays), 3'ss of exon 4
tcttcattagctttatgtg-tgagaagttggagattgagttttcttgataaacgaaattcttttgatcgcttgttttggtttcttttaatgatctctgcagATTCATACTTCTAGAATGACTATGGCTGATGATGTAAACCTAGAGGAGTTTGTGATGACCAAAGATGAGTTTTCTGGTGCTGACATTAAAGCTATCTGTA
       |   | |||||| ||| |  ||     |   ||| | || || ||  |   |  |||| | | |        ||| |||| ||||     |||||| || || || | ||||||  |||||||||||||||||||||| |||||| | ||| | |||||||||||||| ||||||||||| || || || ||||
------gtgcttctatgtgatgaaagcttctgagtcctgttcttttaattaaaaagcatgatttg-ttgttaccaaaattttgttttgatga-----gcagATACACACATCGAAAATGACACTGGCTGATGATGTAAACCTAGAAGAGTTTATTATGTCAAAAGATGAGTTTTCAGGTGCTGACATCAAGGCCATTTGTA

upper sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G095593_T01 (Zea mays), 3'ss of exon 3
tcttcattagctttatgtgtgagaagttggagattgagttttcttgataaacgaaattcttttgatcgcttgttttggtttcttttaatgatctctgcagATTCATACTTCTAGAATGACTATGGCTGATGATGTAAACCTAGAGGAGTTTGTGATGACCAAAGATGAGTTTTCTGGTGCTGACATTAAAGCTATCTGTA
       ||   | | || ||  ||     | |||  |  ||    ||   |  ||| |  ||  |  ||| || | |    || |||  |  | ||||||| || || || | ||||||  | ||||||||||| ||| | || |||||||| ||||||||||| |||||||| |||||||| ||||| || ||||| |
------gtactgtgacgtctgtaaatgataatattt-gcattaacaatgttcttaataccctttgtt-cttattatagaaggttgtaa--acttgtgcagATACACACATCGAAAATGACATTAGCTGATGATGTGAACTTGGAAGAGTTTGTTATGACCAAAGACGAGTTTTCGGGTGCTGATATTAAGGCAATCTGCA

upper sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G056569_T01 (Zea mays), 3'ss of exon 3
tcttcattagctttatgtgtgagaagttggagattgagttttcttgataaacgaaattcttttgatcgcttgttttggtttcttttaatgatctctgcagATTCATACTTCTAGAATGACTATGGCTGATGATGTAAACCTAGAGGAGTTTGTGATGACCAAAGATGAGTTTTCTGGTGCTGACATTAAAGCTATCTGTA
  | |  || |   || |||    |||   | |||  |  || |  ||   || ||| | |||     ||| |  ||     | | ||    |  |||||||||| || || | ||||||  | ||||| ||||| ||| | || |||||||| ||||||||||||||||| || || ||||| ||||| || ||||| |
-gtgctgtaac---atctgtagacagt--aatattt-gcattatcaatgttcgtaatacctttttgtccttataatgaaggttgtaaa----ccgtgcagATTCACACATCAAAAATGACATTAGCTGACGATGTGAACTTGGAAGAGTTTGTTATGACCAAAGATGAGTTCTCGGGCGCTGATATTAAGGCCATCTGCA

upper sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA19G35510.1 (Glycine max), 3'ss of exon 4
tcttcattagctttatgtgtgagaagttggagattgagttttcttgataaa-cgaaattcttttgatc-gcttgttttggtttcttttaatgatctc------------tgcagATTCATACTTCTAGAATGACTATGGCTGATGATGTAAACCTAGAGGAGTTTGTGATGACCAAAGATGAGTTTTCTGGTGCTGACATTAAAGCTATCTGTA
     | |  ||   | ||||| ||  ||    |||  |||   ||| | | |  |||  |  |  ||  |||  ||   | ||  | || | |||             |  |||| |||||||| || |||||  | ||||||||||| ||| |||| || ||||| ||||| || |||||||| ||||| ||||| || ||||| || ||||
gtcggaatgactagttctgtgaaaacatgttt-ttggttttcactgacatatcttaatattcctattctacttagttatatctcactaaaaggtcttatacttttgatatttagATACATACTTCAAGGATGACATTAGCTGATGATGTCAACTTAGAAGAATTTGTTATGACTAAGGATGAGTTCTCTGGAGCTGATATAAAAGCAATATGTA

upper sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT4G29040.1 (Arabidopsis thaliana), 3'ss of exon 4
tcttcattagctttatgtgtgagaagttggagattgagttttcttgataaacgaaattcttttgatcgctt--gttttggtttcttttaatgatctctgcagATTCATACTTCTAGAATGACTATGGCTGATGATGTAAACCTAGAGGAGTTTGTGATGACCAAAGATGAGTTTTCTGGTGCTGACATTAAAGCTATCTGTA
      | |  | ||  | |    || |||  | | | |   |||| |   ||||| | | ||| ||  |   ||| ||| |||| || || |  |    |||| || || || |  |||||| |  | || ||||||||||| || |||||||||||||| ||||| ||||| || || ||||| || || ||||| || |
-----gtaatatataattctactgagatggcaaatcaatga-cttgtt---cgaaactttcttgttcattgaggttgtgggttctgtttataaaat----agATACACACATCGAAGATGACTCTCTCGGAAGATGTAAACCTCGAAGAGTTTGTGATGACGAAAGACGAGTTCTCAGGAGCTGATATAAAGGCTATATGCA

