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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattatttaggttgtatcgacccttcgcttagaggagtaccgactcttcttcttcctctttttcttcttattcttgtcaatactccttcaatagctgaaagcagtgcgttttattgcagGCAGATATATGGTCATTGGGAATCACTGCCATTGAAATGGCGAAAGGGGAACCACCTTATGCTGATTTACACCCTATGCGGGTGCTCTTTCTAATTCCCA

Basic information

species Physcomitrella patens
transcript PP1S98_82V6.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S98_82V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: LOC_Os07g32400.2 (Oryza sativa), 3'ss of exon 8
gtaattatttaggttgtatcgacccttcgcttagaggagtaccgactcttcttcttcctctttttcttcttattcttgtcaatactccttcaatagctgaaagcagtgcgttttattgcagGCAGATATATGGTCATTGGGAATCACTGCCATTGAAATGGCGAAAGGGGAACCACCTTATGCTGATTTACACCCTATGCGGGTGCTCTTTCTAATTCCCA
                                             || | | | || || |      | |  | |||    | |||  ||      |  ||  |  || ||  |  ||||||||||||| ||||| || || || ||||| ||||||||||| ||||| ||||| ||||  || ||| | || || ||| | || || ||  | || ||  
-----------------------------------------gtagctgtgcgtttttctttaaacagtttgctgcttactga-acttttt-----acccaagtc--tgtgtcctgatgcagGCAGATATCTGGTCGTTAGGTATAACTGCTATTGAAATGGCAAAAGGTGAACCCCCTTTGGCAGATATCCATCCCATGAGAGTTCTTTTCATGATACCTC

upper sequence: PP1S98_82V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GRMZM2G027756_T02 (Zea mays), 3'ss of exon 5
gtaattatttaggttgtatcgacccttcgcttagaggagtaccgactcttcttcttcctctttttcttcttattcttgtcaatactc--cttcaatagctgaaagcagtgcgttttattgcagGCAGATATATGGTCATTGGGAATCACTGCCATTGAAATGGCGAAAGGGGAACCACCTTATGCTGATTTACACCCTATGCGGGTGCTCTTTCTAATTCCCA
                                                   | |||   | ||| ||   ||   || | | || |   |||  ||||   || ||     |||| | ||||||||||||| ||||| || || |||||||||||||||||||| ||||| ||||| |||   || ||| | || || ||| | || || ||  | || ||  
--------------------------------------------------gtacttgtgcatttgctaaataaatttattagtagtgagcttttatagac-aaggc----tgtttcaatgcagGCAGATATCTGGTCTTTAGGTATCACTGCCATTGAAATGGCTAAAGGTGAACCCCCTCTGGCAGATATTCATCCCATGAGAGTTCTTTTCATCATACCTC

upper sequence: PP1S98_82V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA12G35510.1 (Glycine max), 3'ss of exon 8
---gtaat-tatttaggttgtatcgacccttcgcttagaggagtaccgactcttcttcttcctctttttcttc---ttattcttgtcaatactccttcaatagctgaaagcagtgcgttttat---tgcagGCAGATATATGGTCATTGGGAATCACTGCCATTGAAATGGCGAAAGGGGAACCACCTTATGCTGATTTACACCCTATGCGGGTGCTCTTTCTAATTCCCA
   ||||| |||||||  |  |||   | || | |  |         |  |||  || | |  |||| | |||   || |  | |||| |     ||  | |      |   | |  || | |   ||||||||||||| |||||  ||||||||||||| ||||| ||||| || ||||| || ||   ||||||| | ||||| ||| | ||||| ||  | || ||| 
gttgtaatatatttagtctaaatc--tcttttgttatgtttctctttggttctgtttttccacctttattttcagtttgtgatagtcattggattttttagaatcatcactggagtattctgtttttgcagGCAGATATCTGGTCTCTGGGAATCACTGCAATTGAGATGGCAAAGGGGGAGCCGCCACTTGCTGATCTTCACCCAATGAGAGTGCTTTTCATTATACCCC

upper sequence: PP1S98_82V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: GLYMA13G34970.1 (Glycine max), 3'ss of exon 9
---gtaat-tatttaggttgtatcgacccttcgcttagaggagtaccgactcttcttcttcctcttt-ttcttcttattcttgtcaatactccttcaatagctgaaagcagtgcgttttatt---gcagGCAGATATATGGTCATTGGGAATCACTGCCATTGAAATGGCGAAAGGGGAACCACCTTATGCTGATTTACACCCTATGCGGGTGCTCTTTCTAATTCCCA
   ||||| |||||||  |  |||   | || | |  |         |  |||  || |||  |||| || ||  | |  | |||| |  |  |   | |      |   | |   | | ||   |||||||||||| |||||  ||||||||||||| ||||| ||||| || ||||| || ||   ||||||| | ||||| ||| | ||||| ||  | || ||| 
gttgtaatatatttagtctaaatc--tcttttgttatgtttctctttggttctgttttttcacctttatttttagtttgttagtcattgtttttcttagaatcatcactggagtaatctgtttttgcagGCAGATATCTGGTCTCTGGGAATCACTGCAATTGAGATGGCAAAGGGGGAGCCTCCACTTGCTGATCTTCACCCAATGAGAGTGCTTTTCATTATACCCC

upper sequence: PP1S98_82V6.1 (Physcomitrella patens), 3'ss of exon 8
lower sequence: EFJ32910 (Selaginella moellendorffii), 3'ss of exon 8
gtaattatttaggttgtatcgacccttcgcttagaggagtaccgactcttcttcttcctctttttcttcttattcttgtcaatactccttcaatagctgaaagcagtgcgttttattg-cagGCAGATATATGGTCATTGGGAATCACTGCCATTGAAATGGCGAAAGGGGAACCACCTTATGCTGATTTACACCCTATGCGGGTGCTCTTTCTAATTCCCA
                                                                            ||| | |  ||   || ||      |    |  |||| |||| |||||||||||||||||  | ||||| ||| |||| |||||||| || || ||||| |||| ||| |||||||| || ||| | || || ||| | ||||| |
-------------------------------------------------------------------------gtatgtta-tgttctagcagtacggctcattcatctgtttcattgacagGCAGATATATGGTCCCTTGGAATAACTACCATCGAAATGGCAAAGGGTGAACCGCCTTTTGCCGATTTACATCCCATGAGAGTTCTTTTTTTGATTCCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttattcttgtcaatactccttcaatagctgaaagcagtgcgttttattgcagGCAGATATATGGTCATTGGGAATCACTGCCATTGAAATGGCGAAAGGGGAACCACCTTATGCTGATTTACACCCTATGCGGGTGCTCTTTCTAATTCCCA
                                            ttttatt  CT-rich tract
                                            ttttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaattatttaggttgtatcgacccttcgcttagaggagtaccgactcttcttcttcctctttttcttcttattcttgtcaatactccttcaatagctgaaagcagtgcgttttattgcagGCAGATATATGGTCATTGGGAATCACTGCCATTGAAATGGCGAAAGGGGAACCACCTTATGCTGATTTACACCCTATGCGGGTGCTCTTTCTAATTCCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT