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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtacaagaactcgatcattttgatttggatccagtttctaagcattggattgtgctggctggcag

Basic information

species Selaginella moellendorffii
transcript EFJ34304
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ34304 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: LOC_Os03g38000.2 (Oryza sativa), 5'ss of exon 3
CGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtacaagaactcgatcattttgatttggatccagtttctaagcattg-gattgtgctggctggcag-----------------------
 |||||||| |||||||||||||| || ||||||||||| |||||    || || || |||| |||||||  ||| ||| | ||||| ||  || | |||||        | | |||  |  |      |    |||  || | |   |||  |  |||||    |                       
AGCCAAGTCCATGAAGTTCAAGGATGGTTACATGATCTCATCTGGTCAGCCAGTCAATGAGTACATTGACTCGGCTGTGAGACACGTGCTCCTGAGACAGgtttgt---ttggttcaactcaagcatcgtagtatttaaaaacctcatgatctttttggctcaacgcacttgttcattatcttttgcag

upper sequence: EFJ34304 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: LOC_Os07g41750.1 (Oryza sativa), 5'ss of exon 5
CGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgt----acaagaactcgatcattttgatttggatc---cagtttctaagcattggattg----tgctggctggcag-----------------
 || || || |||||||||||||||||||||||||| || |||||    || || |||  ||  ||||||   || ||  | || || ||| || | |||||    |||  || || |||  ||||| |   ||    | || ||   |   | | |||    |  |   | | ||                 
TGCTAAATCCATGAAGTTCAAGGACGGATACATGATTTCTTCTGGTTATCCTGTTAACTTGTATATTGACTCTGCTGTTAGACATGTTCTTCTGAGACAGgtttgtacataaaatccatccgtttgaataaaatgttgctgtctccttgtgatagcttgaatttttttcttagaagctgcttcttgttttcag

upper sequence: EFJ34304 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: GRMZM2G099352_T01 (Zea mays), 5'ss of exon 3
CGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtacaagaact-cgatcattttgat-ttggatccagtttctaagcattggattgtgctggctggcag-----------------------------------------
 |||||||| |||||||||||||| || ||||||||||| |||||    || |||||||||| |||||||  ||| ||| | ||||| ||| |  | |||||       ||   |||   |  || || | ||   | || |      ||| |  | |  |     |                                         
AGCCAAGTCCATGAAGTTCAAGGATGGCTACATGATCTCATCTGGTCAGCCAGTGAACGAGTACATTGACTCGGCTGTGAGACACGTTCTTCTCAGACAGgtttgtttgctgtaatctcctcaatgtttggtcgtctctcaagagcagggactacgttttccacgtgcttcaatttaattacccaactaacttcaatctgtcgcgcag

upper sequence: EFJ34304 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: GRMZM2G074300_T03 (Zea mays), 5'ss of exon 3
CGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtaca------agaactcgatcattttgatttggatccagtttc---taagcattggattgtgctggctggcag-------------------------------------
 |||||||| |||||||||||||| || ||||||||||| |||||    || ||||| |||| ||| |||   || ||| | ||||||||  |  | |||||            | | |  | || | || |   |     |     |||||| |  ||| |    | |   |                                      
AGCCAAGTCCATGAAGTTCAAGGATGGCTACATGATCTCATCTGGTCAGCCAGTGAATGAGTACATCGACTCAGCTGTGAGACACGTCCTCCTCAGACAGgtttgttttgctacaattgcccgttgtaatgtctgtttgtctctgggtaagcacttcattttcgacgttccaaatgtaatttctcaacaaacatctttttctgtcgtgcag

upper sequence: EFJ34304 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: PP1S31_178V6.1 (Physcomitrella patens), 5'ss of exon 5
CGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtac----aagaactcgatcattttgat--ttggatccagtttctaagcat--tggattgtgctggct------ggcag--------------------------------------------------------
 || ||||| |||||||||||||||||||||||||| || ||||| ||||| || ||||| | |||||| || || ||  | |||||| | ||||| ||||||      | | ||   | || ||| |  |   | ||  |  || ||  |  |  ||| |  ||  |      || ||                                                        
TGCAAAGTCCATGAAGTTCAAGGACGGATACATGATATCATCTGGAAGCCCTGTCAACGACTACATTGATAGTGCTGTAAGACACGTCATGTTGCGACAGgtattcttgacagctttttaatcttgttagtctcaaccgttcactgagtttcttcaattattgtgatttcattcggaaggctcgtttattagttttttactacgaatctcaggttttggatgtatgtttttgcag

upper sequence: EFJ34304 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: PP1S127_74V6.1 (Physcomitrella patens), 5'ss of exon 5
CGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtacaagaactcgatcattttgatttggatccagtttctaagcattggattgtgctggctggcag-----------------------------------------------------
 || ||||| |||||||||||||| || ||||||||||| ||||| ||||| || ||||| | ||| ||||| ||||| || |||||  | ||||| ||||||||  |  |   | || |   |  | | |   ||| |     | | |   |  ||  ||  ||                                                     
TGCTAAGTCCATGAAGTTCAAGGATGGTTACATGATCTCATCTGGGAGCCCTGTCAACGATTACATCGACAGTGCCGTCCGACACGTTATGTTGCGTCAGgtacacaagatgcttgatgtccgtcagtagctcctttttcgtactagaaagatattgattgatagtcggtgttcccgaagtgaatctgaagtggaggattactttggtatgtttacag

upper sequence: EFJ34304 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: PP1S41_146V6.1 (Physcomitrella patens), 5'ss of exon 5
CGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgt-------acaagaactcgat--cattttgatttggatccagtttctaagcattgg-attgtgctggctggcag---------------------------------------------------------------
 |||||||| |||||||||||||| || |||||||| || || || |||||||| ||||| | ||| || || || ||  | |||||| | || || |||||        ||   | ||  |    |  |   |  | ||   || || |    |   |  ||  | | |  ||                                                                
AGCCAAGTCTATGAAGTTCAAGGATGGCTACATGATTTCATCAGGAAGCCCCGTCAACGATTACATCGATAGTGCTGTCAGACACGTCATGTTACGACAGgtttgtcgagcagctattcagtggtgtcctctctgtggtctccttgctgatttctcctacggtctttgttttcaagaaaaaatctcgtttgcaagttgtctgtaatgtatcttagaaatgtttcgttatttttttcag

upper sequence: EFJ34304 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: PP1S454_3V6.1 (Physcomitrella patens), 5'ss of exon 5
CGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgta-----caagaactcgatcattttgatttggatccagtt--tctaagcattggattgtgctggctgg--cag------------------------------------------------------------------------------
 |||||||| ||||||||||||||||| |||||||| || || || ||||| || || || | ||| ||||| || ||  | |||||| | ||||| ||||||     ||    || |  |||||   | |  |   ||||  |||     ||   || | ||   ||   ||                                                                               
GGCCAAGTCTATGAAGTTCAAGGACGGCTACATGATTTCATCCGGAAGCCCTGTCAATGATTACATCGACAGTGCTGTTAGGCACGTCATGTTGCGTCAGgtatgttacatatccttggccatttctctgttaactgagtttttctggctcttcccttatacttcttgtatcaaattgagttatctcagcatttcggtaatgctttcagtttgccgttgtgaaactgaatcgaagatattgctgtcttctag

upper sequence: EFJ34304 (Selaginella moellendorffii), 5'ss of exon 5
lower sequence: PP1S29_222V6.1 (Physcomitrella patens), 5'ss of exon 5
CGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtacaagaa------ctcgatcattttgatttggatccagtttcta-agcattggattgtgctggctggcag-----------------------------------------------------------------------------------------
 |||||||| ||||| |||||||| || ||||||||||| || || |||||||| || || |  |||||||| |||||  | |||||  |  |||| ||||||  |  |       | |||     |   ||   |||   || |  || |||    |  | | | |  ||                                                                                          
GGCCAAGTCTATGAAATTCAAGGATGGCTACATGATCTCATCCGGAAGCCCCGTCAATGATTATATTGACAGTGCCGTTAGACACGTTATGCTGCGTCAGgtattaacagatttttttgatacccctatgtttactcctccttgtgcagaattaatcttcgattgtttccatccttgcattatactaaatagttctataattgaggtttcattattccgttggctctactgagcctgaattgaagctattccttcttgcag

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|169072227|gb|FE479359.1|FE479359
EST:     CCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAG                         GGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGC
genomic: CCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtacaagaac ... tggctggcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGC
EST: gi|169038060|gb|FE446658.1|FE446658
EST:     CCGTGAACGAGTTCATCGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAG                         GGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGC
genomic: CCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtacaagaac ... tggctggcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGC
EST: gi|169043108|gb|FE454022.1|FE454022
EST:     CCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAG                         GGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGC
genomic: CCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtacaagaac ... tggctggcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGC
EST: gi|70671143|gb|DN839720.1|DN839720
EST:     CCGTGAACGAGTTCATCGACTGGGCCGTGCGCCACGTCCTTTTGCGCCAG                         GGGGTTTTGGGGATCCAGGTGAAGATCATGCTGGACTGGGATCCTAAGGGC
genomic: CCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtacaagaac ... tggctggcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGC
EST: gi|169038061|gb|FE446659.1|FE446659
EST:     CCGTGAACGAGTTCATCGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAG                         GGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGC
genomic: CCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtacaagaac ... tggctggcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGC
EST: gi|169103365|gb|FE507342.1|FE507342
EST:     CCGTGAACGAGTTCATCGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAG                         GGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGC
genomic: CCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtacaagaac ... tggctggcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGC
EST: gi|169044789|gb|FE454104.1|FE454104
EST:     CCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAG                         GGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGC
genomic: CCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtacaagaac ... tggctggcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGC
EST: gi|169073958|gb|FE481670.1|FE481670
EST:     CCGTGAACGAGTTCATCGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAG                         GGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGC
genomic: CCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtacaagaac ... tggctggcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGC
EST: gi|169067196|gb|FE474964.1|FE474964
EST:     CCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAG                         GGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGC
genomic: CCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtacaagaac ... tggctggcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGC
EST: gi|169034020|gb|FE444210.1|FE444210
EST:     CCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAG                         GGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGC
genomic: CCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtacaagaac ... tggctggcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGC
EST: gi|169073959|gb|FE481671.1|FE481671
EST:     CCGTGAACGAGTTCATCGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAG                         GGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGC
genomic: CCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtacaagaac ... tggctggcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGC
EST: gi|169034021|gb|FE444211.1|FE444211
EST:     CCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAG                         GGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGC
genomic: CCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtacaagaac ... tggctggcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGC
EST: gi|169055910|gb|FE465111.1|FE465111
EST:     CCGTGAACGAGTTCATCGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAG                         GGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGC
genomic: CCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtacaagaac ... tggctggcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGC
EST: gi|169055911|gb|FE465112.1|FE465112
EST:     CCGTGAACGAGTTCATCGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAG                         GGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGC
genomic: CCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtacaagaac ... tggctggcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGC
EST: gi|169043107|gb|FE454021.1|FE454021
EST:     CCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAG                         GGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGC
genomic: CCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtacaagaac ... tggctggcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGC

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), 35 (downstream exon)
Score: 124

CGCCAAGTCGATGAAGTTCAAGGACGGATACATGATCTCGTCTGGCAGCCCCGTGAACGAGTTCATTGACAGGGCCGTGCGCCACGTCCTTTTGCGCCAGgtacaagaac ... tggctggcagGGGGTTTTGGGGATCAAGGTGAAGATCATGCTGGACTGGGATCCAAAGGGCAAGACCGGGCCGTCGACACCGCTGCCGGACATGGTGACGATCCAAGTAC




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