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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGACGCAATGGGGATGAACATGATCTCCAAGGGGGTCCAAAACGTTTTGGACTATCTTCACGATGTATTCCCCGACATGTGTGTTATCAGCGTCTCTGgtaaatttccttgaagatttcttgtcctttggtctgagttgcaaacttgtcttcccag

Basic information

species Selaginella moellendorffii
transcript EFJ19556
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ19556 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: LOC_Os09g31970.1 (Oryza sativa), 5'ss of exon 2
GGTGACGCAATGGGGATGAACATGATCTCCAAGGGGGTCCAAAACGTTTTGGACTATCTTCACGATGTATTCCCCGACATGTGTGTTATCAGCGTCTCTGgtaaatttccttgaagatttc--ttgtcctttggtctgagttgcaaacttgtcttcccag------------------------------------------
|| || || ||||||||||||||| | |||||||| ||||| |||||  ||||||| ||||| ||||  ||||| ||||||  ||| |||||| | || |||   ||| ||| ||  |||      | |  ||  |     | |   |||  |||   |                                           
GGGGATGCCATGGGGATGAACATGGTGTCCAAGGGCGTCCAGAACGTGCTGGACTACCTTCAGGATGACTTCCCTGACATGGATGTCATCAGCATATCAGgtt--tttacttcaatttttaagccatgccatgaaccagtatacttgctttacttttgaagtttattagtctgcggtcacacggcggcttatactcttgtca

upper sequence: EFJ19556 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA11G09330.2 (Glycine max), 5'ss of exon 2
GGTGACGCAATGGGGATGAACATGATCTCCAAGGGGGTCCAAAACGTTTTGGACTATCTTCACGATGTATTCCCCGACATGTGTGTTATCAGCGTCTCTGgtaa---atttccttgaagatttcttgtcctttggtctgagttgcaaacttgtcttcccag-----------------------------------------------------
|| || || ||||||||||||||| ||||||| || |||||||||||  |    | ||| ||   ||  || || || |||  ||||||  |  | ||||||||   |||   || ||     | || | |    ||    ||     |||   |    |                                                      
GGGGATGCCATGGGGATGAACATGGTCTCCAAAGGAGTCCAAAACGTGCTTACTTTTCTCCAGAGTGATTTTCCAGATATGGATGTTATTGGGATATCTGgtaattaattaaattaaattaaacatggcatgacatcacccttctttgctttattcattaaggtcaaagttgatgtcacgatgaattaagaattggaacatatttatgtaacag

upper sequence: EFJ19556 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA20G05530.1 (Glycine max), 5'ss of exon 2
GGTGACGCAATGGGGATGAACATGATCTCCAAGGGGGTCCAAAACGTTTTGGACTATCTTCACGATGTATTCCCCGACATGTGTGTTATCAGCGTCTCTGgtaaatttccttgaagatttcttgtc-ctttggtctgagttgcaaacttgtcttcccag---------------------------------------------
|||||||| ||||||||||||||| | ||||| |||||||| || ||| | || |  |||||   ||  ||||| || |||  ||||||  || ||||||||||||||   ||    |   || || |||| ||  |  |   | | ||   |   ||                                              
GGTGACGCCATGGGGATGAACATGGTTTCCAAAGGGGTCCAGAATGTTCTTGATTTCCTTCAAAGTGATTTCCCTGATATGGATGTTATTGGCATCTCTGgtaaatttttatg----tcctttatcactttagtggggctccaatagttcattaatcaacttgcattaatgccaaagatatatgtctgtcagatgctgataaat

upper sequence: EFJ19556 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: Vv03s0038g04100.t01 (Vitis vinifera), 5'ss of exon 2
GGTGACGCAATGGGGATGAACATGATCTCCAAGGGGGTCCAAAACGTTTTGGACTATCTTCACGATGTATTCCCCGACATGTGTGTTATCAGCGTCTCTGgtaaatttccttgaagatttcttgtcctttggtctgagttgcaaactt--gtcttcccag-------------------------------
|| || |||||||||||||||||||||||||| || ||||| || |||||||| |  |||||  |||  ||||||||||||  ||| ||| || |||||||||  ||  |||    |   |  || ||| |  ||  ||  ||   ||  |      | |                               
GGAGATGCAATGGGGATGAACATGATCTCCAAAGGCGTCCAGAATGTTTTGGATTTCCTTCAGAATGATTTCCCCGACATGGATGTCATCGGCATCTCTGgtatgtt--cttattcacagcaagttcttcgaactacgtaacagtttttgggaaattcggattgaattgaatgcaatgaatccaatttcag

