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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgctagcacattgagaaaagatgaagttaattaaactgatgcagatttattgtatgaaggttttccattggtacgatacattttatttataatgtacaagtgttgctaactttgtgtattttgttgtgtagTCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACTCACGTGATAACCCATTAACTAAGGCAAAAGAATGTAGTCCCGTATTTTA

Basic information

species Physcomitrella patens
transcript PP1S70_131V6.1
intron # 5
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|208355961|gb|DC926680.1|DC926680
EST:     AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAG                         TCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
genomic: AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAGgtactgctag ... tgttgtgtagTCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
EST: gi|208382824|gb|DC923871.1|DC923871
EST:     AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAG                         TCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
genomic: AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAGgtactgctag ... tgttgtgtagTCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
EST: gi|67691633|gb|BJ951866.1|BJ951866
EST:     AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAG                         TCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
genomic: AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAGgtactgctag ... tgttgtgtagTCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
EST: gi|67697597|gb|BJ957830.1|BJ957830
EST:     AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAG                         TCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
genomic: AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAGgtactgctag ... tgttgtgtagTCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
EST: gi|37841109|gb|BJ599117.1|BJ599117
EST:     AAGGATTATACGAAGGGCTGGATTGGTTGTNGAGCAACATTGCCAATAAG                         TCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTNTGGGGACT
genomic: AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAGgtactgctag ... tgttgtgtagTCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
EST: gi|37845648|gb|BJ603656.1|BJ603656
EST:     AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAG                         TCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
genomic: AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAGgtactgctag ... tgttgtgtagTCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
EST: gi|67574235|gb|BJ947059.1|BJ947059
EST:     AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAG                         TCTTGAATGATGGTGCCTGTGAA
genomic: AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAGgtactgctag ... tgttgtgtagTCTTGAATGATGGTGCCTGTGAA
EST: gi|37831694|gb|BJ589706.1|BJ589706
EST:     AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAG                         TCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
genomic: AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAGgtactgctag ... tgttgtgtagTCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
EST: gi|37844007|gb|BJ602015.1|BJ602015
EST:     AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAG                         TCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
genomic: AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAGgtactgctag ... tgttgtgtagTCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
EST: gi|67578337|gb|BJ950504.1|BJ950504
EST:     AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAG                         TCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
genomic: AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAGgtactgctag ... tgttgtgtagTCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
EST: gi|162261371|gb|FC437804.1|FC437804
EST:     AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAG                         TCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
genomic: AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAGgtactgctag ... tgttgtgtagTCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
EST: gi|37827495|gb|BJ585507.1|BJ585507
EST:     AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAG                         TCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
genomic: AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAGgtactgctag ... tgttgtgtagTCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
EST: gi|208363816|gb|DC943273.1|DC943273
EST:     ANGATTATACGAAGGGCTGGAATTGGTTGTCGANCAACATTGCCAATAAN                         TCTNGAANGGATGGTGCCTGTGA
genomic: AGGATTATACGAAGGGCTGGA-TTGGTTGTCGAGCAACATTGCCAATAAGgtactgctag ... tgttgtgtagTCTTGAATG-ATGGTGCCTGTGA
EST: gi|162245120|gb|FC421594.1|FC421594
EST:     AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAG                         TCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCCAAACTTTGAGGACT
genomic: AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAGgtactgctag ... tgttgtgtagTCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
EST: gi|162261370|gb|FC437803.1|FC437803
EST:     AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAG                         TCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
genomic: AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAGgtactgctag ... tgttgtgtagTCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
EST: gi|208380989|gb|DC919871.1|DC919871
EST:     AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAG                         TCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
genomic: AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAGgtactgctag ... tgttgtgtagTCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
EST: gi|67697639|gb|BJ957872.1|BJ957872
EST:     AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAG                         TCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
genomic: AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAGgtactgctag ... tgttgtgtagTCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
EST: gi|67695107|gb|BJ955340.1|BJ955340
EST:     AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAG                         TCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
genomic: AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAGgtactgctag ... tgttgtgtagTCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
EST: gi|22132696|gb|BQ827292.1|BQ827292
EST:     AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAG                         TCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
genomic: AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAGgtactgctag ... tgttgtgtagTCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
EST: gi|162245687|gb|FC420731.1|FC420731
EST:     AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAG                         TCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
genomic: AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAGgtactgctag ... tgttgtgtagTCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
EST: gi|208386273|gb|DC952986.1|DC952986
EST:     AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAG                         TCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
genomic: AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAGgtactgctag ... tgttgtgtagTCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
EST: gi|37831484|gb|BJ589496.1|BJ589496
EST:     AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAG                         TCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
genomic: AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAGgtactgctag ... tgttgtgtagTCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
EST: gi|162240921|gb|FC415200.1|FC415200
EST:     AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAG                         TCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
genomic: AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAGgtactgctag ... tgttgtgtagTCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
EST: gi|67574196|gb|BJ947020.1|BJ947020
EST:     AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAG                         TCTTGAATGATGGTGCCTGTGAATATGG
genomic: AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAGgtactgctag ... tgttgtgtagTCTTGAATGATGGTGCCTGTGAATATGG
EST: gi|67701220|gb|BJ961453.1|BJ961453
EST:     AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAG                         TCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
genomic: AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAGgtactgctag ... tgttgtgtagTCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
EST: gi|67700135|gb|BJ960368.1|BJ960368
EST:     AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAG                         TCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
genomic: AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAGgtactgctag ... tgttgtgtagTCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
EST: gi|37844741|gb|BJ602749.1|BJ602749
EST:     AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAG                         TCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
genomic: AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAGgtactgctag ... tgttgtgtagTCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
EST: gi|18336372|gb|BJ168394.1|BJ168394
EST:     AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAG                         TCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
genomic: AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAGgtactgctag ... tgttgtgtagTCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
EST: gi|18334356|gb|BJ166373.1|BJ166373
EST:     AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAG                         TCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
genomic: AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAGgtactgctag ... tgttgtgtagTCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
EST: gi|37853307|gb|BJ611315.1|BJ611315
EST:     AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAG                         TCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT
genomic: AAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAGgtactgctag ... tgttgtgtagTCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACT

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: 85

GTACATCCAGAGTACCTGCGCGACGTCTGGAGAAGGATTATACGAAGGGCTGGATTGGTTGTCGAGCAACATTGCCAATAAGgtactgctag ... tgttgtgtagTCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACTCACGTGATAACCCATTAACTAAGGCAAAAGAATGTAGTCCCGTATTTTA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacattttatttataatgtacaagtgttgctaactttgtgtattttgttgtgtagTCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACTCACGTGATAACCCATTAACTAAGGCAAAAGAATGTAGTCCCGTATTTTA
                           tgctaac  putative branch site (score: 85)
                                          ttttgtt  putative PPT
     tttatttataatgtac  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgctagcacattgagaaaagatgaagttaattaaactgatgcagatttattgtatgaaggttttccattggtacgatacattttatttataatgtacaagtgttgctaactttgtgtattttgttgtgtagTCTTGAATGATGGTGCCTGTGAATATGGCGAGATGCGAAACTTTGGGGACTCACGTGATAACCCATTAACTAAGGCAAAAGAATGTAGTCCCGTATTTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA