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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACGATGAAGCTGAGAGGAGGAGGGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCAgttgagtttccaatttgagtatctgataggcctttctaacttcgctcatggtacag

Basic information

species Selaginella moellendorffii
transcript EFJ08409
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ08409 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: LOC_Os04g41470.1 (Oryza sativa), 5'ss of exon 10
TACGATGAAGCTGAGAGGAGGAGGGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCAgttgagtttccaatttgag------tatctga-taggcctttctaactt-cgctcatggtacag---------------------------------------------------------------
|| |||||| |||| ||||| || |||||||| ||||||||| | |||||||||||||| || || || || |||||  | ||  | || ||    | |    |   ||      || ||||  |   | || |   || |     | ||| |                                                                
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCGgtaagttattgggtacaagaaaagttacctgaacaaagcattgtgttttacataagtagtaaaaaagatttccaatcaatactcaagaagaacttttctggtttcttaatatcttctcgttatgcag

upper sequence: EFJ08409 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: GRMZM2G006428_T02 (Zea mays), 5'ss of exon 10
TACGATGAAGCTGAGAGGAGGAGGGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCAgttgagtttccaatttga-gtatctgataggcctttctaacttcgctcatggtacag--------------------------------------------
|| |||||| |||| ||||| || |||||||| ||||||||| | ||||||||||||||||| || || ||||||||  | ||  | || ||  ||| |  ||| ||    |  |||   |    | ||| |   |  |   |  ||                                            
TATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCGgt-aagtattgaatgtggcagaaatgacctgaaactttaaatctacatagcatggagttcagattgacaattgatgcatgccaagcatcctgttggctgga

upper sequence: EFJ08409 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: Vv00s0207g00090.t01 (Vitis vinifera), 5'ss of exon 10
TACGATGAAGCTGAGAGGAGGAGGGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCAgttgagtttccaatttgagtatctgataggcctttctaacttcgctcatggtacag--------------------------------------------
|| ||||| |||||||   | ||||| |||||||||||||| || ||||||||||| ||||| || || |||||||| || ||| |||| ||    ||  |  ||  ||   ||  |       | |||  | |    |  | |||                                            
TATGATGAGGCTGAGAAACGAAGGGATATGGCTAAGAACTCTTTGGAGAGATATACTCATTATTATGAACGATGGGCGACCAACCAATCTgtatgtttgacttttccagatcctcctcttttgctgtaatatggacattatttcagaaacccattatttcagaatttagtccaagattgtcctcatttgc

upper sequence: EFJ08409 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: PP1S114_2V6.1 (Physcomitrella patens), 5'ss of exon 10
TACGATGAAGCTGAGAGGAGGAGGGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCAgtt---------gagtttcca-atttgagtatctga--taggcctttctaacttcgctcatggtacag---------------------------------------------------------------------------------------------
|| |||||||| ||| |||| ||||||||||||||||||||| | ||  | |||||||||||||| || || ||||| || |||||||| ||          || | | || ||||    ||||||  ||||  || || | ||||| ||||| |  |                                                                                             
TATGATGAAGCAGAGCGGAGAAGGGAAATGGCTAAGAACTCGCTTGAACGCTATACACATTACTATGAACGTTGGGCTACAAACGAATCTgtaagtggtgcagaatctgcacattttcccatctgaattaggttttcctcagttcgc-catgggattgcacctattgtttaggatcttaactctctctcaatttaaagacgtgatctgcgtttgtgttttcttgacttttgaaatctcctttgtttttcag

upper sequence: EFJ08409 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: PP1S178_72V6.2 (Physcomitrella patens), 5'ss of exon 11
TACGATGAAGCTGAGAGGAGGAGGGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCAgttgagtttccaatttgagtatctgataggcctttctaacttcgctcatggtacag-------------------------------------------------------------------------------------------------
||||||||||| ||| |||||||||||||||||||||||||  | ||  | || ||||||||||| || || ||||| || || || || ||      |  | |  |  | |    |    ||||     |||| | |||   | |                                                                                                 
TACGATGAAGCAGAGCGGAGGAGGGAAATGGCTAAGAACTCTCTTGAACGCTACACACATTACTATGAACGTTGGGCTACAAATGAGTCTgtaagtgctggattgcgtttgtgcattttttcttttgtcattcggtaatgaatctgcatgaactgtttaggattttgacatcatcctaacttgaggagatgtggtctgcatttgtttattcttgactatcgagagtttggtggtgttgtgcag

upper sequence: EFJ08409 (Selaginella moellendorffii), 5'ss of exon 10
lower sequence: PP1S156_28V6.1 (Physcomitrella patens), 5'ss of exon 10
TACGATGAAGCTGAGAGGAGGAGGGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCAgttgagtttccaatttgagtatctgataggcctttctaacttcgctcatggtacag----------------------------------------------------------------------------------------------------
|| |||||||| ||| |||||||||| ||||||||||||||  | ||  | || |||||||| || || || ||||| ||||| ||||| || ||||  ||  ||||||| |     ||   | |   || |   |   | |                                                                                                        
TATGATGAAGCAGAGCGGAGGAGGGAGATGGCTAAGAACTCCCTTGAACGTTACACACATTATTATGAACGCTGGGCAACGAATGAATCTgt-gagtg-ccggtttgagtttgcacgagttttcttctaccttaattgcgctgtcttttctcacactgcagatacattgactatgtaaattttaggcaatgatgtagtgtgagcttatatttatcatttctgttctaatttcttttatgtgtgcag

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: 22

TACGATGAAGCTGAGAGGAGGAGGGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCAgttgagtttc ... catggtacagTCCAAAACGAAAGCGATTTCAGATCTACAACAGATGCAAACGGTTCAG




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