Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGGATGATGCTGTAATCTTTGTTGACAGCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctacattgcaatgctgtctgttttgtggagtgaggtgttttctttgaacacagtaatcaggatatggccatttaggttgttccgatcatagtat...

Basic information

species Physcomitrella patens
transcript PP1S79_254V6.2
intron # 2
splice site 5'
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|100398771|gb|BY990507.1|BY990507
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|18373696|gb|BJ205274.1|BJ205274
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|100398308|gb|BY972539.1|BY972539
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|208395729|gb|DC911822.1|DC911822
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|18365099|gb|BJ197173.1|BJ197173
EST:     GCAGTATCAGGCCAGTGCACTTAANGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATT
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATT
EST: gi|18375106|gb|BJ206684.1|BJ206684
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|18372904|gb|BJ204506.1|BJ204506
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|18358733|gb|BJ190792.1|BJ190792
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|100404436|gb|BY973577.1|BY973577
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|100422683|gb|BY957948.1|BY957948
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|208346919|gb|DC905449.1|DC905449
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|208400165|gb|DC904813.1|DC904813
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|18352604|gb|BJ184658.1|BJ184658
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|18343422|gb|BJ175460.1|BJ175460
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|208350210|gb|DC901594.1|DC901594
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|100407245|gb|BY974075.1|BY974075
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|18364014|gb|BJ196087.1|BJ196087
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|18368897|gb|BJ200982.1|BJ200982
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|100363297|gb|BY984455.1|BY984455
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|100390136|gb|BY989216.1|BY989216
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|18357173|gb|BJ189232.1|BJ189232
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|100437331|gb|BY961467.1|BY961467
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|208398960|gb|DC912119.1|DC912119
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|100439349|gb|BY980219.1|BY980219
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|208391691|gb|DC942281.1|DC942281
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATCTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|100353619|gb|BY964897.1|BY964897
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|18354389|gb|BJ186445.1|BJ186445
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|100399784|gb|BY972891.1|BY972891
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|18345187|gb|BJ177228.1|BJ177228
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|208378690|gb|DC914664.1|DC914664
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|18356417|gb|BJ188476.1|BJ188476
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|100432416|gb|BY960464.1|BY960464
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|100408155|gb|BY955925.1|BY955925
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|18351698|gb|BJ183750.1|BJ183750
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|18328272|gb|BJ160276.1|BJ160276
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|100413319|gb|BY956613.1|BY956613
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
EST: gi|18361754|gb|BJ193821.1|BJ193821
EST:     GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAG                         GCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA
genomic: GCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTA

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: 14

GCGGATGATGCTGTAATCTTTGTTGACAGCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctac ... atgtatgcagGCGTTTTCATTTAACGATGTTGCGACGTCATTGGCAGTCCTTCTTGGAGTAGTCCCAAAAGCTGTTGATGAAAAAGTTGCCTCCAAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGGATGATGCTGTAATCTTTGTTGACAGCAGTATCAGGCCAGTGCACTTAAGGACAACTCCTCCTATCGAAAAAGAGgtatgtctacattgcaatgctgtctgttttgtggagtgaggtgttttctttgaacacagtaatcaggatatggccatttaggttgttccgatcatagtat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC