Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcaaacagttgtggaaattggtggtcgtgagattacgcattggaacagaagctaatgtagtccccgtgttgtttttcttttttgtctctttcttttgcagTCCTGATGACACCCCGTGGGATGGAG

Basic information

species Physcomitrella patens
transcript PP1S91_88V6.1
intron # 1
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|67701080|gb|BJ961313.1|BJ961313
EST:     GGACAACAACATCATGTTGTGGAATGCTGTCATATTCGG                         TCCTGATGACACCCCGTGGGATGGAG
genomic: GGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaac ... tcttttgcagTCCTGATGACACCCCGTGGGATGGAG
EST: gi|67569580|gb|BJ942404.1|BJ942404
EST:     GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGG                         TCCTGATGACACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaac ... tcttttgcagTCCTGATGACACCCCGTGGGATGGAG
EST: gi|67570577|gb|BJ943401.1|BJ943401
EST:     GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGG                         TCCTGATGACACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaac ... tcttttgcagTCCTGATGACACCCCGTGGGATGGAG
EST: gi|208380555|gb|DC914944.1|DC914944
EST:     GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGG                         TCCTGATGACACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaac ... tcttttgcagTCCTGATGACACCCCGTGGGATGGAG
EST: gi|18368607|gb|BJ200692.1|BJ200692
EST:     GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGG                         TCCTGATGACACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaac ... tcttttgcagTCCTGATGACACCCCGTGGGATGGAG
EST: gi|67508398|gb|BJ941265.1|BJ941265
EST:     GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGG                         TCCTGATGACACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaac ... tcttttgcagTCCTGATGACACCCCGTGGGATGGAG
EST: gi|18349879|gb|BJ181930.1|BJ181930
EST:     GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGG                         TCCTGATGACACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaac ... tcttttgcagTCCTGATGACACCCCGTGGGATGGAG
EST: gi|67572289|gb|BJ945113.1|BJ945113
EST:     GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGG                         TCCTGATGACACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaac ... tcttttgcagTCCTGATGACACCCCGTGGGATGGAG
EST: gi|67727247|gb|BJ977506.1|BJ977506
EST:     CCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGG                         TCCTGATGACACCCCGTGGGATGGAG
genomic: CCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaac ... tcttttgcagTCCTGATGACACCCCGTGGGATGGAG
EST: gi|162259058|gb|FC436391.1|FC436391
EST:     GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGG                         TCCTGATGACACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaac ... tcttttgcagTCCTGATGACACCCCGTGGGATGGAG
EST: gi|67578213|gb|BJ950380.1|BJ950380
EST:     GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGG                         TCCTGATGACACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaac ... tcttttgcagTCCTGATGACACCCCGTGGGATGGAG
EST: gi|67569740|gb|BJ942564.1|BJ942564
EST:     GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGG                         TCCTGATGACACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaac ... tcttttgcagTCCTGATGACACCCCGTGGGATGGAG
EST: gi|208393858|gb|DC928694.1|DC928694
EST:     GCGCCCCGCA-GACAACAACATCATGTTGTGGAATGCTGTCATATTCGT                         TCCTGATGACACCCCGTGGGATGGAG
genomic: GCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaac ... tcttttgcagTCCTGATGACACCCCGTGGGATGGAG
EST: gi|208399565|gb|DC908562.1|DC908562
EST:     GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGG                         TCCTGATGACACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaac ... tcttttgcagTCCTGATGACACCCCGTGGGATGGAG
EST: gi|162229344|gb|FC405535.1|FC405535
EST:     GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGG                         TCCTGATGACACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaac ... tcttttgcagTCCTGATGACACCCCGTGGGATGGAG
EST: gi|162268444|gb|FC444317.1|FC444317
EST:     GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGG                         TCCTGATGACACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaac ... tcttttgcagTCCTGATGACACCCCGTGGGATGGAG
EST: gi|67576821|gb|BJ949645.1|BJ949645
EST:     GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGG                         TCCTGATGACACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaac ... tcttttgcagTCCTGATGACACCCCGTGGGATGGAG
EST: gi|18357799|gb|BJ189858.1|BJ189858
EST:     GGCGCCCCGCAGGACGACAACATCATGTTGTGGAATGCTGTCATATTCGG                         TCCTGATGACACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaac ... tcttttgcagTCCTGATGACACCCCGTGGGATGGAG
EST: gi|67569162|gb|BJ941986.1|BJ941986
EST:     GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGG                         TCCTGATGACACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaac ... tcttttgcagTCCTGATGACACCCCGTGGGATGGAG
EST: gi|37837159|gb|BJ595167.1|BJ595167
EST:     GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGG                         TCCTGATGACACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaac ... tcttttgcagTCCTGATGACACCCCGTGGGATGGAG
EST: gi|67692848|gb|BJ953081.1|BJ953081
EST:     GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGG                         TCCTGATGACACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaac ... tcttttgcagTCCTGATGACACCCCGTGGGATGGAG
EST: gi|67695657|gb|BJ955890.1|BJ955890
EST:     GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATANTCGG                         TCCTGATGACACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaac ... tcttttgcagTCCTGATGACACCCCGTGGGATGGAG
EST: gi|18366035|gb|BJ198113.1|BJ198113
EST:     GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGG                         TCCTGATGACACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaac ... tcttttgcagTCCTGATGACACCCCGTGGGATGGAG
EST: gi|18331935|gb|BJ163947.1|BJ163947
EST:     GGAATGCTGNCATATTCGG                         TCCTGATGACACCCCGTGGGATGGAG
genomic: GGAATGCTGTCATATTCGGgtacccaaac ... tcttttgcagTCCTGATGACACCCCGTGGGATGGAG
EST: gi|67576245|gb|BJ949069.1|BJ949069
EST:     GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGG                         TCCTGATGACACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaac ... tcttttgcagTCCTGATGACACCCCGTGGGATGGAG
EST: gi|162268443|gb|FC444316.1|FC444316
EST:     GGCGCCCCGCAGGACAACAACATCATGTTGT-GAATGCTGTCATATTCGG                         TCCTGATGACACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaac ... tcttttgcagTCCTGATGACACCCCGTGGGATGGAG
EST: gi|18371730|gb|BJ203332.1|BJ203332
EST:     GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGG                         TCCTGATGACACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaac ... tcttttgcagTCCTGATGACACCCCGTGGGATGGAG
EST: gi|162229343|gb|FC405534.1|FC405534
EST:     GCTGTCATATTCGG                         TCCTGATGACACCCCGTGGGATGGAG
genomic: GCTGTCATATTCGGgtacccaaac ... tcttttgcagTCCTGATGACACCCCGTGGGATGGAG
EST: gi|67699746|gb|BJ959979.1|BJ959979
EST:     GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGG                         TCCTGATGACACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaac ... tcttttgcagTCCTGATGACACCCCGTGGGATGGAG
EST: gi|67718896|gb|BJ969155.1|BJ969155
EST:     GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGG                         TCCTGATGACACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaac ... tcttttgcagTCCTGATGACACCCCGTGGGATGGAG
EST: gi|37846151|gb|BJ604159.1|BJ604159
EST:     GCGCCCCGCAGGACAACAACATCCATGTTGTGGAATGCTGTCATATTCGG                         TCCTGATGACACCCCGTGGGATGGAG
genomic: GCGCCCCGCAGGACAACAACAT-CATGTTGTGGAATGCTGTCATATTCGGgtacccaaac ... tcttttgcagTCCTGATGACACCCCGTGGGATGGAG
EST: gi|208391714|gb|DC942290.1|DC942290
EST:     GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGG                         TCCTGATGACACCCCGTGGGATGGAG
genomic: GGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaac ... tcttttgcagTCCTGATGACACCCCGTGGGATGGAG

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), 34 (downstream exon)
Score: 117

TGATGCGCGACTTCAAGCGCCTGCAGCATGATCCTCCGGCCGGCATCAGCGGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaac ... tcttttgcagTCCTGATGACACCCCGTGGGATGGAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagaagctaatgtagtccccgtgttgtttttcttttttgtctctttcttttgcagTCCTGATGACACCCCGTGGGATGGAG
    agctaat  putative branch site (score: 117)
               tccccgtgttgttttt  putative PPT
                       ttgtttttctttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcaaacagttgtggaaattggtggtcgtgagattacgcattggaacagaagctaatgtagtccccgtgttgtttttcttttttgtctctttcttttgcagTCCTGATGACACCCCGTGGGATGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA