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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACTCACACAATCAAGGCTATGGAGCCGTTTTTCTCTGTTCTTCTATCGGCTATGTTCCTTGGCGAGgtatgatacgttcgcagaaaaggttctatatcaattgcctttgcag

Basic information

species Selaginella moellendorffii
transcript EFJ05868
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ05868 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os09g12600.2 (Oryza sativa), 5'ss of exon 3
CAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACTCACACAATCAAGGCTATGGAGCCGTTTTTCTCTGTTCTTCTATCGGCTATGTTCCTTGGCGAGgtatgat----acgttcgcagaaaaggttctatatcaatt--gcctttgcag-----------------------------------------------------------
 ||||||||||||||||||||||| ||||||||||| || || ||||||||||||||||| || || || ||||| || || ||  | ||||| || ||||||   |    | ||||         |  |  |   || |  ||    |||                                                            
GAACATGAGCCTTGGAAAGGTTGCAGTGTCATTTACACATACTATCAAGGCTATGGAGCCTTTCTTTTCAGTTCTGCTTTCAGCACTTTTCCTCGGAGAGgtaattttttaatgttctgcactggtgcccagtgataactatgcaaccgcatataatcttagaaaaaccatctgtttcttggtttggttctcatacataatcactttgcag

upper sequence: EFJ05868 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os08g25624.2 (Oryza sativa), 5'ss of exon 3
CAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACTCACACAATCAAGGCTATGGAGCCGTTTTTCTCTGTTCTTCTATCGGCTATGTTCCTTGGCGAGgta--tgatacgttcgcagaaaaggtt--ctatatcaattgcctttgcag--------------------------------------------------
 ||||||||||| || |||||||| |||||||| || || || ||||| |||||||| || || || |||||||| || || || || |||||||||||||||  |  ||   ||  | | || |||   |    ||||    | || |                                                   
TAACATGAGCCTGGGGAAGGTTGCTGTGTCATTCACACATACCATCAAAGCTATGGAACCTTTCTTTTCTGTTCTCCTCTCTGCAATTTTCCTTGGCGAGgtaacttgtagtgtcctatataatgttgattgctgcaatatattatgtatatctgagagaactacctgggttttctttcaataattgaatggcatggcag

upper sequence: EFJ05868 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GRMZM2G174107_T01 (Zea mays), 5'ss of exon 3
CAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACTCACACAATCAAGGCTATGGAGCCGTTTTTCTCTGTTCTTCTATCGGCTATGTTCCTTGGCGAGgta----tgatacgttcgcagaaaaggttctatatcaattgcctttgcag----------------------------------------------
||||||||||||||| || ||||| ||||||||||| ||||| ||||||||||||||||| || || |||||| |||| || || || |||||||||||||||    |   |     | | ||| | |   | | |||     |||| |                                               
CAACATGAGCCTTGGGAAAGTTGCAGTGTCATTTACGCACACCATCAAGGCTATGGAGCCTTTCTTTTCTGTTATTCTTTCTGCAATTTTCCTTGGCGAGgtaattttttcatccctgtacaaatgctaggaaagcaacatgttttgaattttaagaaatttctttgtcttcttatactaagtattcgtatggcag

upper sequence: EFJ05868 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GRMZM2G103047_T01 (Zea mays), 5'ss of exon 3
CAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACTCACACAATCAAGGCTATGGAGCCGTTTTTCTCTGTTCTTCTATCGGCTATGTTCCTTGGCGAGgtatgatacgttcgcagaaaaggt-tctatatcaattgcc------tttgcag-------------------------------------------------------
 ||||||||||||||||||||||||||||||||||| || || |||||||| ||||| || || ||||| ||||| || || || || |||||||| |||||| |     |   ||     |    |||||| || | |       | ||||                                                        
AAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACACATACTATCAAGGCCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGTGAGgtaagtcttctcttcaactctgaagcctatattaactacacaactatctgcaatatgatgaaactttgtgcttcttgctttttctttgacaaatgagtgattttgcag

upper sequence: EFJ05868 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GRMZM2G047404_T01 (Zea mays), 5'ss of exon 3
CAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACTCACACAATCAAGGCTATGGAGCCGTTTTTCTCTGTTCTTCTATCGGCTATGTTCCTTGGCGAGgtatgatac-gttcgcagaaaaggttctatatcaattgc------ctttgcag-------------------------------------------------
 ||||||||||||||||||||||| ||||||||||| || || || ||||| ||||| || || ||||| ||||| || || || || |||||||| |||||| | | | ||||       | |    |||  || | |      || |||                                                   
AAACATGAGCCTTGGAAAGGTTGCAGTGTCATTTACACATACTATAAAGGCCATGGAACCTTTCTTCTCAGTTCTCCTTTCAGCAATTTTCCTTGGGGAGgtaagtttctgttcaactctgaagcctaatagtaactacacaactctctgcgatatgataaaatctttcttgctttcctatgacaaatgagtgattttgcag

upper sequence: EFJ05868 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA17G09630.1 (Glycine max), 5'ss of exon 2
CAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACTCACACAATCAAGGCTATGGAGCCGTTTTTCTCTGTTCTTCTATCGGCTATGTTCCTTGGCGAGgtatga---tacgttcgcagaaaaggttcta------tatcaattgcctttgcag---------------------------------------------
||||||||| || ||| ||||||| ||||| || |||||||| || || || |||||||| ||||| || || || || || |||||||||||||| |||||  ||   ||    |  | |      |  |       || | ||   |||| ||                                             
CAACATGAGTCTCGGACAGGTTGCTGTGTCTTTCACTCACACTATAAAAGCGATGGAGCCTTTTTTTTCAGTGCTCCTTTCTGCTATGTTCCTTGGAGAGgttagaacttagaaccttatatgttactgcaaccaggcattatttttttttgtagcctaagtttttgttcctgttgtttcttttcaacgaattttatgat

upper sequence: EFJ05868 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA19G00270.1 (Glycine max), 5'ss of exon 3
CAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACTCACACAATCAAGGCTATGGAGCCGTTTTTCTCTGTTCTTCTATCGGCTATGTTCCTTGGCGAGgtatgatacgttcgcagaaaaggttctatatcaattgcctttgcag------------------------------------------------------
|||||| || ||||| |||||||| || || || |||||||||||||| ||||||||||| || ||| ||||  |||| || ||  | || || || ||||||   | |       ||     || | |     |    | | ||                                                       
CAACATTAGTCTTGGCAAGGTTGCTGTATCTTTCACTCACACAATCAAAGCTATGGAGCCTTTCTTCACTGTAGTTCTTTCTGCCCTTTTACTGGGTGAGgtaatgttcaagtcttgactttattttttccttgtaatttgtacataacataattaagtattattaatttttttctcataaattaaaaaacttgaataca

upper sequence: EFJ05868 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: Vv14s0066g01000.t01 (Vitis vinifera), 5'ss of exon 4
CAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACTCACACAATCAAGGCTATGGAGCCGTTTTTCTCTGTTCTTCTATCGGCTATGTTCCTTGGCGAGgtatgatacgttcgcagaaaaggttctatatcaattgcctttgcag------------------------------------------------------------
|||| | |||||  |||| ||||| || ||||| |||||||||||||| ||||||||||| |||||  | ||| ||||  |  |  | || ||||| |||||| ||    |  ||        ||| ||    ||||  ||||||                                                             
CAACTTAAGCCTCAGAAAAGTTGCTGTTTCATTCACTCACACAATCAAAGCTATGGAGCCCTTTTTTACAGTTGTTCTTGCTACCCTCTTTCTTGGGGAGgtaagaattttatgctc------ttccattattattgtttttgcattgtatcatttgggggcttaatctagtggaattttatggaaatttatatacattagatgtg

upper sequence: EFJ05868 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: Vv17s0000g08560.t01 (Vitis vinifera), 5'ss of exon 3
CAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACTCACACAATCAAGGCTATGGAGCCGTTTTTCTCTGTTCTTCTATCGGCTATGTTCCTTGGCGAGgt-----------atgatacgttcgcagaaaaggttctatatcaattgcctttgcag-------------------------------------------
 || ||||| ||||| || ||  | || ||||| ||||||||||| || ||||||||||| |||||||| ||| | || || |||||||| || || |||||           ||| | | |||          |||   || | |||| |   | |                                           
TAATATGAGTCTTGGGAAAGTGTCTGTTTCATTCACTCACACAATTAAAGCTATGGAGCCCTTTTTCTCAGTTGTCCTCTCTGCTATGTTTCTAGGAGAGgtgagcatttctcatgtttctttcttgcctccctttcctaattagttgcatcacctgaaatcctgcattgagatttagtttctatactccaatttcatga

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|169057504|gb|FE464456.1|FE464456
EST:     CTATCGGCTATGTTCCTTGGCGAG                         GCTCCAAGTGCTTGGATTATCGCTTCTCTCTTGCCAATTGTTGGAGGTGTG
genomic: CTATCGGCTATGTTCCTTGGCGAGgtatgatacg ... gcctttgcagGCTCCAAGTGCTTGGATTATCGCTTCTCTCTTGCCAATTGTTGGAGGTGTG
EST: gi|169055811|gb|FE465377.1|FE465377
EST:     CTATGGAGCCGTTTTTCTCTGTTCTTCTATCGGCTATGTTCCTTGGCGAG                         GCTCCAAGTGCTTGGATTATCGCTTCTCTCTTGCCAATTGTTGGAGGTGTG
genomic: CTATGGAGCCGTTTTTCTCTGTTCTTCTATCGGCTATGTTCCTTGGCGAGgtatgatacg ... gcctttgcagGCTCCAAGTGCTTGGATTATCGCTTCTCTCTTGCCAATTGTTGGAGGTGTG

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), 27 (downstream exon)
Score: 4

CAACATGAGCCTTGGAAAGGTTGCGGTGTCATTTACTCACACAATCAAGGCTATGGAGCCGTTTTTCTCTGTTCTTCTATCGGCTATGTTCCTTGGCGAGgtatgatacg ... gcctttgcagGCTCCAAGTGCTTGGATTATCGCTTCTCTCTTGCCAATTGTTGGAGGTGTGGCGTTGGCATCCTTGACTGAGGCGTCTTTCAACTG




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