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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGTTAGGAGCTGCTACGACGAGGGAAAACGCGTGGCCGAAACGTTGATGTTTGACTATCACAGGCAGCACGGGATTGgtgtgctcgattgctttagcttgatgacgctggttctgacgtccagtaattctcag

Basic information

species Selaginella moellendorffii
transcript EFJ35029
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ35029 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: LOC_Os03g16980.5 (Oryza sativa), 5'ss of exon 8
GTGTTAGGAGCTGCTACGACGAGGGAAAACGCGTGGCCGAAACGTTGATGTTTGACTATCACAGGCAGCACGGGATTGgtgtgctcgattgctt-tagcttgatgacgctggttctgacgtccagtaattctcag------------------------------
| || ||||| ||||| |||||||| || || || || |||||  ||||||||||||||||||||||||| || ||||||    |   | | |  || |||  || |    | | |   |    ||| |||||                                
GAGTCAGGAGTTGCTATGACGAGGGTAAGCGTGTCGCAGAAACACTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaatatttttagttcatacctttttgtcttgtgatgtactggattgtagttctccttaataagtattttccaatctatctctgtag

upper sequence: EFJ35029 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: GRMZM2G382038_T01 (Zea mays), 5'ss of exon 9
GTGTTAGGAGCTGCTACGACGAGGGAAAACGCGTGGCCGAAACGTTGATGTTTGACTATCACAGGCAGCACGGGATTGgtg-tgctcgattgctttagcttgatgacgctggttctgacgtccagtaattctcag----------------------------------------------------------------
|||||||||| || || || ||||| || || || || || | ||||||||||||||||||||||||||| || ||||||    ||  ||  ||||  ||| |  ||     |  |     |   ||   |||                                                                  
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGATGTTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaacacttcat--ctttcacttaa--acttcaatattagtagctcatagccctctttgttatgtgataactctgggcttatgatttttttcttgacagtatttatcatctatgtctgtag

upper sequence: EFJ35029 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: GRMZM2G177373_T02 (Zea mays), 5'ss of exon 8
GTGTTAGGAGCTGCTACGACGAGGGAAAACGCGTGGCCGAAACGTTGATGTTTGACTATCACAGGCAGCACGGGATTGgtg-tgctcgattgctttagcttgatgacgctggttctgacgtccagtaattctcag----------------------------------------------------------------
|||||||||| || || || ||||| || || || || || | ||||||||||||||||||||||||||| || ||||||    ||  ||  ||||  ||| |  ||     |  |     |   ||   |||                                                                  
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAGAGATGTTGATGTTTGACTATCACAGGCAGCATGGCATTGgtaacacttcat--ctttcacttaa--acttcaatattagtagctcatagccctctttgttatgtgataactctgggcttatgatttttttcttaacggtatttatcatctatgtctgtag

upper sequence: EFJ35029 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: GRMZM2G300412_T01 (Zea mays), 5'ss of exon 14
GTGTTAGGAGCTGCTACGACGAGGGAAAACGCGTGGCCGAAACGTTGATGTTTGACTATCACAGGCAGCACGGGATTGgtg-tgctcgattgctttagcttgatgacgctggttctgacgtccagtaattctcag-----------------------------------------------------------------
|||||||||| || || || ||||| || || || || || |||||||||||||||||||||| |||||| || ||||||    ||  ||  ||||  ||| |  ||     |  |     |   || | |||                                                                   
GTGTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCTGAGACGTTGATGTTTGACTATCACAAGCAGCATGGCATTGgtaacacttcat--ctttcacttaa--acttcaatattagtagctcatagtcctctttgttatgtgataactctgggcttatgattttttttcttaacagtgtttatcatctatgtctgtag

upper sequence: EFJ35029 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: GRMZM2G157772_T01 (Zea mays), 5'ss of exon 5
GTGTT-AGGAGCTGCTACGACGAGGGAAAACGCGTGGCC-GAAACGTTGATGTTTGACTATCACAGGCAGCACGGGATTGgtg-----tgctcgattgctttagctt-gatgacgctggttctgacgtccagtaattctcag-------------------------------------------------------
||||| ||||| || || || ||||| || || || ||  || ||||||||||| ||||||||||||||||| || ||||||      |  ||  |  ||| | |||  ||     | | ||  |   |   |  || | ||                                                       
GTGTTTAGGAGTTGTTATGATGAGGGTAAGCGTGTAGCAAGAGACGTTGATGTTCGACTATCACAGGCAGCATGGCATTGgtaacacttcatctttcacttaaacttcaatattagtagctcatagccctctttgttatgagataactctgggcttatgatttttttcttaacagtatttatcatctatgtctgtag

upper sequence: EFJ35029 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: GLYMA13G40960.1 (Glycine max), 5'ss of exon 9
GTGTTAGGAGCTGCTACGACGAGGGAAAACGCGTGGCCGAAACGTTGATGTTTGACTATCACAGGCAGCACGGGATTGgtg--tgctcgattgctttagcttgatgacgctggttctgacgtccagtaattctcag----------------------------------------------------------
| ||| | || ||||| || ||||| ||||| |||||||| || ||||||||||| || || |||||||| |||||||||   | || |  | ||||  ||||      ||  |  |   ||  |   ||   |||                                                          
GAGTTCGTAGTTGCTATGATGAGGGGAAACGGGTGGCCGAGACATTGATGTTTGATTACCATAGGCAGCATGGGATTGgtaatttcttgtcttcttttccttgtaatttcttctcattttgtttacacatatccagtagagatttatctttgtttcttaactccttgtggtgtttatgtctcctttcaacatag

upper sequence: EFJ35029 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: GLYMA11G15020.1 (Glycine max), 5'ss of exon 8
GTGTTAGGAGCTGCTACGACGAGGGAAAACGCGTGGCCGAAACGTTGATGTTTGACTATCACAGGCAGCACGGGATTGgtg-tgctcgattgctttagcttgatgacgctggtt--ctgacgtccagtaattctcag---------------------------------------------------------------------------------
| ||| | || ||||| || ||||| ||||| ||||| ||||| ||||||||||| ||||| |||||||| || || |||  |    | |    ||  ||| ||     | |||   ||  ||    |  |||  ||                                                                                 
GAGTTCGTAGTTGCTATGATGAGGGGAAACGTGTGGCTGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATAGgtaatttctgctcttcttttcttcatagttgttgttgattgttgttgttttcttcatagttgtcttttgttccttgttatagctggtagaaaattttcttttgtaagttaactgagttttttatatttctttcaacatag

upper sequence: EFJ35029 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: GLYMA12G06990.1 (Glycine max), 5'ss of exon 8
GTGTTAGGAGCTGCTACGACGAGGGAAAACGCGTGGCCGAAACGTTGATGTTTGACTATCACAGGCAGCACGGGATTGgtg---tgctcgattgctttagcttgatgac-gctggttctgacgtccagtaattctcag--------------------------------------------------
| ||| | || ||||| || ||||| ||||| ||||| ||||| ||||||||||| ||||| |||||||| || || |||    |  ||  ||  |||  ||| ||    |   |||    | |    ||| |   ||                                                  
GAGTTCGTAGTTGCTATGATGAGGGGAAACGTGTGGCTGAAACTTTGATGTTTGATTATCATAGGCAGCATGGAATAGgtaatttcttctcttcttttttcttcatagttgtctgttgctccttgttataactggtagaaatttttctctgtaatttaactgagttttctatatttctttcaacatag

upper sequence: EFJ35029 (Selaginella moellendorffii), 5'ss of exon 7
lower sequence: Vv13s0019g00840.t01 (Vitis vinifera), 5'ss of exon 8
GTGTTAGGAGCTGCTACGACGAGGGAAAACGCGTGGCCGAAACGTTGATGTTTGACTATCACAGGCAGCACGGGATTGgtgtgctcgattgctttagcttgatgacgc-tggttctgacgtccagtaattctcag-----------------------------------------------------------------------------------------------------------------------------------
| || ||||| ||||| || |||||||| || ||||| |||||  |||||||||| |||||||||||||| || || |||    | |   |||    ||   |||  | |    |  ||   |||  |  | ||                                                                                                                                    
GAGTCAGGAGTTGCTATGATGAGGGAAAGCGAGTGGCTGAAACTCTGATGTTTGATTATCACAGGCAGCATGGAATAGgtaaaattgg--gctccctctctctgatccatacacccaacacacagacacccccacacctacacacattcactcagtcactgatgggatgtgtaaaattgttcactcccttcccctccctctctctatctgaaactctactttccaatgcactctcactttattttgaaatggtgatcctataacag

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|169050505|gb|FE458884.1|FE458884
EST:     ACGCGTGGCCGAAACGTTGATGTTTGACTATCACAGGCAGCACGGGATTG                         AGATAAGGATCGCTCGCATTTTCAACACTTACGGGCCCCGGATGAATATCG
genomic: ACGCGTGGCCGAAACGTTGATGTTTGACTATCACAGGCAGCACGGGATTGgtgtgctcga ... taattctcagAGATAAGGATCGCTCGCATTTTCAACACTTACGGCCCCCGGATGAATATCG
EST: gi|169078730|gb|FE489606.1|FE489606
EST:     ACGCGTGGCCGAAACGTTGATGTTTGACTATCACAGGCAGCACGGGATTG                         AGATAAGGATCGCTCGCATTTTCAACACTTACGGGCCCCGGATGAATATCG
genomic: ACGCGTGGCCGAAACGTTGATGTTTGACTATCACAGGCAGCACGGGATTGgtgtgctcga ... taattctcagAGATAAGGATCGCTCGCATTTTCAACACTTACGGCCCCCGGATGAATATCG

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), 34 (downstream exon)
Score: 31

GTGTTAGGAGCTGCTACGACGAGGGAAAACGCGTGGCCGAAACGTTGATGTTTGACTATCACAGGCAGCACGGGATTGgtgtgctcga ... taattctcagAGATAAGGATCGCTCGCATTTTCAACACTTACGGCCCCCGGATGAATATCGACGATGGACGGGTCGTTAGCAACTTCATTGCCCAAGCTCTAAG




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