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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactttcatcctgcgtgctcatttacctgtttgattatttgtcatatttacttgctcatttgccggtgtgatcgtcacttgagtcatgtcaaatgtctggtgacatgtatattacatttctctgcagcttagctttgcatttgagtgttccaaactgtaacgttatttggtctgtccctcgcagGTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCATGATGCGAATGAGGAAGTGGATGGAGACGAGGACAGTGACCAAGAGGATC

Basic information

species Physcomitrella patens
transcript PP1S55_319V6.1
intron # 7
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|162160259|gb|FC336545.1|FC336545
EST:     AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGACCG                         GTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
genomic: AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCGgtactttcat ... tccctcgcagGTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
EST: gi|162237618|gb|FC413051.1|FC413051
EST:     AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCG                         GTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
genomic: AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCGgtactttcat ... tccctcgcagGTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
EST: gi|162236800|gb|FC413479.1|FC413479
EST:     AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCG                         GTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
genomic: AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCGgtactttcat ... tccctcgcagGTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
EST: gi|162189159|gb|FC365979.1|FC365979
EST:     AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCG                         GTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
genomic: AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCGgtactttcat ... tccctcgcagGTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
EST: gi|162217507|gb|FC393183.1|FC393183
EST:     AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCG                         GTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
genomic: AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCGgtactttcat ... tccctcgcagGTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
EST: gi|162236799|gb|FC413478.1|FC413478
EST:     AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCG                         GTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
genomic: AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCGgtactttcat ... tccctcgcagGTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
EST: gi|162223922|gb|FC398928.1|FC398928
EST:     AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCG                         GTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
genomic: AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCGgtactttcat ... tccctcgcagGTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
EST: gi|162206580|gb|FC382949.1|FC382949
EST:     AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCG                         GTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
genomic: AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCGgtactttcat ... tccctcgcagGTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
EST: gi|208351200|gb|DC921535.1|DC921535
EST:     AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCG                         GTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAGATCTTCAT
genomic: AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCGgtactttcat ... tccctcgcagGTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
EST: gi|208345408|gb|DC917319.1|DC917319
EST:     AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCG                         GTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
genomic: AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCGgtactttcat ... tccctcgcagGTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
EST: gi|162160260|gb|FC336546.1|FC336546
EST:     AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCG                         GTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
genomic: AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCGgtactttcat ... tccctcgcagGTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
EST: gi|208372240|gb|DC948043.1|DC948043
EST:     AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCG                         GTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
genomic: AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCGgtactttcat ... tccctcgcagGTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
EST: gi|162189158|gb|FC365978.1|FC365978
EST:     AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCG                         GTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
genomic: AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCGgtactttcat ... tccctcgcagGTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
EST: gi|67694015|gb|BJ954248.1|BJ954248
EST:     AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCG                         GTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
genomic: AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCGgtactttcat ... tccctcgcagGTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
EST: gi|208389139|gb|DC945715.1|DC945715
EST:     AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCG                         GTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
genomic: AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCGgtactttcat ... tccctcgcagGTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
EST: gi|37832680|gb|BJ590692.1|BJ590692
EST:     AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCG                         GTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
genomic: AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCGgtactttcat ... tccctcgcagGTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
EST: gi|162259954|gb|FC435257.1|FC435257
EST:     AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCG                         GTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
genomic: AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCGgtactttcat ... tccctcgcagGTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
EST: gi|6166827|gb|AW145091.1|AW145091
EST:     AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCG                         GTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
genomic: AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCGgtactttcat ... tccctcgcagGTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
EST: gi|162202498|gb|FC380039.1|FC380039
EST:     AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCG                         GTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
genomic: AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCGgtactttcat ... tccctcgcagGTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
EST: gi|162206579|gb|FC382948.1|FC382948
EST:     GATTGAGAAAGCCCAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCG                         GTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
genomic: GATTGAG-AAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCGgtactttcat ... tccctcgcagGTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
EST: gi|162163621|gb|FC339531.1|FC339531
EST:     AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCG                         GTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
genomic: AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCGgtactttcat ... tccctcgcagGTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
EST: gi|22491982|gb|BU051905.1|BU051905
EST:     AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCG                         GTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
genomic: AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCGgtactttcat ... tccctcgcagGTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
EST: gi|208353396|gb|DC946302.1|DC946302
EST:     AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCG                         GTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
genomic: AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCGgtactttcat ... tccctcgcagGTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
EST: gi|162223923|gb|FC398929.1|FC398929
EST:     AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCG                         GTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
genomic: AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCGgtactttcat ... tccctcgcagGTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
EST: gi|208386257|gb|DC952970.1|DC952970
EST:     AGATTGAGAGGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCG                         GTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
genomic: AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCGgtactttcat ... tccctcgcagGTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
EST: gi|208398568|gb|DC916089.1|DC916089
EST:     AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCG                         GTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
genomic: AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCGgtactttcat ... tccctcgcagGTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
EST: gi|162238555|gb|FC417410.1|FC417410
EST:     AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCG                         GTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
genomic: AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCGgtactttcat ... tccctcgcagGTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
EST: gi|37836440|gb|BJ594448.1|BJ594448
EST:     AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCG                         GTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT
genomic: AGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCGgtactttcat ... tccctcgcagGTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCAT

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: 34 (upstream exon), 31 (downstream exon)
Score: 12

GACCTTGGAATTACAGTGTTGGAGAATGCTATCAAAGCTTGTACGAAAGAGATTGAGAAGCACAAAGGAAAGCTTCTTGTCAAGGAGCCACCACGAGCGgtactttcat ... tccctcgcagGTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCATGATGCGAATGAGGAAGTGGATGGAGACGAGGACAGTGACCAAGAGGATC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagctttgcatttgagtgttccaaactgtaacgttatttggtctgtccctcgcagGTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCATGATGCGAATGAGGAAGTGGATGGAGACGAGGACAGTGACCAAGAGGATC
                         ctgtaac  putative branch site (score: 12)
                                         tctgtccctc  putative PPT
                                 ttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactttcatcctgcgtgctcatttacctgtttgattatttgtcatatttacttgctcatttgccggtgtgatcgtcacttgagtcatgtcaaatgtctggtgacatgtatattacatttctctgcagcttagctttgcatttgagtgttccaaactgtaacgttatttggtctgtccctcgcagGTGAGTGAGAGAGAGGAGCGGTTCCTCGCAGAAACTATTAAAAATCTTCATGATGCGAATGAGGAAGTGGATGGAGACGAGGACAGTGACCAAGAGGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT