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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTGGCCGGATCGGCAGGCTTGTGGCCCGCGTCGCGCTCTTTCGCGACGACATCGAGCTCGTGGCAGTCAACGATCCATTCATCAGCACGGATTACATGgtaacattcgctgttcttggtggattcccctctccaatcgcttggatttctttctcccag

Basic information

species Selaginella moellendorffii
transcript EFJ30760
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ30760 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: LOC_Os02g38920.1 (Oryza sativa), 5'ss of exon 3
ATTTGGCCGGATCGGCAGGCTTGTGGCCCGCGTCGCGCTCTTTCGCGACGACATCGAGCTCGTGGCAGTCAACGATCCATTCATCAGCACGGATTACATGgtaacattcgctgttcttggtggattcccctctccaatcgcttggatttctttctcccag---------------------------------------------
 || ||||| ||||||||||| |||||| | || |||||     |||| ||  |||||||||| || ||||||||||| ||||||| ||| || ||||||||| | |    |   || |        ||| | | |||   |||   |  |   |   ||                                             
GTTCGGCCGCATCGGCAGGCTGGTGGCCAGGGTGGCGCTGCAGAGCGAGGATGTCGAGCTCGTTGCCGTCAACGATCCCTTCATCACCACCGAGTACATGgtaccgtctctttccctcg-----cctcccccgcgaattagttgatctggtgcttttgagaatgtatgatatgatgattgtgctcgcttcggttaaattgaattg

upper sequence: EFJ30760 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GRMZM2G071630_T01 (Zea mays), 5'ss of exon 3
ATTTGGCCGGATCGGCAGGCTTGTGGCCCGCGTCGCGCTCTTTCGCGACGACATCGAGCTCGTGGCAGTCAACGATCCATTCATCAGCACGGATTACATGgtaacattcgctgttcttggtggattcccctctccaat-cgcttggatttctttctcccag-----------------------------------------
 |||||| ||||||| ||||| |||||| | || || ||     |||||||| |||||||||| || || ||||| || ||||||||||| ||||||||||||     |  |||     |   ||  |    ||   | |    ||| |    | |  ||                                          
GTTTGGCAGGATCGGAAGGCTGGTGGCCAGGGTGGCCCTGCAGAGCGACGACGTCGAGCTCGTCGCCGTGAACGACCCCTTCATCAGCACCGATTACATGgtatagccccttgtatc--gcttatcgcttgatctggtacttagggagtgtgctgtaacatggtaatatgccccctcgtatcgctaatcccttgatctgcta

upper sequence: EFJ30760 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GRMZM2G180625_T02 (Zea mays), 5'ss of exon 3
ATTTGGCCGGATCGGCAGGCTTGTGGCCCGCGTCGCGCTCTTTCGCGACGACATCGAGCTCGTGGCAGTCAACGATCCATTCATCAGCACGGATTACATGgtaacattcgctgttcttggtggattcccctctccaatcgcttggatttctttctcccag------------------------------------------
 || ||  ||||||||||||| |||||| | ||||| ||     |||| ||  |||||||||| || |||||||| || ||||||| |||||||||||||||| |   |   | ||| | ||  | |    |      ||  | ||| |  |  |  | |                                          
TTTCGGAAGGATCGGCAGGCTCGTGGCCAGGGTCGCCCTGCAGAGCGAGGATGTCGAGCTCGTCGCCGTCAACGACCCCTTCATCACCACGGATTACATGgta-cgcgcctcgatct-gatgcctccgttccgtgccacgagtagatctggtggtttccggtgggggtttagctttagcaccgatccgtatgccagcatgct

upper sequence: EFJ30760 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GRMZM2G046804_T02 (Zea mays), 5'ss of exon 3
ATTTGGCCGGATCGGCAGGCTTGTGGCCCGCGTCGCGCTCTTTCGCGACGACATCGAGCTCGTGGCAGTCAACGATCCATTCATCAGCACGGATTACATGgta-acat-tcgctgttcttggtggattcccctctcc-aatcgcttggatttctttctcccag-------------------------------------
 || ||  ||||||||||||| |||||| | ||||| |||    |||| ||  |||||||||| || |||||||| || ||||||| |||||| |||||||||  |   ||| | | ||  ||   ||||   |    | | | |  | |    | | |   |                                     
CTTCGGAAGGATCGGCAGGCTCGTGGCCAGGGTCGCCCTCCAGAGCGAGGATGTCGAGCTCGTCGCCGTCAACGACCCCTTCATCACCACGGACTACATGgtacgcgcctcgatctgctgcgtctgttccgtgccgtgagtagatctggtggtgtacgcggggtttgcgccgggtttaccatcgatccgtcgcaagccag

upper sequence: EFJ30760 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA11G37360.1 (Glycine max), 5'ss of exon 3
ATTTGGCCGGATCGGCAGGCTTGTGGCCCGCGTCGCGCTCTTTCGCGACGACATCGAGCTCGTGGCAGTCAACGATCCATTCATCAGCACGGATTACATGgtaacattcgctgttc------------ttggtggattcccctctccaatcgcttggatttctt--tctcccag---------------------------
||||||  |||| ||| |  | |||||| | || || ||     |  | ||| | || || || || ||||||||||| ||||||| ||| ||||||||||||| |      |||              | | | | |  | | || |||    || |||  ||  | |   |                            
ATTTGGAAGGATTGGCCGTTTGGTGGCCAGGGTTGCTCTTCAGAGGAATGACGTTGAACTTGTTGCTGTCAACGATCCTTTCATCACCACTGATTACATGgtaaaaacaagggttaaaatattgcatactagagtagtagcttttctaataatgtgcattgtttaatgttttaaacgttgttacgttgattgttctggcag

upper sequence: EFJ30760 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: GLYMA18G01330.1 (Glycine max), 5'ss of exon 3
ATTTGGCCGGATCGGCAGGCTTGTGGCCCGCGTCGCGCTCTTTCGCGACGACATCGAGCTCGTGGCAGTCAACGATCCATTCATCAGCACGGATTACATGgtaa-cattcgctgttcttggtggattcccctctccaatcgcttggatttctttctcccag------------------------------------------------------------------------------------
||||||  |||| ||| |  | |||||| | || || ||     |  | ||  | || || || || ||||||||||| ||||||| ||| |||||||||||||   ||   |  | |   |  |||  |||    || | |    |          | ||                                                                                    
ATTTGGAAGGATTGGCCGTTTGGTGGCCAGGGTTGCCCTTCAAAGGAATGATGTTGAACTTGTTGCTGTCAACGATCCTTTCATCACCACTGATTACATGgtaaatgtttttttctttgactctattgtcctgaaaaaacacacacacacacacacacaagggtttgcaatattgaatatgagagtagtaggttttgctaataatgtgcgttgtttaatgttttaaacattgattgctctggcag

upper sequence: EFJ30760 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: Vv17s0000g10430.t01 (Vitis vinifera), 5'ss of exon 3
ATTTGGCCGGATCGGCAGGCTTGTGGCCCGCGTCGCGCTCTTTCGCGACGACATCGAGCTCGTGGCAGTCAACGATCCATTCATCAGCACGGATTACATGgtaa-----cattcgctgttcttggtggattcccctctcca--at-cgcttggatttctttctcccag--------------------------------
||||||  |||||||| |  | |||||| | || || ||     | |||||  | ||| | || |||||||||||||||||||||| ||| ||||||||||||      |||    || | || ||   |||   |    |  ||    |||||  |   | |    |                                
ATTTGGAAGGATCGGCCGATTGGTGGCCAGAGTGGCACTGCAGAGAGACGATGTTGAGTTGGTTGCAGTCAACGATCCATTCATCACCACTGATTACATGgtatagtgtcatctcatgattttagtatgttcttgttgtgatgatgtatttggaactggatttggatgtagagcgtagttgatcagacttttctagccat

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|169069052|gb|FE477744.1|FE477744
EST:     ACATCGAGCTCGTGGCAGTCAACGATCCATTCATCAGCACGGATTACATG                         GCCTACATGTTTAAGTACGATAGCGTCCATGGAAAGTGGAAGAGGGAGGAT
genomic: ACATCGAGCTCGTGGCAGTCAACGATCCATTCATCAGCACGGATTACATGgtaacattcg ... tttctcccagGCCTACATGTTTAAGTACGATAGCGTCCATGGAAAGTGGAAGAGGGAGGAT




















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), 15 (downstream exon)
Score: 14

ATTTGGCCGGATCGGCAGGCTTGTGGCCCGCGTCGCGCTCTTTCGCGACGACATCGAGCTCGTGGCAGTCAACGATCCATTCATCAGCACGGATTACATGgtaacattcg ... tttctcccagGCCTACATGTTTAAGTACGATAGCGTCCATGGAAAGTGGAAGAGGGAGGATGTGGAGGTCAAGGACTCCGAGACGCTCTCCTTTGGCGGCAAGCCCGTGA




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