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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gattagggttttagggttttggtgctcttttggtcccgactgtgtccgttggtattggagttgcaatacctaatagatggctgttttttctcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG

Basic information

species Physcomitrella patens
transcript PP1S84_153V6.1
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|162242036|gb|FC419409.1|FC419409
EST:     CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAG                         ATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
genomic: CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAGgtaccactct ... tcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
EST: gi|162200859|gb|FC377054.1|FC377054
EST:     CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAG                         ATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
genomic: CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAGgtaccactct ... tcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
EST: gi|18344903|gb|BJ176944.1|BJ176944
EST:     CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAG                         ATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
genomic: CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAGgtaccactct ... tcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
EST: gi|162200093|gb|FC376555.1|FC376555
EST:     CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAG                         ATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
genomic: CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAGgtaccactct ... tcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
EST: gi|162240450|gb|FC416016.1|FC416016
EST:     CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAG                         ATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
genomic: CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAGgtaccactct ... tcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
EST: gi|19788851|gb|BQ040961.1|BQ040961
EST:     CGCACGAATTTGTGCGCAACTACACTGCCCACTTGAAGCGCTCTGGCAAG                         ATTGAAGATCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
genomic: CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAGgtaccactct ... tcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
EST: gi|162200888|gb|FC377083.1|FC377083
EST:     CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAG                         ATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
genomic: CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAGgtaccactct ... tcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
EST: gi|19781146|gb|BQ039660.1|BQ039660
EST:     CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAG                         ATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
genomic: CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAGgtaccactct ... tcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
EST: gi|162199841|gb|FC376707.1|FC376707
EST:     CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAG                         ATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
genomic: CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAGgtaccactct ... tcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
EST: gi|37824109|gb|BJ582175.1|BJ582175
EST:     CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAG                         ATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
genomic: CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAGgtaccactct ... tcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
EST: gi|67726367|gb|BJ976626.1|BJ976626
EST:     CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAG                         ATTGAAGTTCCCGCATGGGCTGATCTTGTGTTAAGACCGCTACCTTCAAGG
genomic: CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAGgtaccactct ... tcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTG--AAGACCGCTACCTTCAAGG
EST: gi|162204915|gb|FC380597.1|FC380597
EST:     CGCACGAATTTGTGCGCAATTACGCTGCCCACTTGAAGCGCTCTGGCAAG                         ATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
genomic: CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAGgtaccactct ... tcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
EST: gi|19786736|gb|BQ040532.1|BQ040532
EST:     CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAG                         ATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
genomic: CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAGgtaccactct ... tcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
EST: gi|162239228|gb|FC416497.1|FC416497
EST:     CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAG                         ATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
genomic: CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAGgtaccactct ... tcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
EST: gi|162214855|gb|FC390990.1|FC390990
EST:     CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAG                         ATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
genomic: CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAGgtaccactct ... tcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
EST: gi|67508621|gb|BJ941483.1|BJ941483
EST:     CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAG                         ATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
genomic: CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAGgtaccactct ... tcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
EST: gi|162200860|gb|FC377055.1|FC377055
EST:     CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAG                         ATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
genomic: CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAGgtaccactct ... tcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
EST: gi|67717860|gb|BJ968119.1|BJ968119
EST:     CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAG                         ATTGAAGTTCCCGCATGGGCTGATCTTGTGTTAAGACCGCTACCTTCAAGG
genomic: CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAGgtaccactct ... tcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTG--AAGACCGCTACCTTCAAGG
EST: gi|162246164|gb|FC423600.1|FC423600
EST:     CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAG                         ATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
genomic: CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAGgtaccactct ... tcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
EST: gi|7047316|gb|AW477210.1|AW477210
EST:     CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAG                         ATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
genomic: CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAGgtaccactct ... tcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
EST: gi|162274330|gb|FC450298.1|FC450298
EST:     CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAG                         ATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
genomic: CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAGgtaccactct ... tcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
EST: gi|162204916|gb|FC380598.1|FC380598
EST:     CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAG                         ATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
genomic: CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAGgtaccactct ... tcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
EST: gi|7207529|gb|AW561528.1|AW561528
EST:     CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAG                         ATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
genomic: CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAGgtaccactct ... tcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
EST: gi|162218915|gb|FC394861.1|FC394861
EST:     CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAG                         ATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
genomic: CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAGgtaccactct ... tcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
EST: gi|162214237|gb|FC390283.1|FC390283
EST:     CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAG                         ATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
genomic: CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAGgtaccactct ... tcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
EST: gi|18340129|gb|BJ172157.1|BJ172157
EST:     CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAG                         ATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
genomic: CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAGgtaccactct ... tcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
EST: gi|162219483|gb|FC396961.1|FC396961
EST:     CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAG                         ATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
genomic: CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAGgtaccactct ... tcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
EST: gi|162276832|gb|FC452514.1|FC452514
EST:     CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAG                         ATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
genomic: CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAGgtaccactct ... tcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
EST: gi|7207470|gb|AW561471.1|AW561471
EST:     CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAG                         ATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
genomic: CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAGgtaccactct ... tcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
EST: gi|162236411|gb|FC412778.1|FC412778
EST:     CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAG                         ATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
genomic: CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAGgtaccactct ... tcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
EST: gi|7047136|gb|AW477030.1|AW477030
EST:     CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAG                         ATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA
genomic: CGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAGgtaccactct ... tcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAA

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), 35 (downstream exon)
Score: 56

CGCCCATAGTCGCACCTCCGCCATGGCCAAAACTGTTAAAGACGTGCCCTCGCACGAATTTGTGCGCAACTACGCTGCCCACTTGAAGCGCTCTGGCAAGgtaccactct ... tcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgttggtattggagttgcaatacctaatagatggctgttttttctcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG
                      acctaat  putative branch site (score: 56)
                                   ctgttttttctcgtct  putative PPT
                         taatagat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gattagggttttagggttttggtgctcttttggtcccgactgtgtccgttggtattggagttgcaatacctaatagatggctgttttttctcgtctgcagATTGAAGTTCCCGCATGGGCTGATCTTGTGAAGACCGCTACCTTCAAGGAACTTGCCCCTTACGATGCTGACTGGTACTACATCAGAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT