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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtgttcaatctcggcaaagttatttatgaacggagcctctctttgcaaattgtgaaggtgtttttaccgagattgatacagatctttactcgttgtgttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGGCTCAGATCGATCAATGGATTGATTTCGCCGCTCTTGAGATCGACATCAA

Basic information

species Physcomitrella patens
transcript PP1S172_22V6.1
intron # 3
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|100443039|gb|BY981665.1|BY981665
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
EST: gi|208376452|gb|DC902749.1|DC902749
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
EST: gi|67717448|gb|BJ967707.1|BJ967707
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
EST: gi|208389492|gb|DC942199.1|DC942199
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
EST: gi|100369785|gb|BY967385.1|BY967385
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
EST: gi|162174625|gb|FC350280.1|FC350280
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
EST: gi|18347384|gb|BJ179430.1|BJ179430
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
EST: gi|18356387|gb|BJ188446.1|BJ188446
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
EST: gi|67718156|gb|BJ968415.1|BJ968415
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
EST: gi|18330838|gb|BJ162844.1|BJ162844
EST:     TTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: TTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
EST: gi|67704223|gb|BJ964456.1|BJ964456
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTC
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTC
EST: gi|18369160|gb|BJ201245.1|BJ201245
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
EST: gi|100353391|gb|BY964783.1|BY964783
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
EST: gi|67716670|gb|BJ966930.1|BJ966930
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
EST: gi|208390428|gb|DC933685.1|DC933685
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
EST: gi|67717265|gb|BJ967524.1|BJ967524
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
EST: gi|100355882|gb|BY946086.1|BY946086
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
EST: gi|100424887|gb|BY976866.1|BY976866
EST:     GAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: GAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
EST: gi|67712935|gb|BJ966384.1|BJ966384
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
EST: gi|162229414|gb|FC405605.1|FC405605
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
EST: gi|18366975|gb|BJ199055.1|BJ199055
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
EST: gi|18346613|gb|BJ178658.1|BJ178658
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTAC
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTAC
EST: gi|18354799|gb|BJ186857.1|BJ186857
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
EST: gi|208367162|gb|DC935962.1|DC935962
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
EST: gi|18341969|gb|BJ174004.1|BJ174004
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
EST: gi|18356942|gb|BJ189001.1|BJ189001
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
EST: gi|67571497|gb|BJ944321.1|BJ944321
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
EST: gi|100363442|gb|BY966391.1|BY966391
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
EST: gi|18372682|gb|BJ204284.1|BJ204284
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
EST: gi|67703235|gb|BJ963468.1|BJ963468
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGGGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
EST: gi|67717486|gb|BJ967745.1|BJ967745
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCGAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
EST: gi|67569243|gb|BJ942067.1|BJ942067
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
EST: gi|18364140|gb|BJ196213.1|BJ196213
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
EST: gi|100415505|gb|BY992875.1|BY992875
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
EST: gi|100360303|gb|BY966108.1|BY966108
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
EST: gi|100427995|gb|BY959230.1|BY959230
EST:     GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACG                         TTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG
genomic: GGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGG

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: 34 (upstream exon), 32 (downstream exon)
Score: 15

GTTCCAGTTCTGGAAACTCCAGAAGGATCCATCTTTGAGAGTAACGCTATTGCTCGATACGgttagtgttc ... ttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGGCTCAGATCGATCAATGGATTGATTTCGCCGCTCTTGAGATCGACATCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaggtgtttttaccgagattgatacagatctttactcgttgtgttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGGCTCAGATCGATCAATGGATTGATTTCGCCGCTCTTGAGATCGACATCAA
                  gattgat  putative branch site (score: 15)
      tgttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtgttcaatctcggcaaagttatttatgaacggagcctctctttgcaaattgtgaaggtgtttttaccgagattgatacagatctttactcgttgtgttgaatgcagTTGCTGGCCTCAAGGATGTCGGCTTGCTCGGTGTCCCTGGGTACAATAAGGCTCAGATCGATCAATGGATTGATTTCGCCGCTCTTGAGATCGACATCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC