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'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCGCAAGTTTTTCATCTTTGTGCAGAACTATGACGAGGAGGATGCCAAAACACACGAGGGAATGGACTTGCGGACAGTAACAACCAAGGAAGTTTTCGAgtatgtgtctttctttggccggaatctgtaggttgatttgcgaggtgcatgtgtgttgggcatggtcgcttgacgtgtgttggattgtaggggtggttgtgaccacggcagtaagcttgtggggggtaattctggcgggtgctgcgtctcatcgtgtaaactgtggtgcag

Basic information

species Physcomitrella patens
transcript PP1S167_1V6.1
intron # 5
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|100364022|gb|BY966287.1|BY966287
EST:     ACACACGAGGGAATGGACTTGCGGACAGTAACAACAAAGGAAGTTTTCGA                         GAAGTTCGGGCTGGATGCTAACACAGTAGACTTTATTGGACACTCTTT
genomic: ACACACGAGGGAATGGACTTGCGGACAGTAACAACCAAGGAAGTTTTCGAgtatgtgtct ... tgtggtgcagGAAGTTCGGGCTGGATGCTAACACAGTAGACTTTATTGGACACTCTTT
EST: gi|162239319|gb|FC415405.1|FC415405
EST:     ACACACGAGGGAATGGACTTGCGGACAGTAACAACCAAGGAAGTTTTCGA                         GAAGTTCGGGCTGGATGCTAACACAGTAGACTTTATTGGACACTCTTTGGC
genomic: ACACACGAGGGAATGGACTTGCGGACAGTAACAACCAAGGAAGTTTTCGAgtatgtgtct ... tgtggtgcagGAAGTTCGGGCTGGATGCTAACACAGTAGACTTTATTGGACACTCTTTGGC
EST: gi|100411963|gb|BY992426.1|BY992426
EST:     ACACACGAGGGAATGGACTTGCGGACAGTAACAACCAAGGAAGTTTTCGA                         GAAGTTCGGGCTGGATGCTAACACAGTAGACTTTATTGGACACTCTTTGGC
genomic: ACACACGAGGGAATGGACTTGCGGACAGTAACAACCAAGGAAGTTTTCGAgtatgtgtct ... tgtggtgcagGAAGTTCGGGCTGGATGCTAACACAGTAGACTTTATTGGACACTCTTTGGC
EST: gi|100351814|gb|BY964563.1|BY964563
EST:     ACACACGAGGGAATGGACTTGCGGACAGTGACAACCAAGGAGGTTTTCGA                         GAAGTTCGGGCTGGATGCCA-CACAGTAGACTTTATTGGA
genomic: ACACACGAGGGAATGGACTTGCGGACAGTAACAACCAAGGAAGTTTTCGAgtatgtgtct ... tgtggtgcagGAAGTTCGGGCTGGATGCTAACACAGTAGACTTTATTGGA
EST: gi|67718774|gb|BJ969033.1|BJ969033
EST:     ACACACGAGGGAATGGACTTGCGGACAGTAACAACCAAGGAAGTTTTCGA                         GAAGTTCGGGCTGGATGCTAACACAGTANACTTTATTGGACACTCTTTGGC
genomic: ACACACGAGGGAATGGACTTGCGGACAGTAACAACCAAGGAAGTTTTCGAgtatgtgtct ... tgtggtgcagGAAGTTCGGGCTGGATGCTAACACAGTAGACTTTATTGGACACTCTTTGGC
EST: gi|208391457|gb|DC937605.1|DC937605
EST:     ACACACGAGGGAATGGACTTGCGGACAGTAACAACCAAGGAAGTTTTCGA                         GAAGTTCGGGCTGGATGCTAACACAGTAGACTTTATTGGACACTCTTTGGC
genomic: ACACACGAGGGAATGGACTTGCGGACAGTAACAACCAAGGAAGTTTTCGAgtatgtgtct ... tgtggtgcagGAAGTTCGGGCTGGATGCTAACACAGTAGACTTTATTGGACACTCTTTGGC
EST: gi|100386544|gb|BY951340.1|BY951340
EST:     ACACACGAGGGAATGGACTTGCGGACAGTGACAACCAAGGAGGTTTTCGA                         GAAGTTCGGGCTGGATGCCAACACAGTAGACTTTATTGGACACTCTTTGGC
genomic: ACACACGAGGGAATGGACTTGCGGACAGTAACAACCAAGGAAGTTTTCGAgtatgtgtct ... tgtggtgcagGAAGTTCGGGCTGGATGCTAACACAGTAGACTTTATTGGACACTCTTTGGC
EST: gi|208388870|gb|DC932898.1|DC932898
EST:     ACACACGAGGGAATGGACTTGCGGACAGTGACAACCAAGGAGGTTTTCGA                         GAAGTTCGGGCTGGATGCCAACACAGTAGACTTTATTGGACACTCTTTGGC
genomic: ACACACGAGGGAATGGACTTGCGGACAGTAACAACCAAGGAAGTTTTCGAgtatgtgtct ... tgtggtgcagGAAGTTCGGGCTGGATGCTAACACAGTAGACTTTATTGGACACTCTTTGGC
EST: gi|100420810|gb|BY993515.1|BY993515
EST:     ACACACGAGGGAATGGACTTGCGGACAGTAACAACCAAGGAAGTTTTCGA                         GAAGTTCGGGCTGGATGCTAACACAGTAGACTTTATTGGACACTCTTTGGC
genomic: ACACACGAGGGAATGGACTTGCGGACAGTAACAACCAAGGAAGTTTTCGAgtatgtgtct ... tgtggtgcagGAAGTTCGGGCTGGATGCTAACACAGTAGACTTTATTGGACACTCTTTGGC
EST: gi|67572040|gb|BJ944864.1|BJ944864
EST:     ACACACGAGGGAATGGACTTGCGGACAGTGACAACCAAGGAGGTTTTCGA                         GAAGTTCGGGCTGGATGCCAACACAGTAGACTTTATTGGACACTCTTTGGC
genomic: ACACACGAGGGAATGGACTTGCGGACAGTAACAACCAAGGAAGTTTTCGAgtatgtgtct ... tgtggtgcagGAAGTTCGGGCTGGATGCTAACACAGTAGACTTTATTGGACACTCTTTGGC
EST: gi|162249711|gb|FC426825.1|FC426825
EST:     ACACACGAGGGAATGGACTTGCGGACAGTAACAACCAAGGAAGTTTTCGA                         GAAGTTCGGGCTGGATGCTAACACAGTAGACTTTATTGGACACTCTTTGGC
genomic: ACACACGAGGGAATGGACTTGCGGACAGTAACAACCAAGGAAGTTTTCGAgtatgtgtct ... tgtggtgcagGAAGTTCGGGCTGGATGCTAACACAGTAGACTTTATTGGACACTCTTTGGC
EST: gi|100432371|gb|BY960451.1|BY960451
EST:     CACACGAGGGAATGGACTTGCGGACAGGTA-CAACCAAGGAAGTTTTCGA                         GGAGTTCGGGCTGGA
genomic: CACACGAGGGAATGGACTTGCGGACAG-TAACAACCAAGGAAGTTTTCGAgtatgtgtct ... tgtggtgcagGAAGTTCGGGCTGGA
EST: gi|162167541|gb|FC343712.1|FC343712
EST:     ACACACGAGGGAATGGACTTGCGGACAGTAACAACCAAGGAAGTTTTCGA                         GAAGTTCGGGCTGGATGCTAACACAGTAGACTTTATTGGACACTCTTTGGC
genomic: ACACACGAGGGAATGGACTTGCGGACAGTAACAACCAAGGAAGTTTTCGAgtatgtgtct ... tgtggtgcagGAAGTTCGGGCTGGATGCTAACACAGTAGACTTTATTGGACACTCTTTGGC
EST: gi|162202240|gb|FC378096.1|FC378096
EST:     ACACACGAGGGAATGGACTTGCGGACAGTGACAACCAAGGAGGTTTTCGA                         GAAGTTCGGGCTGGATGCCAACACAGTAGACTTTATTGGACACTCTTTGGC
genomic: ACACACGAGGGAATGGACTTGCGGACAGTAACAACCAAGGAAGTTTTCGAgtatgtgtct ... tgtggtgcagGAAGTTCGGGCTGGATGCTAACACAGTAGACTTTATTGGACACTCTTTGGC
EST: gi|100390164|gb|BY989244.1|BY989244
EST:     ACACACGAGGGAATGGACTTGCGGACAGTGACAACCAAGGAGGTTTTCGA                         GAAGTTCGGGCTGGATGCCAACACAGTAGACTTTAT-GGNACACTCTTTGG
genomic: ACACACGAGGGAATGGACTTGCGGACAGTAACAACCAAGGAAGTTTTCGAgtatgtgtct ... tgtggtgcagGAAGTTCGGGCTGGATGCTAACACAGTAGACTTTATTGG-ACACTCTTTGG
EST: gi|208400746|gb|DC904924.1|DC904924
EST:     ACACACGAGGGAATGGACTTGCGGACAGTGACAACCAANGAGGTTTTCGA                         GAAGTTCGGGCTGGATGCCAACACAGTAGACTTTATTGGACACTCTTTGGC
genomic: ACACACGAGGGAATGGACTTGCGGACAGTAACAACCAAGGAAGTTTTCGAgtatgtgtct ... tgtggtgcagGAAGTTCGGGCTGGATGCTAACACAGTAGACTTTATTGGACACTCTTTGGC
EST: gi|162179697|gb|FC355755.1|FC355755
EST:     ACACACGAGGGAATGGACTTGCGGACAGTAACAACCAAGGAAGTTTTCGA                         GAAGTTCGGGCTGGATGCTAACACAGTAGACTTTATTGGACACTCTTTGGC
genomic: ACACACGAGGGAATGGACTTGCGGACAGTAACAACCAAGGAAGTTTTCGAgtatgtgtct ... tgtggtgcagGAAGTTCGGGCTGGATGCTAACACAGTAGACTTTATTGGACACTCTTTGGC
EST: gi|100410627|gb|BY992191.1|BY992191
EST:     ACACACGAGGGAATGGACTTGCGGACAGTAACAACCAAGGAAGTTTTCGA                         GAAGTTCGGGCTGGATGCTAACACAGTAGACTTTATTGGACACTCTTTGGC
genomic: ACACACGAGGGAATGGACTTGCGGACAGTAACAACCAAGGAAGTTTTCGAgtatgtgtct ... tgtggtgcagGAAGTTCGGGCTGGATGCTAACACAGTAGACTTTATTGGACACTCTTTGGC
EST: gi|208359628|gb|DC934615.1|DC934615
EST:     ACACACGAGGGAATGGACTTGCGGACAGTGACAACCAAGGAGGTTTTCGA                         GAAGTTCGGGCTGGATGCCAACACAGTAGACTTTATTGGACACTCTTTGGC
genomic: ACACACGAGGGAATGGACTTGCGGACAGTAACAACCAAGGAAGTTTTCGAgtatgtgtct ... tgtggtgcagGAAGTTCGGGCTGGATGCTAACACAGTAGACTTTATTGGACACTCTTTGGC
EST: gi|67704562|gb|BJ964795.1|BJ964795
EST:     ACACACGAGGGAATGGACTTGCGGACAGTAACAACCAAGGAAGTTTTCGA                         GAAGTTCGGGCTGGATGCTAACACAGTAGACTTTATTGGACACTCTTTGGC
genomic: ACACACGAGGGAATGGACTTGCGGACAGTAACAACCAAGGAAGTTTTCGAgtatgtgtct ... tgtggtgcagGAAGTTCGGGCTGGATGCTAACACAGTAGACTTTATTGGACACTCTTTGGC
EST: gi|162194881|gb|FC368998.1|FC368998
EST:     ACACACGAGGGAATGGACTTGCGGACAGTGACAACCAAGGAGGTTTTCGA                         GAAGTTCGGGCTGGATGCCAACACAGTAGACTTTATTGGACACTCTTTGGC
genomic: ACACACGAGGGAATGGACTTGCGGACAGTAACAACCAAGGAAGTTTTCGAgtatgtgtct ... tgtggtgcagGAAGTTCGGGCTGGATGCTAACACAGTAGACTTTATTGGACACTCTTTGGC

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), 29 (downstream exon)
Score: 23

CTCGCAAGTTTTTCATCTTTGTGCAGAACTATGACGAGGAGGATGCCAAAACACACGAGGGAATGGACTTGCGGACAGTAACAACCAAGGAAGTTTTCGAgtatgtgtct ... tgtggtgcagGAAGTTCGGGCTGGATGCTAACACAGTAGACTTTATTGGACACTCTTTGGCTCTGCATCGCGATGATCGGTTCTTGTCGGAGCCAGCGTTGGACTTTGTG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCGCAAGTTTTTCATCTTTGTGCAGAACTATGACGAGGAGGATGCCAAAACACACGAGGGAATGGACTTGCGGACAGTAACAACCAAGGAAGTTTTCGAgtatgtgtctttctttggccggaatctgtaggttgatttgcgaggtgcatgtgtgttgggcatggtcgcttgacgtgtgttggattgtaggggtggttgtgaccacggcagtaagcttgtggggggtaattctggcgggtgctgcgtctcatcgtgtaaactgtggtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA