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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGATGCAGGGCGCTGCTGGGAAATTGTGGACAAGTATAACGTGACCATTTTTTACACAGCCCCAACTGCAATTCGTTCATTGATGCGGTCAGGTGACGAGgtatttatgtcaacaatctcagacctgctttttaaagcaaccgaaacaagcaatcatctcgaaccttattttagggttttttttggtcattttgttttaatcatcagcctggtggttctggcag

Basic information

species Physcomitrella patens
transcript PP1S61_296V6.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S61_296V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: LOC_Os02g32490.1 (Oryza sativa), 5'ss of exon 10
AGATGCAGGGCGCTGCTGGGAAATTGTGGACAAGTATAACGTGACCATTTTTTACACAGCCCCAACTGCAATTCGTTCATTGATGCGGTCAGGTGACGAGgtatttatgtcaacaatctcagacctgctttttaaagcaaccgaaacaagcaatcatctcgaaccttattttag-ggttttttttggtcattttgttttaatcatcagcctggtggttctggcag
 ||| | || || |||||||| |||||||||||||| || ||||| || |||||||| || |||||     |||| ||| | |||||    ||   |||||||   |||   |   |||      |||| | | |     ||   |||||  ||  | ||  |   | |   || | |        | || | || |  | ||                      
TGATTCTGGTCGGTGCTGGGACATTGTGGACAAGTACAAGGTGACAATATTTTACACTGCACCAACACTCGTTCGATCACTCATGCGTGATGGCACCGAGgtacgcatggtgat--tctgtattgtgctctctcatttttccagtacaagatatactttcacaaaatctgcaagtgatacgaacgagccaatctggtg-attc----------------------

upper sequence: PP1S61_296V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: GRMZM2G162663_T03 (Zea mays), 5'ss of exon 9
AGATGCAGGGCGCTGCTGGGAAATTGTGGACAAGTATAACGTGACCATTTTTTACACAGCCCCAACTGCAATTCGTTCATTGATGCGGTCAGGTGACGAGgtatttatgtcaacaatctcagacctgctttttaaagcaaccgaaacaagcaatcatctcgaaccttattttagggttttttttggtcattttgttttaatcatcagcctggtggttctggcag
 ||| | || || |||||||| |||||||||||||| || ||||| || ||||| || |||||||||    |||||||| | |||||    ||    |||||||  ||  |  |  || || |       |||||            |     | | || |||||  ||    ||       | ||    |  || | ||  || | ||               
TGATTCGGGCCGATGCTGGGATATTGTGGACAAGTACAATGTGACAATATTTTATACTGCCCCAACTCTTGTTCGTTCACTCATGCGTGATGGCACTGAGgtatgcatagcttc--tcaca-atacatgatttaattttgtaactttacatggttacct-gaaccagatgcatgg---cccatgggatgctgggtatcaa--attaccc---------------

upper sequence: PP1S61_296V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: EFJ18689 (Selaginella moellendorffii), 5'ss of exon 10
AGATGCAGGGCGCTGCTGGGAAATTGTGGACAAGTATAACGTGACCATTTTTTACACAGCCCCAACTGCAATTCGTTCATTGATGCGGTCAGGTGACGAGgtatttatgtcaacaatctcagacctgctttttaaagcaaccgaaacaagcaatcatctcgaaccttattttagggttttttttggtcattttgttttaatcatcagcctggtggttctggcag
 || || || || || ||||| ||||||||||| ||  |||| |||||||| ||||| ||||| || || |||||  |||||||| | ||||| || |||||||| ||  |   | |||  ||   | |    ||       |   | ||                                                                          
CGACGCTGGTCGGTGTTGGGAGATTGTGGACAAATACCACGTTACCATTTTCTACACGGCCCCGACAGCGATTCGAGCATTGATGAGATCAGGAGATGAGgtattgattaccttattctgtgaatcgttgaagaattttcttgtttccag--------------------------------------------------------------------------

upper sequence: PP1S61_296V6.1 (Physcomitrella patens), 5'ss of exon 9
lower sequence: EFJ36126 (Selaginella moellendorffii), 5'ss of exon 10
AGATGCAGGGCGCTGCTGGGAAATTGTGGACAAGTATAACGTGACCATTTTTTACACAGCCCCAACTGCAATTCGTTCATTGATGCGGTCAGGTGACGAGgtatttatgtcaacaatctcagacctgctttttaaagcaaccgaaacaagcaatcatctcgaaccttattttagggttttttttggtcattttgttttaatcatcagcctggtggttctggcag
 || || || || || ||||| ||||||||||| ||  |||| |||||||| ||||| ||||| || || |||||  |||||||| | ||||| || |||||||| ||  |   | |||  ||   | |    |        |   | ||                                                                          
CGACGCTGGTCGGTGTTGGGAGATTGTGGACAAATACCACGTTACCATTTTCTACACGGCCCCCACAGCGATTCGAGCATTGATGAGATCAGGAGATGAGgtattgattaccttattctgtgaatcgttgaagagttttcttgtttccag--------------------------------------------------------------------------

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: 35 (upstream exon), 32 (downstream exon)
Score: 7

AGATGCAGGGCGCTGCTGGGAAATTGTGGACAAGTATAACGTGACCATTTTTTACACAGCCCCAACTGCAATTCGTTCATTGATGCGGTCAGGTGACGAGgtatttatgt ... gttctggcagCCTGTAAAACGGCACTCGCGTAAGTCACTACGAGTACTTGGCAGTGTCGGAGAACCCATTAATCCAAGCGCATGGAAGTGGTACTACGAAGTAGTTGGCG




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