upper sequence: EFJ19556 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: Vv04s0044g01740.t01 (Vitis vinifera), 5'ss of exon 3
GGTGACGCAATGGGGATGAACATGATCTCCAAGGGGGTCCAAAACGTTTTGGACTATCTTCACGATGTATTCCCCGACATGTGTGTTATCAGCGTCTCTGgtaaatttc---cttgaagatttcttgtcctttggtctgag--ttgcaaacttgtcttcccag----------------------------
||||| |||||||| ||||||||| ||||||| || |||||||||||  |||| |  |||||    |  ||||| ||||||  ||| ||| || |||| |||||| ||    || | |||    || | |    | | ||    ||| ||  | |    |||                             
GGTGATGCAATGGGTATGAACATGGTCTCCAAAGGAGTCCAAAACGTCCTGGATTTCCTTCAAACCGATTTCCCTGACATGGATGTCATCGGCATCTCCGgtaaaattttaactggcagaccaattctaccaatgcccgatgcatgctaaagtttgaatccatctgaatcaatgtttttgaatcgccccag

upper sequence: EFJ19556 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: PP1S1_155V6.1 (Physcomitrella patens), 5'ss of exon 2
GGTGACGCAATGGGGATGAACATGATCTCCAAGGGGGTCCAAAACGTTTTGGACTATCTTCACGATGTATTCCCCGACATGTGTGTTATCAGCGTCTCTG-
||||| || ||||||||||||||||| ||||| || || |||||||||||||| |||||||| ||||||| ||| || |||   || ||||| || ||||    || |  | ||||||   |||   | ||    ||  ||       |    ||||  |  ||                                                                                            
GGTGATGCGATGGGGATGAACATGATATCCAAAGGTGTTCAAAACGTTTTGGATTATCTTCAGGATGTATACCCAGATATGGAGGTCATCAGTGTATCTGgttcgtgacataccttgattctttgttcctgatgattaatccagaacacgggattgtagttgcataattttctacaggcatgatagtattagtgcatgcgtagaatctcactagcaagtgggtttacgtgtactaacgtactctgtttgcatgcag

upper sequence: EFJ19556 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: PP1S139_2V6.1 (Physcomitrella patens), 5'ss of exon 2
GGTGACGCAATGGGGATGAACATGATCTCCAAGGGGGTCCAAAACGTTTTGGACTATCTTCACGATGTATTCCCCGACATGTGTGTTATCAGCGTCTCTGgtaaatttccttgaagatttcttgtcctttggtctgagtt-gcaaacttgtcttcccag-----------------------------------------------
|||||||||||||||||||||||||| ||||| || || || || |||||||| || ||||| ||| ||  ||| ||||||   || |||||||| ||||||      | |     | || |||  | || || | ||||       | |  |  | ||                                               
GGTGACGCAATGGGGATGAACATGATATCCAAAGGCGTACAGAATGTTTTGGATTACCTTCAGGATATAAACCCGGACATGGAGGTCATCAGCGTGTCTGgtttgcaacatgacccagttgttggtccttcgtttcagttcattttttcgcttgtctagcgcttgtttagctgtacagtatactcacgtagtctgtacatgtgcag

upper sequence: EFJ19556 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: PP1S61_10V6.1 (Physcomitrella patens), 5'ss of exon 2
GGTGACGCAATGGGGATGAACATGATCTCCAAGGGGGTCCAAAACGTTTTGGACTATCTTCACGATGTATTCCCCGACATGTGTGTTATCAGCGTCTCTGgtaaat--------ttccttgaagatttcttgtcctttggtctgagttgcaaacttgtcttcccag--------------------------------------------------------------------------------------------------------
|| || |||||||| ||||||||||| |||||||| || || || |||||||| |||||||| ||||| | ||| || |||      || ||||| |||||||  |         | ||||   || || ||||      |  ||| |    |  | | ||   |                                                                                                         
GGCGATGCAATGGGAATGAACATGATATCCAAGGGCGTTCAGAATGTTTTGGATTATCTTCAGGATGTGTACCCTGATATGGAGACCATAAGCGTGTCTGgtatgtaacacatcctgcttgtgtatgtcatgtctcaaaattagaggtttctatgtatattgatatgctccatccaatggtacaaggtcgtacatgatgctgttctgagacttggtggttgtagtatctcttaatgaattggtgtactaacacaatattttcatttgcag

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: 29 (upstream exon), 35 (downstream exon)
Score: 18

GGTGACGCAATGGGGATGAACATGATCTCCAAGGGGGTCCAAAACGTTTTGGACTATCTTCACGATGTATTCCCCGACATGTGTGTTATCAGCGTCTCTGgtaaatttcc ... gtcttcccagGGAACTTATGCGCTGACAAGAAGGCAACATCAGTGAACTGGATCGAGGGGCGAGGGAAGTCCGTCGTCTGCGAAGCGGTGATAAAGGGCGACGTGGTCTC




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