upper sequence: PP1S109_234V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: Vv07s0005g05160.t01 (Vitis vinifera), 3'ss of exon 4
-----------------tcttcattagctttatgtgtgagaagttggagattgagttttcttgataaacgaaattct--------tttgatcgct-tgttttggtttcttttaatgatct---ctgcagATTCATACTTCTAGAATGACTATGGCTGATGATGTAAACCTAGAGGAGTTTGTGATGACCAAAGATGAGTTTTCTGGTGCTGACATTAAAGCTATCTGTA
                   |     |     || |     |  ||       || || |  ||| ||  |||   |          |||||  || |   |  |    | | | | || |    ||||||| ||||| || || |||||  ||||||||||||| ||| | || || ||||| ||||| || |||||||||||||| ||||| || || || || || |
gtacatgtgtgtttaagattatgcaaatgcaatattcactatattttcatccgacttcttgtgacaactgaatcaccaaacctggcttgattactattactaagcaaatctcatttatttaaattgcagATACATACATCAAGGATGACATTGGCTGATGATGTTAACTTGGAAGAATTTGTTATGACTAAGGATGAGTTTTCTGGAGCTGATATAAAGGCAATATGCA

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|37852217|gb|BJ610225.1|BJ610225
EST:     AGATTGAGTTTCCATTGCCAGATATCAAAACCAAGAGGAGAATTTTCCAG                         ATTCATACTTCTAGAATGACTATGGCTGATGATGTAAACCTAGAGGAGTTT
genomic: AGATTGAGTTTCCATTGCCAGATATCAAAACCAAGAGGAGAATTTTCCAGgtctggttat ... atctctgcagATTCATACTTCTAGAATGACTATGGCTGATGATGTAAACCTAGAGGAGTTT
EST: gi|67694035|gb|BJ954268.1|BJ954268
EST:     AGATTGAGTTTCCATTGCCAGATATCAAAACCAAGAGGAGAATTTTCCAG                         ATTCATACTTCTAGAATGACTATGGCTGATGATGTAAACCTAGAGGAGTTT
genomic: AGATTGAGTTTCCATTGCCAGATATCAAAACCAAGAGGAGAATTTTCCAGgtctggttat ... atctctgcagATTCATACTTCTAGAATGACTATGGCTGATGATGTAAACCTAGAGGAGTTT
EST: gi|162186727|gb|FC362763.1|FC362763
EST:     AGATTGAGTTTCCATTGCCAGATATCAAAACCAAGAGGAGAATTTTCCAG                         ATTCATACTTCTAGAATGACTATGGTTGATGATGTAAACCTAGAGGAGTTT
genomic: AGATTGAGTTTCCATTGCCAGATATCAAAACCAAGAGGAGAATTTTCCAGgtctggttat ... atctctgcagATTCATACTTCTAGAATGACTATGGCTGATGATGTAAACCTAGAGGAGTTT
EST: gi|162197603|gb|FC374437.1|FC374437
EST:     AGATTGAGTTTCCATTGCCAGATATCANAACCAAGAGGAGAATTTTCCAG                         ATTCATACTTCTAGAATGACTATGGCTGATGATGTAAACCTA
genomic: AGATTGAGTTTCCATTGCCAGATATCAAAACCAAGAGGAGAATTTTCCAGgtctggttat ... atctctgcagATTCATACTTCTAGAATGACTATGGCTGATGATGTAAACCTA

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: 30 (upstream exon), 34 (downstream exon)
Score: 8

TATCGAAAGCCTGGATCCGGCTCTGCTTCGACCTGGTAGAATTGATCGCAAGATTGAGTTTCCATTGCCAGATATCAAAACCAAGAGGAGAATTTTCCAGgtctggttat ... atctctgcagATTCATACTTCTAGAATGACTATGGCTGATGATGTAAACCTAGAGGAGTTTGTGATGACCAAAGATGAGTTTTCTGGTGCTGACATTAAAGCTATCTGTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gataaacgaaattcttttgatcgcttgttttggtttcttttaatgatctctgcagATTCATACTTCTAGAATGACTATGGCTGATGATGTAAACCTAGAGGAGTTTGTGATGACCAAAGATGAGTTTTCTGGTGCTGACATTAAAGCTATCTGTA
                                     ttttaat  putative branch site (score: 8)
                                              tctctgc  putative PPT
                                 tttcttttaatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcttcattagctttatgtgtgagaagttggagattgagttttcttgataaacgaaattcttttgatcgcttgttttggtttcttttaatgatctctgcagATTCATACTTCTAGAATGACTATGGCTGATGATGTAAACCTAGAGGAGTTTGTGATGACCAAAGATGAGTTTTCTGGTGCTGACATTAAAGCTATCTGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG