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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttgactcttgaaaccattctggtattcattggctttggcttttctgctgatctgcaagaagttgtatatatgaatcacgtgtgtgctagccgattctttatctccttgtttacatggaatatggatgcag

Basic information

species Physcomitrella patens
transcript PP1S47_46V6.3
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GLYMA14G07750.1 (Glycine max), 5'ss of exon 7
AGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtac-tcttgactcttgaaaccattctg---gtattcattggctttggcttttctgctgatctgcaagaagttgtatatatgaatcacgtgtgtgctagccgattctttatctccttgtttacatggaatatggatgcag
 || ||| | || || || || |||||||| ||||| ||||||||  | ||||| ||||||||  | |||||||||||||| |||||||| ||||| ||||||  |||||  || | |  |||||  |   || || |    |  |       ||     | |  ||  |  ||      |   | ||   | ||   |                                         
TGGTCGTCGTTTCAGTGAGGGAACAAGTGCTGATCGTGAGATTCAGAGAACACTAATGGAGTTGCTTAATCAACTTGATGGGTTTGATCAACTTGGGAAGgtatatcttgcttcgtaaccccatttagtttgttttgaaaacccataatcacactttacttttagaaacacctgctccctttcctaacaaatttgaaggt----------------------------------------

upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GLYMA04G03180.1 (Glycine max), 5'ss of exon 7
AGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttgactcttgaaaccattctggtattcattggctttggcttttctgctgatctgcaagaagttgtatatatgaatcacgtgtgtgctagccgattctttatctccttgtttacatggaatatggatgcag
||| ||  | || || || || |||||||||||||| ||||||||  | || || |||||| |  | |||||||||||||| |||||||| ||||||||||||   || | ||   || ||           ||||    || | |       ||||| |       |||||      |||  |   |  | ||    ||| ||| |||  || |||   ||||            
AGGTCGCCGTTTCAGTGAGGGAACAAGTGCAGATCGTGAGATTCAGAGAACGCTAATGGAGCTGCTTAATCAACTTGATGGATTTGATCAACTTGGAAAGgtatatttaattccataatcc-----------catttaacttagttaaaagcttgatccg-------ttgta---gcaaattcc---taggttaaggaatt-tttgtctttttatttttgtggag-----------

upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GLYMA17G37220.1 (Glycine max), 5'ss of exon 7
-AGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttgactcttgaaaccattctggtattcattgg---ctttggcttttctgctgatctgcaagaagttgtatatatgaatcacgtgtgtgctagccgattctttatctccttgtttacatggaatatggatgcag
  || ||| | || || || || |||||||| ||||| ||||||||  | ||||| ||||||||  | |||||||||||||| |||||||| ||||| ||||||    |  ||    || ||    | || |   |||    |  |       ||     | |  ||  |  ||      |   | ||   | ||   |                                         
GTGGTCGTCGTTTCAGTGAGGGAACAAGTGCTGATCGTGAGATTCAGAGAACACTAATGGAGTTGCTTAATCAACTTGATGGGTTTGATCAACTTGGGAAggtatatcttgcttagtaaccccacttagtttgttttgaaaaccataatcacactttacttttagaaacacctgctccctttcttaacaaatttgaaggt----------------------------------------

upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 5'ss of exon 7
lower sequence: GLYMA06G03230.1 (Glycine max), 5'ss of exon 7
AGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttgactcttgaaaccattctggtattcattggctttggcttttctgctgatctgcaagaagttgtatatatgaatcacgtgtgtgctagccgattctttatctccttgtttacatggaatatggatgcag
||| ||  | || || || || |||||||||||||| ||||||||  | || || |||||| |  | |||||||| ||||| |||||||| ||||||||||||   || | ||   || ||  | |        ||||  ||      |       | || |  || ||  |    | |   || | |||  |      || |||                               
AGGTCGCCGTTTCAGTGAGGGAACAAGTGCAGATCGTGAGATTCAGAGAACGCTAATGGAGCTGCTTAATCAACTCGATGGATTTGATCAACTTGGAAAGgtatattttattccataatcccatttaac-----ttggagttaaaagcttgatccgt-tgtagcaaattccaaggttaaggaacttttgtcttctttttttttttg------------------------------

upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 5'ss of exon 7
lower sequence: Vv03s0038g04350.t01 (Vitis vinifera), 5'ss of exon 7
AGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttgact---cttgaaaccattctggt-attcattggctttggct-tttctgctgatctgcaagaagttgtatata--tgaat---cacgtgtgtgc-tagccgattctttatctccttgtttacatggaat-atggatgcag-----------------------------------
 || ||| | || ||||| || |||||||| ||||| || |||||  | ||||||||||||||  | || || || ||||| |||||||||||||| |||||| | ||   |    |   |   | |||| |   || || | ||||  | ||| |    ||| |   ||| |||  | ||  || ||    |  ||  ||| |   |    || ||  |  || | ||  |||  |  ||  ||                                      
TGGGCGTCGTTTCAGCGAGGGAACAAGTGCTGATCGTGAAATTCAGAGAACACTCATGGAGTTGCTCAACCAGCTGGATGGATTTGATCAGCTTGGGAAGgtatttttatttgtgttatcagtaactctgtttgctcttttgatttgattgtttataaccatcagtt-gaacttgcttctagttgcatgcatatatgaatgcatcaacatccctctacatgtttttgtatttggctttgtgattgtccaaaaggtgactaaatgtgaagtgtgggtttcctag

upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 5'ss of exon 7
lower sequence: EFJ13668 (Selaginella moellendorffii), 5'ss of exon 7
AGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttgactcttgaaaccattctggtattcattggctttggcttttctgctgatctgcaagaagttgtatatatgaatcacgtgtgtgctagccgattctttatctccttgtttacatggaatatggatgcag
 ||||| ||||| || |||||||| ||||| ||  |||| || ||| | ||||| |||||  | || ||||| || ||||| |||||||||||||||||||||     |    | |||   |||||  | |||  |    ||||| | |   |                                                                                   
CGGACGAAGGTTCAGTGAAGGTACCAGTGCTGACAGAGAAATCCAAAGAACACTTATGGAACTCTTAAATCAGCTAGATGGGTTTGATCAGCTTGGAAAGgta-----gggattggaag--attctcatgttctatatagttggcctcttgtccag--------------------------------------------------------------------------------

upper sequence: PP1S47_46V6.2 (Physcomitrella patens), 5'ss of exon 7
lower sequence: EFJ28962 (Selaginella moellendorffii), 5'ss of exon 7
AGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttgactcttgaaaccattctggtattcattggctttggcttttctgctgatctgcaagaagttgtatatatgaatcacgtgtgtgctagccgattctttatctccttgtttacatggaatatggatgcag
 ||||| ||||| || |||||||| ||||| ||  |||| || ||| | ||||| |||||  | || ||||| || ||||| |||||||||||||||||||||          ||||||   ||||  | |||  |    ||||| | |   |                                                                                   
CGGACGGAGGTTCAGTGAAGGTACCAGTGCTGACAGAGAAATCCAAAGAACACTTATGGAACTCTTAAATCAGCTAGATGGGTTTGATCAGCTTGGAAAGgta------gggattgaaagt-ttctcatgttctatatagttggcctcttgtccag--------------------------------------------------------------------------------

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|162266638|gb|FC441998.1|FC441998
EST:     CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAG                         GTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
genomic: CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttga ... atggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
EST: gi|162266639|gb|FC441999.1|FC441999
EST:     CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAG                         GTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
genomic: CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttga ... atggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
EST: gi|37837457|gb|BJ595465.1|BJ595465
EST:     CACTCATGGAGTTATNGAATCAACTTGATGGTTTTGATCAGCTTGGAAAG                         GTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
genomic: CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttga ... atggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
EST: gi|37836411|gb|BJ594419.1|BJ594419
EST:     CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAG                         GTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
genomic: CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttga ... atggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
EST: gi|162269526|gb|FC445082.1|FC445082
EST:     CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAG                         GTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
genomic: CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttga ... atggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
EST: gi|37834916|gb|BJ592928.1|BJ592928
EST:     CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAG                         GTTAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
genomic: CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttga ... atggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
EST: gi|208353233|gb|DC926158.1|DC926158
EST:     CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAG                         GTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
genomic: CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttga ... atggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
EST: gi|37823384|gb|BJ581450.1|BJ581450
EST:     CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAG                         GTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
genomic: CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttga ... atggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
EST: gi|37833453|gb|BJ591465.1|BJ591465
EST:     CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAG                         GTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG
genomic: CACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttga ... atggatgcagGTAAAGATGATAATGGCCACTAATCGGCCTGATGTTCTTGATCCTGCTTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGACGTAGGTTTAGCGAAGGTACAAGTGCAGATCGAGAGATTCAACGCACACTCATGGAGTTATTGAATCAACTTGATGGTTTTGATCAGCTTGGAAAGgtactcttgactcttgaaaccattctggtattcattggctttggcttttctgctgatctgcaagaagttgtatatatgaatcacgtgtgtgctagccgattctttatctccttgtttacatggaatatggatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT