Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgttggtgaggttttgtttgttttttcgagtggggtattttgtaaaagatttggatattatttgttaattggaagatgcaactgcgttcttttgttatagGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG

Basic information

species Physcomitrella patens
transcript PP1S97_74V6.1
intron # 1
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|37829134|gb|BJ587146.1|BJ587146
EST:     CCTTTCGGGTTCGCTTGGGCGCTGCATCCNTTCTCCTCCCTTTCGCAATG                         GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
genomic: CCTTTCGGGTTCGCTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATGgtatggttct ... tttgttatagGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
EST: gi|162274404|gb|FC450431.1|FC450431
EST:     TTCGCTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATG                         GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
genomic: TTCGCTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATGgtatggttct ... tttgttatagGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
EST: gi|162274878|gb|FC451113.1|FC451113
EST:     TTCGCTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATG                         GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
genomic: TTCGCTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATGgtatggttct ... tttgttatagGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
EST: gi|162262677|gb|FC438472.1|FC438472
EST:     TTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATG                         GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
genomic: TTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATGgtatggttct ... tttgttatagGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
EST: gi|18369346|gb|BJ201432.1|BJ201432
EST:     TTTCGGGTTCGCTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATG                         GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
genomic: TTTCGGGTTCGCTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATGgtatggttct ... tttgttatagGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
EST: gi|162274403|gb|FC450430.1|FC450430
EST:     CCCTTTCGCAATG                         GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
genomic: CCCTTTCGCAATGgtatggttct ... tttgttatagGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
EST: gi|162266465|gb|FC442501.1|FC442501
EST:     CTTCTCCTCCCTTTCGCAATG                         GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
genomic: CTTCTCCTCCCTTTCGCAATGgtatggttct ... tttgttatagGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
EST: gi|18346854|gb|BJ178899.1|BJ178899
EST:     CCTTTCGGGTTCGCTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATG                         GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
genomic: CCTTTCGGGTTCGCTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATGgtatggttct ... tttgttatagGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
EST: gi|18360908|gb|BJ192972.1|BJ192972
EST:     GGTTCGCTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATG                         GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
genomic: GGTTCGCTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATGgtatggttct ... tttgttatagGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
EST: gi|18353902|gb|BJ185957.1|BJ185957
EST:     CCTTTCGGGTTCGCTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATG                         GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
genomic: CCTTTCGGGTTCGCTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATGgtatggttct ... tttgttatagGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
EST: gi|162272845|gb|FC448820.1|FC448820
EST:     TTCGCTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATG                         GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
genomic: TTCGCTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATGgtatggttct ... tttgttatagGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
EST: gi|18348254|gb|BJ180301.1|BJ180301
EST:     CCTTTCGGGTTCGCTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATG                         GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
genomic: CCTTTCGGGTTCGCTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATGgtatggttct ... tttgttatagGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
EST: gi|37838798|gb|BJ596806.1|BJ596806
EST:     GGTTCGCTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATG                         GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
genomic: GGTTCGCTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATGgtatggttct ... tttgttatagGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
EST: gi|18343066|gb|BJ175104.1|BJ175104
EST:     CCTTTCGGGTTCGCTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATG                         GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
genomic: CCTTTCGGGTTCGCTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATGgtatggttct ... tttgttatagGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
EST: gi|162203338|gb|FC378785.1|FC378785
EST:     CTTTCGGGTTCGCTTGGGCGCTGCATCCCTTCACCTCCCTTTCGCAATG                         GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
genomic: CTTTCGGGTTCGCTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATGgtatggttct ... tttgttatagGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
EST: gi|18373967|gb|BJ205545.1|BJ205545
EST:     CCTTTCGGGTTCGCTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATG                         GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
genomic: CCTTTCGGGTTCGCTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATGgtatggttct ... tttgttatagGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
EST: gi|162266464|gb|FC442500.1|FC442500
EST:     CCCTTTCGCAATG                         GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
genomic: CCCTTTCGCAATGgtatggttct ... tttgttatagGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
EST: gi|18367163|gb|BJ199244.1|BJ199244
EST:     GGTTCGCTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATG                         GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
genomic: GGTTCGCTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATGgtatggttct ... tttgttatagGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
EST: gi|18350164|gb|BJ182215.1|BJ182215
EST:     CCTTTCGGGTTCGCTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATG                         GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
genomic: CCTTTCGGGTTCGCTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATGgtatggttct ... tttgttatagGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
EST: gi|162230491|gb|FC407406.1|FC407406
EST:     GGGCGCTGCATCCCTTCACCTCCCTTTCGCAATG                         GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
genomic: GGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATGgtatggttct ... tttgttatagGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
EST: gi|162201674|gb|FC377478.1|FC377478
EST:     CTTGGGCGCTGCATCCCTTCACCTCCCTTTCGCAATG                         GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
genomic: CTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATGgtatggttct ... tttgttatagGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
EST: gi|18344711|gb|BJ176752.1|BJ176752
EST:     CCTTTCGGGTTCGCTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATG                         GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
genomic: CCTTTCGGGTTCGCTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATGgtatggttct ... tttgttatagGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
EST: gi|18375101|gb|BJ206679.1|BJ206679
EST:     GGGTTCGCTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATG                         GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
genomic: GGGTTCGCTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATGgtatggttct ... tttgttatagGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
EST: gi|162262676|gb|FC438471.1|FC438471
EST:     CCCTTTCGCAATG                         GTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
genomic: CCCTTTCGCAATGgtatggttct ... tttgttatagGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG

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: 41

GTTTCTCTCCTTCACTTCTCCCTTTCGGGTTCGCTTGGGCGCTGCATCCCTTCTCCTCCCTTTCGCAATGgtatggttct ... tttgttatagGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagatttggatattatttgttaattggaagatgcaactgcgttcttttgttatagGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG
                 tgttaat  putative branch site (score: 41)
                                         ttcttttgtt  putative PPT
         atattatttgttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgttggtgaggttttgtttgttttttcgagtggggtattttgtaaaagatttggatattatttgttaattggaagatgcaactgcgttcttttgttatagGTGAAGTACGCGAGAGATCCGGATAATGCGACGAAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC