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

CATCGAAACCTTGTGAAGCTAATTGGCATCTGCACCGAGAAAATTCGGTGTTTGGTTTATGAACTCATCACGAATGGCAGTGTGGAATCTCATGTGCATGgtacgtacttctgttcattggtgcccactactggacttcatttgtgtggagtcctcttcgatgattagatttatatgtgagtctgaatcatctcattatt...

Basic information

species Physcomitrella patens
transcript PP1S343_14V6.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S343_14V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: LOC_Os01g09860.1 (Oryza sativa), 5'ss of exon 12
CATCGAAACCTTGTGAAGCTAATTGGCATCTGCACCGAGAAAA---TTCGGTGTTTGGTTTATGAACTCATCACGAATGGCAGTGTGGAATCTCATGTGCATGgtacgtacttctgttcattggtgcccactactggacttcatttgtgtggagtcctcttcgatgattagatttatatgtgagtctgaatcatctcattatt
   |||||  | || ||| |  | ||||| ||    ||| | |      | ||| ||||||||||||| ||  ||||||||||||| ||||| ||| ||||||||| ||||||      |||   |||    ||  | ||        ||  |||         ||| |  |   | || ||  | ||| |  | |       
---CGAAATTTGGTCAAGTTGTTAGGCATATGTGTAGAGGAGAACGCAAGATGTCTGGTTTATGAACTTATTCCGAATGGCAGTGTAGAATCCCATTTGCATGgtaagtacttgaaga-attaaggcc----accagcct--------gtaaagtttaagcaattgactgaa---agatctgcctttgacttttgtag-----

upper sequence: PP1S343_14V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GRMZM2G330298_T01 (Zea mays), 5'ss of exon 5
CATCGAAACCTTGTGAAGCTAATTGGCATCTGCACCGAGA---AAATTCGGTGTTTGGTTTATGAACTCATCACGAATGGCAGTGTGGAATCTCATGTGCATGgtacgtacttctgttcattggtgcccactactggacttcatttgtgtggagtcctcttcgatgattagatttatatgtgagtctgaatcatctcattatt--------
    | ||| | || ||||| || || || ||||| |||    | |  || |||||||||||||| ||  |  ||||||||||||||||||||||  |||||||||   | ||   |||  ||    ||   |||  ||||  |  |  |    || | |      || |  | | | | | | | | | |||| | |||           
---AGGAACTTGGTTAAGCTGATAGGTATATGCACAGAGGGGCATAGCCGATGTTTGGTTTATGAGCTTGTTCCGAATGGCAGTGTGGAATCTCACTTGCATGgta---aatttccttctgtg----ccgtaacttcactttctaaggctttcttcatttcatcatataacttctctttcttaattt-agtcattttattggcaagaggtg

upper sequence: PP1S343_14V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA15G18470.1 (Glycine max), 5'ss of exon 7
CATCGAAACCTTGTGAAGCTAATTGGCATCTGCACCGAG---AAAATTCGGTGTTTGGTTTATGAACTCATCACGAATGGCAGTGTGGAATCTCATGTGCATGgtacgta-cttctgttcatt-ggtgcccactactggacttcatttgtgtggagtcctcttcgatgattagatttatatgtgagtctgaatcatctcattatt
    ||||| | || ||| | ||||| || ||| | |||   |   | || ||||| ||||||||||||||  | ||||||||||||||||| ||| | |||||||| || ||| | || |||  ||  | | |||   | | || |||| |  ||| || |  ||| ||    ||  ||| |     |   || |||  |    
---AGAAACTTGGTTAAGTTGATTGGTATATGCGCAGAGGTCAGCTTCCGCTGTTTAGTTTATGAACTCATTCCAAATGGCAGTGTGGAATCCCATTTACATGgtacctaacttttcttgattcagtctcgagtacc--attccaattgttt--agtgctttaagataatggttttcttatat-----ttggtcttctggtag--

upper sequence: PP1S343_14V6.1 (Physcomitrella patens), 5'ss of exon 6
lower sequence: GLYMA09G07140.1 (Glycine max), 5'ss of exon 8
CATCGAAACCTTGTGAAGCTAATTGGCATCTGCACCGAG---AAAATTCGGTGTTTGGTTTATGAACTCATCACGAATGGCAGTGTGGAATCTCATGTGCATGgtacgtacttctgttcattggtgcccactactggacttcatttgtgtggagtcctcttcgatgattagatttatatgtgagtctgaatcatctcattatt
    ||||| | || ||| | ||||| || ||| | |||   |   | || ||| | ||||||||||||||  | ||||||||||||||||| ||| | |||||||| ||  | |  |   |   | |         |||    |||| |  ||| ||    ||| ||  | ||| | | |   | ||  || |||  |    
---AGAAACTTGGTTAAGTTGATTGGTATATGCGCAGAGGTCAGCTTCCGCTGTCTAGTTTATGAACTCATTCCAAATGGCAGTGTGGAATCCCATTTACATGgtacttaacttttcttgattcagtctgaagtaccactctgattgttt--agttcttaaagataat--ggtttttct-tatatttgg-tcttctggtag--

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|100369031|gb|BY984989.1|BY984989
EST:     TTTGGTTTATGAACTCATCACGAATGGCAGTGTGGAATCTCATGTGCATG                         GTTCAGACAAATACACAGATCCTCTCAGCTGGGGAGCGCGCGTTAAAATTG
genomic: TTTGGTTTATGAACTCATCACGAATGGCAGTGTGGAATCTCATGTGCATGgtacgtactt ... ctatctgcagGTTCAGACAAATACACAGATCCTCTCAGCTGGGAAGCGCGCGTTAAAATTG




















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: 17 (upstream exon), 19 (downstream exon)
Score: 1

CATCGAAACCTTGTGAAGCTAATTGGCATCTGCACCGAGAAAATTCGGTGTTTGGTTTATGAACTCATCACGAATGGCAGTGTGGAATCTCATGTGCATGgtacgtactt ... ctatctgcagGTTCAGACAAATACACAGATCCTCTCAGCTGGGAAGCGCGCGTTAAAATTGCTTTAGGATCTGCTCGTGGGCTGGCATACCTACATGAGGATTCTCAGCC




<











<


<