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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGTCATATTACAGCTTATTGAGAAGGCTGGTGATTTTGTTAGTGATGATATATGGTACCGAGTGGTTCAATTTGTTACCAACAATGATGATCTACAGgtactctaaataagtgttttacgtacatattgaattgcgcacttcggtttcttttaaagttaacctagagaagtgtttgggctgaattaactaatacaattattccgttgttatgtttattttcttgaactctttggatacgtag

Basic information

species Physcomitrella patens
transcript PP1S26_36V6.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S26_36V6.1 (Physcomitrella patens), 5'ss of exon 13
lower sequence: LOC_Os03g02150.1 (Oryza sativa), 5'ss of exon 13
TGATGTCATATTACAGCTTATTGAGAAGGCTGGTGATTTTGTTAGTGATGATATATGGTACCGAGTGGTTCAATTTGTTACCAACAATGATGATCTACAGgtactctaaataagtgttttacgtacatattgaattgcgcacttcggtttcttttaaagttaacctagagaagtgtttgggctgaattaactaatacaattattccgttgttatgtttattttcttgaactctttggatacgtag
 ||||| ||  | ||||| || || || || || |||||||| ||||||||||||||||| |||||||| |||||||| ||||||||||| ||||| ||||| ||     |   | |||    |   |   ||  |    |  ||  |||  |||   ||| | || ||    ||  | |  | | || |  |                                                    
CGATGTTATTCTGCAGCTGATAGACAAAGCAGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTCACCAACAATGAAGATCTGCAGgttct-----tgcatatttctgat---tgccga--tagctatctcaattttgttt---gttgaacttgaagtttgacttg--taattttatcag---------------------------------------------------

upper sequence: PP1S26_36V6.1 (Physcomitrella patens), 5'ss of exon 13
lower sequence: GRMZM2G137236_T01 (Zea mays), 5'ss of exon 14
TGATGTCATATTACAGCTTATTGAGAAGGCTGGTGATTTTGTTAGTGATGATATATGGTACCGAGTGGTTCAATTTGTTACCAACAATGATGATCTACAGgtactctaaataagtgttttacgtacatattgaattgcgcacttcggtttcttttaaagttaacctagagaagtgtttgggctgaattaactaatacaattattccgttgttatgtttattttcttgaactctttggatacgtag
|||||| ||  | || ||||| || || ||||| |||||||| ||||||||||||||||| |||||||| ||||||||||| ||||| || || ||||||||  | |  |||  | |  |  |  || | | |  |     || |  ||| |||| || |||   | |   | | ||||     | || |  |                                                    
TGATGTTATTCTTCAACTTATAGACAAAGCTGGAGATTTTGTAAGTGATGATATATGGTATCGAGTGGTACAATTTGTTACGAACAACGAAGACCTACAGgt-ttgtgtatatatatagt-tgagcaaaatcatct-----ctacttttttttttgaattta---tggttcattttttg---caattttatcag---------------------------------------------------

upper sequence: PP1S26_36V6.1 (Physcomitrella patens), 5'ss of exon 13
lower sequence: GLYMA12G30520.1 (Glycine max), 5'ss of exon 13
TGATGTCATATTACAGCTTATTGAGAAGGCTGGTGATTTTGTTAGTGATGATATATGGTACCGAGTGGTTCAATTTGTTACCAACAATGATGATCTACAGgtactctaaataagtgttttacgtacatattgaattgcgcacttcggtttctttta-aagttaacctagagaagtgtttgggctgaattaactaatacaattattccgttgttatgtttattttcttgaactctttggatacgtag
|||||| ||  | ||  | ||||| ||||| ||||||||||| |||||||| |||||||  || |||||||| |||||||| |||||||| ||  |||||||           |||||| |      || ||| |     ||| |    |  |||| |  | |  |   ||   | ||  | ||   | |                                                        
TGATGTGATTCTTCAATTAATTGACAAGGCCGGTGATTTTGTCAGTGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGACTTACAGgt-----------gtgtttgaaacttgtagtgactatgatactgcttcctaatttacacatcattcacaaggcattttccgtctttgtcag-------------------------------------------------------

upper sequence: PP1S26_36V6.1 (Physcomitrella patens), 5'ss of exon 13
lower sequence: GLYMA17G05410.1 (Glycine max), 5'ss of exon 13
TGATGTCATATTACAGCTTATTGAGAAGGCTGGTGATTTTGTTAGTGATGATATATGGTACCGAGTGGTTCAATTTGTTACCAACAATGATGATCTACAGgtactctaaataagtgttttacgtacatattgaattgcgcacttcggtttctttta-aagttaacctagagaagtgtttgggctgaattaactaatacaattattccgttgttatgtttattttcttgaactctttggatacgtag
||| || ||  | ||  | ||||| ||||| || ||||||||||| ||||| |||||||  || |||||||| |||||||| |||||||| ||  |||||||           |||||| |      || ||| |     ||| |    | ||||| |  | |  |   ||   | ||  | ||   | |                                                        
TGACGTGATTCTTCAATTAATTGACAAGGCCGGAGATTTTGTTAGCGATGACATATGGTTTCGGGTGGTTCAGTTTGTTACAAACAATGAAGACTTACAGgt-----------gtgtttgaaacttgtagtgactatgatactgcttcctattttacacatcattcacaaggcattttctgtctttctcag-------------------------------------------------------

upper sequence: PP1S26_36V6.1 (Physcomitrella patens), 5'ss of exon 13
lower sequence: AT5G22770.2 (Arabidopsis thaliana), 5'ss of exon 14
TGATGTCATATTACAGCTTATTGAGAAGGCTGGTGATTTTGTTAGTGATGATATATGGTACCGAGTGGTTCAATTTGTTACCAACAATGATGATCTACAGgtactctaaataagtgtttt-acgtacatattgaattgcgcacttcggtttcttttaaagttaacctagagaagtgtttgggctgaattaactaatacaattattccgttgttatgtttattttcttgaactctttggatacgtag
|||||| ||  | ||| | || || |||||||| ||||||||||| ||||| |||||||  || |||||||| ||||| || || ||||| || || |||||    || |||| ||||   |   | ||||||  |  |  | ||   |  | || ||||||  | || | |  | ||||  ||||                                                            
TGATGTGATCCTTCAGTTGATCGACAAGGCTGGGGATTTTGTTAGCGATGACATATGGTTTCGTGTGGTTCAGTTTGTAACAAATAATGAAGACCTGCAGgt---ttatataattgttaggaaaaatatattgtttatcctattt--atgacattcaaagttg-cttacatatttctttgacctgacag---------------------------------------------------------

upper sequence: PP1S26_36V6.1 (Physcomitrella patens), 5'ss of exon 13
lower sequence: EFJ34224 (Selaginella moellendorffii), 5'ss of exon 13
TGATGTCATATTACAGCTTATTGAGAAGGCTGGTGATTTTGTTAGTGATGATATATGGTACCGAGTGGTTCAATTTGTTACCAACAATGATGATCTACAGgtactctaaataagtgttttacgtacatattgaattgcgcacttcggtttcttttaaagttaacctagagaagtgtttgggctgaattaactaatacaattattccgttgttatgtttattttcttgaactctttggatacgtag
 ||||| || ||||||||||||||||||||||| ||||| ||||| ||||| || |||||| |||| || |||||||| || |||||||||||||| |||||    ||      | |||||    ||| || | |   |  ||||                                                                                                    
GGATGTTATCTTACAGCTTATTGAGAAGGCTGGAGATTTCGTTAGCGATGACATTTGGTACAGAGTAGTCCAATTTGTGACAAACAATGATGATCTGCAGgtggg-tatggcgtttttttattgtcat-ttaactcatgtgcttcacag------------------------------------------------------------------------------------------------

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|100415547|gb|BY992895.1|BY992895
EST:     ATATATGGTACCGAGTGGTTCAATTTGTTACCAACAATGATGATCTACAG                         GTGCATGCTGCAGCTAANGCACTTGACTACTTGGATAAGCCCGCTGTGCAC
genomic: ATATATGGTACCGAGTGGTTCAATTTGTTACCAACAATGATGATCTACAGgtactctaaa ... ggatacgtagGTGCATGCTGCAGCTAAGGCACTTGACTACTTGGATAAGCCCGCTGTGCAC




















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: 26 (upstream exon), 16 (downstream exon)
Score: 2

TGATGTCATATTACAGCTTATTGAGAAGGCTGGTGATTTTGTTAGTGATGATATATGGTACCGAGTGGTTCAATTTGTTACCAACAATGATGATCTACAGgtactctaaa ... ggatacgtagGTGCATGCTGCAGCTAAGGCACTTGACTACTTGGATAAGCCCGCTGTGCACGAAACTATGGTGAAG




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