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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatgtcctttcattttcacggtcctcgactgtgatttggtttgctctatttttttattttttatttccgaaaagaggtatgtaaaatttattcttttgattaacatagtatcatttgagtggtcagATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAAATACAAGAAGCTGTATGATGATTTGACGGCCGGGTTCAGGAATCTCGAG

Basic information

species Physcomitrella patens
transcript PP1S44_102V6.1
intron # 19
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|37836831|gb|BJ594839.1|BJ594839
EST:     ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGT                         ATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
genomic: ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGTgtaagatgtc ... gagtggtcagATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
EST: gi|37838710|gb|BJ596718.1|BJ596718
EST:     ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGT                         ATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
genomic: ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGTgtaagatgtc ... gagtggtcagATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
EST: gi|162276207|gb|FC452899.1|FC452899
EST:     ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGT                         ATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
genomic: ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGTgtaagatgtc ... gagtggtcagATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
EST: gi|37845049|gb|BJ603057.1|BJ603057
EST:     ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGT                         ATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
genomic: ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGTgtaagatgtc ... gagtggtcagATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
EST: gi|37838267|gb|BJ596275.1|BJ596275
EST:     ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGT                         ATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
genomic: ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGTgtaagatgtc ... gagtggtcagATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
EST: gi|22131932|gb|BQ826891.1|BQ826891
EST:     ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGT                         ATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
genomic: ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGTgtaagatgtc ... gagtggtcagATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
EST: gi|18337399|gb|BJ169423.1|BJ169423
EST:     ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGT                         ATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
genomic: ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGTgtaagatgtc ... gagtggtcagATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
EST: gi|37852823|gb|BJ610831.1|BJ610831
EST:     ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGT                         ATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
genomic: ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGTgtaagatgtc ... gagtggtcagATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
EST: gi|15327219|gb|BI487765.1|BI487765
EST:     ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGT                         ATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
genomic: ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGTgtaagatgtc ... gagtggtcagATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
EST: gi|37848114|gb|BJ606122.1|BJ606122
EST:     ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGT                         ATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
genomic: ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGTgtaagatgtc ... gagtggtcagATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
EST: gi|162276206|gb|FC452898.1|FC452898
EST:     ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGT                         ATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
genomic: ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGTgtaagatgtc ... gagtggtcagATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
EST: gi|67578993|gb|BJ951144.1|BJ951144
EST:     ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGT                         ATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
genomic: ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGTgtaagatgtc ... gagtggtcagATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
EST: gi|37834888|gb|BJ592900.1|BJ592900
EST:     ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGT                         ATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
genomic: ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGTgtaagatgtc ... gagtggtcagATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
EST: gi|162186096|gb|FC361300.1|FC361300
EST:     ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGT                         ATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
genomic: ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGTgtaagatgtc ... gagtggtcagATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
EST: gi|37846602|gb|BJ604610.1|BJ604610
EST:     ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGT                         ATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
genomic: ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGTgtaagatgtc ... gagtggtcagATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
EST: gi|162258844|gb|FC434851.1|FC434851
EST:     ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGT                         ATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
genomic: ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGTgtaagatgtc ... gagtggtcagATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
EST: gi|37853133|gb|BJ611141.1|BJ611141
EST:     ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGT                         ATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
genomic: ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGTgtaagatgtc ... gagtggtcagATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
EST: gi|37822114|gb|BJ580180.1|BJ580180
EST:     ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGT                         ATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
genomic: ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGTgtaagatgtc ... gagtggtcagATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
EST: gi|37834988|gb|BJ593000.1|BJ593000
EST:     ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGT                         ATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
genomic: ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGTgtaagatgtc ... gagtggtcagATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
EST: gi|162239653|gb|FC418014.1|FC418014
EST:     ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGT                         ATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
genomic: ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGTgtaagatgtc ... gagtggtcagATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
EST: gi|37848974|gb|BJ606982.1|BJ606982
EST:     ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGT                         ATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
genomic: ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGTgtaagatgtc ... gagtggtcagATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
EST: gi|37850336|gb|BJ608344.1|BJ608344
EST:     ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGT                         ATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
genomic: ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGTgtaagatgtc ... gagtggtcagATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
EST: gi|162179502|gb|FC356542.1|FC356542
EST:     ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGT                         ATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA
genomic: ACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGTgtaagatgtc ... gagtggtcagATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAA

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: 21

GCTGTTGAGCGAGCTGCTGGTCCGGAGGGGCAGAAAATTACGTACAACATCATCAAGCAGCGCTTGAATGATCTCATCTATCGTCTTGTgtaagatgtc ... gagtggtcagATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAAATACAAGAAGCTGTATGATGATTTGACGGCCGGGTTCAGGAATCTCGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagaggtatgtaaaatttattcttttgattaacatagtatcatttgagtggtcagATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAAATACAAGAAGCTGTATGATGATTTGACGGCCGGGTTCAGGAATCTCGAG
                          gattaac  putative branch site (score: 21)
          taaaatttattctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatgtcctttcattttcacggtcctcgactgtgatttggtttgctctatttttttattttttatttccgaaaagaggtatgtaaaatttattcttttgattaacatagtatcatttgagtggtcagATCCATGAAGTTCGAGGATCCCTCCGATGGTGAAGATGTTCTGACTGAGAAATACAAGAAGCTGTATGATGATTTGACGGCCGGGTTCAGGAATCTCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG