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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggttgattttctgtgctcttttcgtcattatcacatgtttgaattcccttttaaccgttctgtgatgtgtgttaatgtttagaggctatgaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTTATGATTCATATCGCGGCTGGATTGACCGCAGAGTTGT

Basic information

species Physcomitrella patens
transcript PP1S76_8V6.2
intron # 4
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|208377393|gb|DC906648.1|DC906648
EST:     AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAG                         GTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
genomic: AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAGgtttggttga ... gaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
EST: gi|100412613|gb|BY974821.1|BY974821
EST:     AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAG                         GTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
genomic: AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAGgtttggttga ... gaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
EST: gi|162249661|gb|FC426801.1|FC426801
EST:     AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAG                         GTATCCAACCATACGTGACACTTTATCACTGGGATCTTCCGCAGTCTCTTT
genomic: AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAGgtttggttga ... gaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
EST: gi|100393326|gb|BY989824.1|BY989824
EST:     AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAG                         GTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
genomic: AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAGgtttggttga ... gaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
EST: gi|100375234|gb|BY948810.1|BY948810
EST:     AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAG                         GTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
genomic: AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAGgtttggttga ... gaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
EST: gi|100396545|gb|BY990178.1|BY990178
EST:     AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAG                         GTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
genomic: AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAGgtttggttga ... gaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
EST: gi|100432068|gb|BY978649.1|BY978649
EST:     AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAG                         GTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
genomic: AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAGgtttggttga ... gaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
EST: gi|100360599|gb|BY984199.1|BY984199
EST:     GAAGGAGTGGCGTACTACAATAACCTTATAAATGGGTCTTTTGAAAAAAG                         GTATCCAACCATACGTGACACTTTATCACTGGGGACCTTCCGCAGTCTCTT
genomic: GAAGGAGTGGCGTACTACAATAACCTTATAAATGG-TCTTTTGAAAAAAGgtttggttga ... gaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGG-ACCTTCCGCAGTCTCTT
EST: gi|67716232|gb|BJ966492.1|BJ966492
EST:     AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAG                         GTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
genomic: AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAGgtttggttga ... gaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
EST: gi|208383670|gb|DC907061.1|DC907061
EST:     AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAG                         GTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
genomic: AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAGgtttggttga ... gaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
EST: gi|100362831|gb|BY947550.1|BY947550
EST:     AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAG                         GTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
genomic: AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAGgtttggttga ... gaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
EST: gi|18329187|gb|BJ161193.1|BJ161193
EST:     AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAG                         GTATCCAACCATACGTGACACTTTATCACTGGGACCTCCCGCAGTCTCTTT
genomic: AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAGgtttggttga ... gaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
EST: gi|100391024|gb|BY953034.1|BY953034
EST:     AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAG                         GTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
genomic: AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAGgtttggttga ... gaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
EST: gi|162183972|gb|FC359342.1|FC359342
EST:     AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAG                         GTATCCAACCATACGTGACACTTTATCACTGGGATCTTCCGCAGTCTCTTT
genomic: AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAGgtttggttga ... gaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
EST: gi|100387996|gb|BY988469.1|BY988469
EST:     AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAG                         GTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
genomic: AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAGgtttggttga ... gaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
EST: gi|162154400|gb|FC330207.1|FC330207
EST:     AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAG                         GTATCCAACCATACGTGACACTTTATCACTGGGATCTTCCGCAGTCTCTTT
genomic: AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAGgtttggttga ... gaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
EST: gi|100445704|gb|CJ970003.1|CJ970003
EST:     AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAG                         GTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
genomic: AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAGgtttggttga ... gaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
EST: gi|162258357|gb|FC434284.1|FC434284
EST:     AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAG                         GTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
genomic: AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAGgtttggttga ... gaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
EST: gi|100358802|gb|BY946698.1|BY946698
EST:     AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAG                         GTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
genomic: AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAGgtttggttga ... gaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
EST: gi|162157552|gb|FC333810.1|FC333810
EST:     AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAG                         GTATCCAACCATACGTGACACTTTATCACTGGGATCTTCCGCAGTCTCTTT
genomic: AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAGgtttggttga ... gaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
EST: gi|100437296|gb|BY961449.1|BY961449
EST:     AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAG                         GTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
genomic: AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAGgtttggttga ... gaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
EST: gi|100452031|gb|CJ975065.1|CJ975065
EST:     AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAG                         GTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
genomic: AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAGgtttggttga ... gaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
EST: gi|67719020|gb|BJ969279.1|BJ969279
EST:     AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAG                         GTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
genomic: AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAGgtttggttga ... gaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
EST: gi|100376261|gb|BY986100.1|BY986100
EST:     AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAG                         GTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
genomic: AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAGgtttggttga ... gaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
EST: gi|208380336|gb|DC907661.1|DC907661
EST:     AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAG                         GTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
genomic: AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAGgtttggttga ... gaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
EST: gi|100417188|gb|BY957211.1|BY957211
EST:     AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAG                         GTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
genomic: AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAGgtttggttga ... gaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
EST: gi|67704515|gb|BJ964748.1|BJ964748
EST:     AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAG                         GTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
genomic: AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAGgtttggttga ... gaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
EST: gi|67718927|gb|BJ969186.1|BJ969186
EST:     AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAG                         GTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
genomic: AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAGgtttggttga ... gaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
EST: gi|100418352|gb|BY957377.1|BY957377
EST:     AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAG                         GTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
genomic: AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAGgtttggttga ... gaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
EST: gi|100365284|gb|BY966902.1|BY966902
EST:     AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAG                         GTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT
genomic: AGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAGgtttggttga ... gaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTT

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), 19 (downstream exon)
Score: 3

GTGGGCCAAACCCAGTCGTGAACCAAGAAGGAGTGGCGTACTACAATAACCTTATAAATGGTCTTTTGAAAAAAGgtttggttga ... gaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTTATGATTCATATCGCGGCTGGATTGACCGCAGAGTTGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcccttttaaccgttctgtgatgtgtgttaatgtttagaggctatgaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTTATGATTCATATCGCGGCTGGATTGACCGCAGAGTTGT
                           ttaatgttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttggttgattttctgtgctcttttcgtcattatcacatgtttgaattcccttttaaccgttctgtgatgtgtgttaatgtttagaggctatgaatgtgcagGTATCCAACCATACGTGACACTTTATCACTGGGACCTTCCGCAGTCTCTTTATGATTCATATCGCGGCTGGATTGACCGCAGAGTTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA