Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATGTGCAAGCCACCAAGGGTCTTCGGTAGCAACGATTGTGCGACGTGCCAGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtccaaaagtagattttttgtctcgtatgtgctgaggggctatattgtattggcctgcttttgaccttcccacattcccgtcttgtcttcttt...

Basic information

species Physcomitrella patens
transcript PP1S69_133V6.3
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|37833065|gb|BJ591077.1|BJ591077
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|37834827|gb|BJ592839.1|BJ592839
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAGTGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|67691964|gb|BJ952197.1|BJ952197
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|37848068|gb|BJ606076.1|BJ606076
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|67701209|gb|BJ961442.1|BJ961442
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|37830962|gb|BJ588974.1|BJ588974
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|37850286|gb|BJ608294.1|BJ608294
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|18338176|gb|BJ170200.1|BJ170200
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|208382592|gb|DC919788.1|DC919788
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|67700323|gb|BJ960556.1|BJ960556
EST:     CAGGACCCAAAGANTCAG                         GAAANGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCA
genomic: CAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAA-GGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCA
EST: gi|67701499|gb|BJ961732.1|BJ961732
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|37844837|gb|BJ602845.1|BJ602845
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|37843392|gb|BJ601400.1|BJ601400
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|208381709|gb|DC928372.1|DC928372
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|37836841|gb|BJ594849.1|BJ594849
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|37850916|gb|BJ608924.1|BJ608924
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|37847199|gb|BJ605207.1|BJ605207
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|37839648|gb|BJ597656.1|BJ597656
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|37847556|gb|BJ605564.1|BJ605564
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|37841081|gb|BJ599089.1|BJ599089
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|37832636|gb|BJ590648.1|BJ590648
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|37839037|gb|BJ597045.1|BJ597045
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|37827635|gb|BJ585647.1|BJ585647
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|37845211|gb|BJ603219.1|BJ603219
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|37850132|gb|BJ608140.1|BJ608140
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|162152065|gb|FC328460.1|FC328460
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCGGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|37822862|gb|BJ580928.1|BJ580928
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|37830832|gb|BJ588844.1|BJ588844
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|37852445|gb|BJ610453.1|BJ610453
EST:     GTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCA
genomic: GTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGAC-TCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCA
EST: gi|37827636|gb|BJ585648.1|BJ585648
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|162278634|gb|FC455032.1|FC455032
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|162278633|gb|FC455031.1|FC455031
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|18340944|gb|BJ172976.1|BJ172976
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|37822569|gb|BJ580635.1|BJ580635
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|208392989|gb|DC946011.1|DC946011
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|67726731|gb|BJ976990.1|BJ976990
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|162248690|gb|FC424543.1|FC424543
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
EST: gi|37827314|gb|BJ585326.1|BJ585326
EST:     AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAG                         GAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC
genomic: AGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCAC

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: 24 (upstream exon), 28 (downstream exon)
Score: 4

GATGTGCAAGCCACCAAGGGTCTTCGGTAGCAACGATTGTGCGACGTGCCAGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtc ... attaccgcagGAAAGGGTGCTGGATGTGCTGATGAATGCTTGCAACCGTATTACTAATCACGTTGATGAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATGTGCAAGCCACCAAGGGTCTTCGGTAGCAACGATTGTGCGACGTGCCAGTTTTTCATTTTAGAGATCAAAATAAAATTGCAGGACCCAAAGACTCAGgtaatcagtccaaaagtagattttttgtctcgtatgtgctgaggggctatattgtattggcctgcttttgaccttcccacattcccgtcttgtcttcttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA