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'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCGAAAAGTACGTTGATTATGCTCTAGACGTTCCTATGTATTTTGTCTACCGTAACGGTCGGTACGTTGACTGTTCTGGTCTGTCATTTAAGgtaatttactttgccacagcaggctttagcatgacaaggcgttcattgctagtttattatacacgattagattgccaattttttaatcatctgtgttgtgtaatgcttcggctaccgaagtttcgggtctttagggcacaaatcatttcatcaacttggagcattgtattttgcag

Basic information

species Physcomitrella patens
transcript PP1S479_14V6.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S479_14V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GLYMA05G37850.3 (Glycine max), 5'ss of exon 10
GTTCGAAAAGTACGTTGATTATGCTCTAGACGTTCCTATGTATTTTGTCTACCGTAACGGTCGGTACGTTGACTGTTCTGGTCTGTCATTTAAGgtaatttactttgccacagcaggctttagcatgacaaggcgttcattgctagtttattatacacgattagattgccaatttt--ttaatcatctgtgttgtgtaatgcttcggctaccgaagtttcgggtctttagggcacaaatcatttcatcaacttggagcattgtattttgcag
||| ||  | || |||||||||||||| || |||||||||||||||||||| || ||     | ||  | |||||  ||||   | | || | |||  |    | |  |          ||   ||   | |   |  |||       |   || |   |||      |  | |||  || | ||         |||| | |||    | |  ||          | ||| | |    | ||||  | |  ||| ||               
GTTTGAGCAATATGTTGATTATGCTCTTGATGTTCCTATGTATTTTGTCTATCGGAAAAACAGATATATCGACTGCACTGGAAAGACCTTCAGGgt--tcccatctatctttaatattcttgtaatttaaggatatctattctagccctgccattctttattgtgaaacttactttgcttgaccacactatacatgtagt-cttgatttgctcaa----------tgtagagaattggttattttttta--ttgcag---------------

upper sequence: PP1S479_14V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GLYMA08G01750.1 (Glycine max), 5'ss of exon 10
GTTCGAAAAGTACGTTGATTATGCTCTAGACGTTCCTATGTATTTTGTCTACCGTAACGGTCGGTACGTTGACTGTTCTGGTCTGTCATTTAAGgtaatttactttgccacagcaggctttagcatgacaaggc-gttcattgctagtttattatacacgattagattgccaatttt--ttaatcatctgtgttgtgtaatgcttcggctaccgaagtttcgggtctttagggcacaaatcatttcatcaacttggagcattgtattttgcag
|||  |  |||| ||||||||||| || || |||||||||||||||||||| || ||     | ||  | |||||| ||||   | | || | |||     |  |  |   |  |  |||  | |    |||||  |  ||||          || |   |||      |  | |||  || | |||         ||| | |||    |    ||          | ||| | |   || ||||  |    ||| ||               
GTTTCAGCAGTATGTTGATTATGCACTTGATGTTCCTATGTATTTTGTCTATCGGAAACACAGATATATCGACTGTACTGGAAAGACCTTCAGGgtt-cccatctatctttaatattctt--gtaatttaaggctatctattgtagccccgacattctttattgtgaaacttactttgcttgaccatagtatacacgtagt-cttgatttgttcaa----------tgtagagaattgattatttttttttattgcag---------------
















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|22131816|gb|BQ826821.1|BQ826821
EST:     TTGTCTACCGTAACGGTCGGTACGTTGACTGTTCTGGTCTGTCATTTAAG                         GATTTTCTGGAA
genomic: TTGTCTACCGTAACGGTCGGTACGTTGACTGTTCTGGTCTGTCATTTAAGgtaatttact ... tattttgcagGATTTTCTGGAA
EST: gi|67725923|gb|BJ976182.1|BJ976182
EST:     TTGTCTACCGTAACGGTCGGTACGTTGACTGTTCTGGTCTGTCATTTAAG                         GATTTTCTGGAAGGAAAGCTATCTGTTCTGCCTGGAGAGAGGCCTACACTG
genomic: TTGTCTACCGTAACGGTCGGTACGTTGACTGTTCTGGTCTGTCATTTAAGgtaatttact ... tattttgcagGATTTTCTGGAAGGAAAGCTATCTGTTCTGCCTGGAGAGAGGCCTACACTG
EST: gi|208346034|gb|DC921279.1|DC921279
EST:     AACGGTCGGTACGTTGACTGTTCTGGTCTGTCATTTAAG                         GATTTTCTGGAAGGAAAGCTATCCGTTCTGCCTGGAGAGAGGCCTACACTG
genomic: AACGGTCGGTACGTTGACTGTTCTGGTCTGTCATTTAAGgtaatttact ... tattttgcagGATTTTCTGGAAGGAAAGCTATCTGTTCTGCCTGGAGAGAGGCCTACACTG
EST: gi|162182551|gb|FC357526.1|FC357526
EST:     TTGTCTACCGTAACGGTCGGTACGTTGACTGTTCTGGTCTGTCATTTAAG                         GATTTTCTGGAAGGCAAGCTATCTGTTCTGCCTGGAGAGAGGCCTACACTG
genomic: TTGTCTACCGTAACGGTCGGTACGTTGACTGTTCTGGTCTGTCATTTAAGgtaatttact ... tattttgcagGATTTTCTGGAAGGAAAGCTATCTGTTCTGCCTGGAGAGAGGCCTACACTG
EST: gi|67725390|gb|BJ975649.1|BJ975649
EST:     TTGTCTACCGTAACGGTCGGTACGTTGACTGTTCTGGTCTGTCATTTAAG                         GATTTTCTGGAAGGAAAGCTATCTGTTCTGCCTGGAGAGAGGCCTACACTG
genomic: TTGTCTACCGTAACGGTCGGTACGTTGACTGTTCTGGTCTGTCATTTAAGgtaatttact ... tattttgcagGATTTTCTGGAAGGAAAGCTATCTGTTCTGCCTGGAGAGAGGCCTACACTG
EST: gi|37840845|gb|BJ598853.1|BJ598853
EST:     TTGTCTACCGTAACGGTCGGTACGTTGACTGTTCTGGTCTGTCATTTAAG                         GATTTTCTGGAAGGAAAGCTATCTGTTCTGCCTGGAGAGAGGCCTACACTG
genomic: TTGTCTACCGTAACGGTCGGTACGTTGACTGTTCTGGTCTGTCATTTAAGgtaatttact ... tattttgcagGATTTTCTGGAAGGAAAGCTATCTGTTCTGCCTGGAGAGAGGCCTACACTG
EST: gi|162239290|gb|FC415389.1|FC415389
EST:     TTGTCTACCGTAACGGTCGGTACGTTGACTGTTCTGGTCTGTCATTTAAG                         GATTTTCTGGAAGGCAAGCTATCTGTTCTGCCTGGAGAGAGGCCTACACTG
genomic: TTGTCTACCGTAACGGTCGGTACGTTGACTGTTCTGGTCTGTCATTTAAGgtaatttact ... tattttgcagGATTTTCTGGAAGGAAAGCTATCTGTTCTGCCTGGAGAGAGGCCTACACTG

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: 29 (upstream exon), 35 (downstream exon)
Score: 10

GTTCGAAAAGTACGTTGATTATGCTCTAGACGTTCCTATGTATTTTGTCTACCGTAACGGTCGGTACGTTGACTGTTCTGGTCTGTCATTTAAGgtaatttact ... tattttgcagGATTTTCTGGAAGGAAAGCTATCTGTTCTGCCTGGAGAGAGGCCTACACTGAGCGATTGGGAGAATCACTTAACAACAATATTTCCCGAG




<











<


<