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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtattgttgcgctgattttattcgaggatttctgtattctcgatttgattagttgttagtgccctcatgcggattcgaatcttgttttcttagatctctatggcgctacctttcaatgttataaatgtagggaggtaaagttattagggtttagtgaggagactttgagtctaatatcctgcacttgcaattgtagTCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCTTGGTGATGAGTTCAAGGGATACGTTTTCAAGATTATGGGAGGATGTGAC

Basic information

species Physcomitrella patens
transcript PP1S311_33V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S311_33V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT5G10360.1 (Arabidopsis thaliana), 3'ss of exon 3
gtgagtattgttgcgctgattttattcgaggatttctgtattctcgatttgattagttgttagtgccctcatgcggattcgaatcttgttttcttagatctctatggcgctacctttcaatgttataaatgtagggaggtaaagttattagggtttagtgaggagactt--tgagtctaatatcctgcacttgcaattgtagTCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCTTGGTGATGAGTTCAAGGGATACGTTTTCAAGATTATGGGAGGATGTGAC
              |   | ||| |||      ||| || || |   | ||||   |||| ||| |  | || |  |   ||||  ||| |  || || || | ||  |  |  ||  |  | ||   ||  | |    |      ||  | |   ||  |||   |    |||  | |  |     ||||       ||   ||||  ||||                                                                                         
--------------gtgaaattttttctcctggttcagtgtttttt-tctgatgtcttgtgagttcagt-atacttaacagaattgtgtgtgttttgagctatttgcagGAA--TTCAAGGGATACGTATTCAAGATCATGGGAGGAT--GTGACAAGCAAGGTTTCCCAATGAAACAAGGAGTTCTCACTCCAGGGCGTGTCCGTC--TTTTGC---------------------------------------------------------------------------------------
















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|208372979|gb|DC940610.1|DC940610
EST:     CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCT                         TCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
genomic: CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCTgtgagtattg ... gcaattgtagTCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
EST: gi|67698486|gb|BJ958719.1|BJ958719
EST:     GTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCT                         TCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
genomic: GTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCTgtgagtattg ... gcaattgtagTCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
EST: gi|208350926|gb|DC910473.1|DC910473
EST:     CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCT                         TCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
genomic: CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCTgtgagtattg ... gcaattgtagTCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
EST: gi|162279665|gb|FC455898.1|FC455898
EST:     CAGAAGAAAGTCGAGATCGATGACGATGCCAAGCT                         TCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
genomic: CAGAAGAAAGTCGAGATCGATGACGATGCCAAGCTgtgagtattg ... gcaattgtagTCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
EST: gi|18374415|gb|BJ205993.1|BJ205993
EST:     CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCT                         TCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
genomic: CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCTgtgagtattg ... gcaattgtagTCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
EST: gi|208394580|gb|DC953619.1|DC953619
EST:     GGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCT                         TCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
genomic: GGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCTgtgagtattg ... gcaattgtagTCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
EST: gi|162236276|gb|FC411200.1|FC411200
EST:     CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGTT                         TCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
genomic: CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCTgtgagtattg ... gcaattgtagTCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
EST: gi|19785812|gb|BQ040399.1|BQ040399
EST:     CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCT                         TCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
genomic: CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCTgtgagtattg ... gcaattgtagTCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
EST: gi|18373396|gb|BJ204974.1|BJ204974
EST:     CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCT                         TCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
genomic: CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCTgtgagtattg ... gcaattgtagTCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
EST: gi|67575041|gb|BJ947865.1|BJ947865
EST:     CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCT                         TCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
genomic: CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCTgtgagtattg ... gcaattgtagTCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
EST: gi|208359876|gb|DC934877.1|DC934877
EST:     CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCT                         TCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
genomic: CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCTgtgagtattg ... gcaattgtagTCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
EST: gi|208377690|gb|DC932226.1|DC932226
EST:     CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCT                         TCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
genomic: CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCTgtgagtattg ... gcaattgtagTCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
EST: gi|162239498|gb|FC417963.1|FC417963
EST:     CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCT                         TCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
genomic: CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCTgtgagtattg ... gcaattgtagTCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
EST: gi|18373564|gb|BJ205142.1|BJ205142
EST:     CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCT                         TCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
genomic: CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCTgtgagtattg ... gcaattgtagTCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
EST: gi|162271070|gb|FC446097.1|FC446097
EST:     CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCT                         TCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
genomic: CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCTgtgagtattg ... gcaattgtagTCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
EST: gi|67571348|gb|BJ944172.1|BJ944172
EST:     CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCT                         TCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
genomic: CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCTgtgagtattg ... gcaattgtagTCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
EST: gi|18367978|gb|BJ200062.1|BJ200062
EST:     CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCT                         TCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
genomic: CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCTgtgagtattg ... gcaattgtagTCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
EST: gi|162271071|gb|FC446098.1|FC446098
EST:     CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCT                         TCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
genomic: CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCTgtgagtattg ... gcaattgtagTCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
EST: gi|18355513|gb|BJ187572.1|BJ187572
EST:     CCCACTACGGGGTGTCAGGAGAAAGTCGAGATCGATGACGATGCCAAGCT                         TCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
genomic: CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCTgtgagtattg ... gcaattgtagTCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
EST: gi|162235066|gb|FC411201.1|FC411201
EST:     CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCT                         TCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
genomic: CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCTgtgagtattg ... gcaattgtagTCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
EST: gi|18342104|gb|BJ174139.1|BJ174139
EST:     CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCT                         TCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
genomic: CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCTgtgagtattg ... gcaattgtagTCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
EST: gi|67694668|gb|BJ954901.1|BJ954901
EST:     GTGTCAGNAGAAAGTCGAGATCGATGACGATGCCAAGCT                         TCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
genomic: GTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCTgtgagtattg ... gcaattgtagTCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
EST: gi|208386094|gb|DC949005.1|DC949005
EST:     CCCANTAC-GGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCT                         TCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
genomic: CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCTgtgagtattg ... gcaattgtagTCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
EST: gi|18371929|gb|BJ203531.1|BJ203531
EST:     CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCT                         TCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
genomic: CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCTgtgagtattg ... gcaattgtagTCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
EST: gi|67698381|gb|BJ958614.1|BJ958614
EST:     GTCAGAAG-AAGTCGAGATCGATGACGATGCCAAGCT                         TCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCCAGC
genomic: GTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCTgtgagtattg ... gcaattgtagTCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGA-CCAGC
EST: gi|162279666|gb|FC455899.1|FC455899
EST:     CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCT                         TCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
genomic: CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCTgtgagtattg ... gcaattgtagTCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
EST: gi|67574954|gb|BJ947778.1|BJ947778
EST:     CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCT                         TCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
genomic: CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCTgtgagtattg ... gcaattgtagTCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
EST: gi|18352184|gb|BJ184238.1|BJ184238
EST:     CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCT                         TCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT
genomic: CCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCTgtgagtattg ... gcaattgtagTCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCT

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: 34

CTAAATATCGCTAACCCCACTACGGGGTGTCAGAAGAAAGTCGAGATCGATGACGATGCCAAGCTgtgagtattg ... gcaattgtagTCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCTTGGTGATGAGTTCAAGGGATACGTTTTCAAGATTATGGGAGGATGTGAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattagggtttagtgaggagactttgagtctaatatcctgcacttgcaattgtagTCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCTTGGTGATGAGTTCAAGGGATACGTTTTCAAGATTATGGGAGGATGTGAC
                           gtctaat  putative branch site (score: 34)
                            tctaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtattgttgcgctgattttattcgaggatttctgtattctcgatttgattagttgttagtgccctcatgcggattcgaatcttgttttcttagatctctatggcgctacctttcaatgttataaatgtagggaggtaaagttattagggtttagtgaggagactttgagtctaatatcctgcacttgcaattgtagTCGTCAATTTTATGACAAGCGTCTTGCTCAAGAGGTCAGTGGTGACCAGCTTGGTGATGAGTTCAAGGGATACGTTTTCAAGATTATGGGAGGATGTGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG