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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtgcaagaactcgatcgttttgatttggatccagtttctaagcattggattgttctggcag

Basic information

species Selaginella moellendorffii
transcript EFJ34676
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ34676 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: LOC_Os03g38000.2 (Oryza sativa), 5'ss of exon 3
CGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtgcaagaactcgatcgttttgatttggatccagtttctaagcattg-gattgttctggcag---------------------------
 |||||||| |||||||||||||| || ||||||||||| |||||    || || || |||| |||||||  ||| ||| | ||||| ||  || | |||||        | | ||   |  |      |    |||  || | |   |||  || ||||                             
AGCCAAGTCCATGAAGTTCAAGGATGGTTACATGATCTCATCTGGTCAGCCAGTCAATGAGTACATTGACTCGGCTGTGAGACACGTGCTCCTGAGACAGgtttgt---ttggttcaactcaagcatcgtagtatttaaaaacctcatgatctttttggctcaacgcacttgttcattatcttttgcag

upper sequence: EFJ34676 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: LOC_Os07g41750.1 (Oryza sativa), 5'ss of exon 5
CGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgt----gcaagaactcgatcgttttgatttggatc---cagtttctaagca-----ttggattgttctggcag--------------------
 || || || |||||||||||||||||||||||||| || |||||    || || |||  ||  ||||||   || ||  | || || ||| || | |||||     ||  || || |||  ||||| |   ||    | || ||   |       ||| ||| || |   ||                    
TGCTAAATCCATGAAGTTCAAGGACGGATACATGATTTCTTCTGGTTATCCTGTTAACTTGTATATTGACTCTGCTGTTAGACATGTTCTTCTGAGACAGgtttgtacataaaatccatccgtttgaataaaatgttgctgtctccttgtgatagcttgaatttttttcttagaagctgcttcttgttttcag

upper sequence: EFJ34676 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: GRMZM2G099352_T01 (Zea mays), 5'ss of exon 3
CGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtgcaagaact-cgatcgttttgat-ttggatccagtttctaagcattggattgttctggcag---------------------------------------------
 |||||||| |||||||||||||| || ||||||||||| |||||    || |||||||||| |||||||  ||| ||| | ||||| ||| |  | |||||       ||   |||   |  || || | ||   | || |      ||| |    |  |                                               
AGCCAAGTCCATGAAGTTCAAGGATGGCTACATGATCTCATCTGGTCAGCCAGTGAACGAGTACATTGACTCGGCTGTGAGACACGTTCTTCTCAGACAGgtttgtttgctgtaatctcctcaatgtttggtcgtctctcaagagcagggactacgttttccacgtgcttcaatttaattacccaactaacttcaatctgtcgcgcag

upper sequence: EFJ34676 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: GRMZM2G074300_T03 (Zea mays), 5'ss of exon 3
CGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgt-------gcaagaactcgatcgttttgatttggatccagtttc---taagcattggattgttctggcag-----------------------------------------
 |||||||| |||||||||||||| || ||||||||||| |||||    || ||||| |||| ||| |||   || ||| | ||||||||  |  | |||||       || | || | |  |||| | || |   |     |     |||||| |  ||| |    |                                            
AGCCAAGTCCATGAAGTTCAAGGATGGCTACATGATCTCATCTGGTCAGCCAGTGAATGAGTACATCGACTCAGCTGTGAGACACGTCCTCCTCAGACAGgtttgttttgctacaatt-gcccgttgtaatgtctgtttgtctctgggtaagcacttcattttcgacgttccaaatgtaatttctcaacaaacatctttttctgtcgtgcag

upper sequence: EFJ34676 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: PP1S31_178V6.1 (Physcomitrella patens), 5'ss of exon 5
CGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtgc----aagaactcgatcgttttgat--ttggatccagtttctaagcat--tggattgttctggcag------------------------------------------------------------------
 || ||||| |||||||||||||||||||||||||| || ||||| ||||| || ||||| | |||||| || || ||  | |||||| | ||||| |||||       | | ||   |  | ||| |  |   | ||  |  || ||  |  |  ||| || ||                                                                      
TGCAAAGTCCATGAAGTTCAAGGACGGATACATGATATCATCTGGAAGCCCTGTCAACGACTACATTGATAGTGCTGTAAGACACGTCATGTTGCGACAGgtattcttgacagctttttaatcttgttagtctcaaccgttcactgagtttcttcaattattgtgatttcattcggaaggctcgtttattagttttttactacgaatctcaggttttggatgtatgtttttgcag

upper sequence: EFJ34676 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: PP1S127_74V6.1 (Physcomitrella patens), 5'ss of exon 5
CGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtgcaagaactcgatcgttttgatttggatccagtttctaagcattggattgttctggcag---------------------------------------------------------
 || ||||| |||||||||||||| || ||||||||||| ||||| ||||| || ||||| | ||| ||||| ||||| || |||||  | ||||| ||||| ||  |  |   |  | |   |  | | |   ||| |     | | |   |  ||   |                                                         
TGCTAAGTCCATGAAGTTCAAGGATGGTTACATGATCTCATCTGGGAGCCCTGTCAACGATTACATCGACAGTGCCGTCCGACACGTTATGTTGCGTCAGgtacacaagatgcttgatgtccgtcagtagctcctttttcgtactagaaagatattgattgatagtcggtgttcccgaagtgaatctgaagtggaggattactttggtatgtttacag

upper sequence: EFJ34676 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: PP1S41_146V6.1 (Physcomitrella patens), 5'ss of exon 5
CGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtg---caagaactcgatc-gttttgatttggatccagtttctaagcattggattgttctggcag----------------------------------------------------------------------------
 |||||||| |||||||||||||| || |||||||| || || || |||||||| ||||| | ||| || || || ||  | |||||| | || || |||||    | || |     || ||  ||   |   |   || ||   ||    ||||  ||   | |                                                                            
AGCCAAGTCTATGAAGTTCAAGGATGGCTACATGATTTCATCAGGAAGCCCCGTCAACGATTACATCGATAGTGCTGTCAGACACGTCATGTTACGACAGgtttgtcgagcagctattcagtggtgtcctctctgtggtctccttgct---gatttctcctacggtctttgttttcaagaaaaaatctcgtttgcaagttgtctgtaatgtatcttagaaatgtttcgttatttttttcag

upper sequence: EFJ34676 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: PP1S454_3V6.1 (Physcomitrella patens), 5'ss of exon 5
CGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtg-----caagaactcgatcgttttgatttggatccagtt--tctaagcattggattgttctggcag------------------------------------------------------------------------------------
 |||||||| ||||||||||||||||| |||||||| || || || ||||| || || || | ||| ||||| || ||  | |||||| | ||||| |||||      ||    || |  | |||   | |  |   ||||  |||     ||   || | ||    |                                                                                    
GGCCAAGTCTATGAAGTTCAAGGACGGCTACATGATTTCATCCGGAAGCCCTGTCAATGATTACATCGACAGTGCTGTTAGGCACGTCATGTTGCGTCAGgtatgttacatatccttggccatttctctgttaactgagtttttctggctcttcccttatacttcttgtatcaaattgagttatctcagcatttcggtaatgctttcagtttgccgttgtgaaactgaatcgaagatattgctgtcttctag

upper sequence: EFJ34676 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: PP1S29_222V6.1 (Physcomitrella patens), 5'ss of exon 5
CGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtgcaagaactcgatcgttttgat----ttggatccagtt-tctaagcattggattgttctggcag--------------------------------------------------------------------------------------------------
 |||||||| ||||| |||||||| || ||||||||||| || || |||||||| || || |  |||||||| |||||  | |||||  |  |||| |||||   |  |   |||  |||||||     |   |  | |  ||   |    | |||  |||   |                                                                                                   
GGCCAAGTCTATGAAATTCAAGGATGGCTACATGATCTCATCCGGAAGCCCCGTCAATGATTATATTGACAGTGCCGTTAGACACGTTATGCTGCGTCAGgtattaaca---gatttttttgatacccctatgtttactcctccttgtgcagaattaatcttcgattgtttccatccttgcattatactaaatagttctataattgaggtttcattattccgttggctctactgagcctgaattgaagctattccttcttgcag

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|169075229|gb|FE484111.1|FE484111
EST:     CCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAG                         GGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGC
genomic: CCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtgcaagaac ... gttctggcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGC




















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: 32 (upstream exon), 34 (downstream exon)
Score: 26

CGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtgcaagaac ... gttctggcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGCAAGACCGGGCCGTCGACACCGCTGCCGGACATGGTGACGATCCAAGTAC




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