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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgtagccgctcggcactagggtatcgatctaactcttggtttcgtgttgcag

Basic information

species Selaginella moellendorffii
transcript EFJ16328
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ16328 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os07g07240.1 (Oryza sativa), 5'ss of exon 1
TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgtagccgctcggcactagggtatcgatctaactcttggtttcgtgttgcag--------------------------------------------
||||||| ||||||||||| || || || || || |||||||| ||||||||||||||||| |||||||||||||||||||||||||| || |||||||||| || | |||| | | | | | | | |||| |||| | || |
TGATGCGGGACTTCAAGCGGCTGCAGCAGGACCCCCCCGCGGGGATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATCTTCGGgtgggtgt-cagcca-tggacgc-ggaattcccatctgcctctacctctctccccccctccccctctcctgcgccggccccccggtgttctagggtttcggtg

upper sequence: EFJ16328 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os03g57790.1 (Oryza sativa), 5'ss of exon 1
TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgtagccgc--tcggcactagggtatcgat--ctaactcttggtttcg------tgttgcag----------------------------------------------------------------------------------------------------------
||||||| ||||||||||| || || || || || ||||| |||||||||||||||||||| |||||||||||||||||||||||||| || || ||||||||| | | ||| | | ||| | || ||| | |||| || | | ||||
TGATGCGGGACTTCAAGCGGCTGCAGCAGGACCCGCCCGCCGGAATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagccacccacgcgccgtagccaccctcatctcaggcgctaggttttggagccgaggggatctcgcagagcttgtgattttcctattcgttgtggagttattttttttaattttttgtgtgggttgatttggttctgatgtcgtttgcttgtcatgtctggtacgattttgcag

upper sequence: EFJ16328 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G074479_T04 (Zea mays), 5'ss of exon 1
TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgtagccgctcggcactagggtatcgatctaactcttggtttcgtgttgcag----------------------------------------------------------------------------------------------------------------------------------------------
||||||| ||||||| |||||| || || || || ||||| || ||||||||||||||||| |||||||||||||||||||||||||| || || ||||||||| || || | | | | |||| | | | |
TGATGCGGGACTTCAGGCGCCTGCAGCAGGACCCGCCCGCCGGGATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtagcc-cgtcccctcccctcccccctcccccgatttcgttaccccacaaacgccccccctggagtccgttaatcccgttcctgttctagggtttgattgagggactccggatctcggggagggagacgggatctcagctattccttttgttcttactcttgtgttcgttgtgctgatgagaggttcgtgtggtttcgcag

upper sequence: EFJ16328 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G022206_T02 (Zea mays), 5'ss of exon 1
TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtagga----------atgtagccgctcggcactagggt--atcgatctaactcttggtttcgtgttgcag-----------------------------------------------------------------------------------------------------------
||||||| ||||||| |||||| || || || || ||||| || ||||||||||||||||| |||||||||||||||||||||||||| || || |||||||| | |||| | | | | | || | ||| ||| || | | | ||| |
TGATGCGGGACTTCAGGCGCCTGCAGCAGGACCCGCCCGCCGGGATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgtacctcatccatcccacagagccccccaccccccgagtccgttaatcccgctcctgttctagggtttgattgacaggttccggatcttgggggggtgagaaacgggttctcatctattcctttccattttcactcgtgtttgttgtgctgatgagagaggttcgtttgattttgcag

upper sequence: EFJ16328 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G007260_T01 (Zea mays), 5'ss of exon 1
TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgtagccgctcggcactagggtatcgatctaact--cttggtttcgtgttgcag------------------------------------------------------------------
||||||| ||||||||||| | || || || || ||||| || ||||||||||||||||| |||||||||||||||||||||||||| || || |||||||| || ||||| || | | | || || | | || || |
TGATGCGGGACTTCAAGCGGTTGCAGCAGGACCCGCCCGCCGGCATCAGCGGCGCGCCGCACGACAACAACATCATGCTCTGGAACGCCGTCATATTCGGgta---atcaggccgcctatttctgtgatgttaggttagctagcctaaggatctgatgaggtgcgaggctgcaatacttacggtgctgactgtgcttttgctattgtcgtttgttgcgattctgcag

upper sequence: EFJ16328 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G120674_T01 (Zea mays), 5'ss of exon 1
TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgtagccgct-cggcactagggtatcgatctaactcttggtttcgtgttgcag-------------------------------------------------------------------------
||||||| |||||||||||||| || || || || ||||| || ||||||||||||||| | |||||||| ||||||||||||||||| || || |||||||| | | | | | | | || | | | ||| ||
TGATGCGGGACTTCAAGCGCCTGCAGCAGGACCCGCCCGCCGGCATCAGCGGCGCGCCGTACGACAACAATATCATGCTCTGGAACGCCGTCATATTCGGgtatcagcccgcctatttctgtgatgttaggttagctagcctaaggatctagtgaggcgtgaggccgcgatacttttggtgggttttaatgctgactgtgctttttctcttggtgtttgttgcgattctgcag

upper sequence: EFJ16328 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA17G10640.1 (Glycine max), 5'ss of exon 2
TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgtagccgctcggcactagggtatcgatctaactcttggtttcgtgttgcag--------------------------------------------------------------------------------------------
| ||| |||| |||||| | || ||||| || ||||| || |||||||| ||||| || ||||| |||||||||||||| ||||| || || || || |||| | || | | | | | || | | ||| || | | ||
TCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagc-tgaattgaaattggataaagataaaactgttctgcttacttgaataatatagttactttgttttttattttattttttttccacactttgtgtaagtatggatggataagcaatttctgctttcttgtctgctttggattgcag

upper sequence: EFJ16328 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA17G10640.3 (Glycine max), 5'ss of exon 2
TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgtagccgctcggcactagggtatcgatctaactcttggtttcgtgttgcag------------------------------------------
| ||| |||| |||||| | || ||||| || ||||| || |||||||| ||||| || ||||| |||||||||||||| ||||| || || || || |||| | || | | | | | || | | ||| || | | ||
TCATGAGAGATTTCAAGAGGCTGCAACAAGACCCTCCTGCAGGAATCAGTGGCGCCCCTCAGGATAACAACATCATGCTGTGGAATGCTGTCATATTTGGgtgagc-tgaattgaaattggataaagataaaactgttctgcttacttgaataatatagttactttgttttttattttattttttttccacactttgtgta

upper sequence: EFJ16328 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S219_106V6.1 (Physcomitrella patens), 5'ss of exon 1
TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgtagccgctcggcactagggtatcgatctaactcttggtttcgtgttgcag------------------------------------------
||||||| |||||||||||| | ||||| |||||||| || || ||||||||||| |||||||||||||| |||||||| ||||| || ||||| |||||||| | || | | || | | | | | || | | ||||| ||| |
TGATGCGTGACTTCAAGCGCTTGCAACATGATCCTCCGGCCGGCATCAGCGGCGCTCCGCAGGACAACAATATCATGCTGTGGAATGCTGTGATATTCGGgtaacgaagtgcctccctggt-ttcgttttttgttcaattgtgtccggtcgtggtgcggaattcgccgggcgtgggaggcgcacgtcggagtgtcggtttt

upper sequence: EFJ16328 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S91_87V6.1 (Physcomitrella patens), 5'ss of exon 1
TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgta--ggaat---------gtagccgctcggca----ctagggtatcgatctaactcttggtttcgtgttgcag--------------------------
||||||| |||||||||||||| || || |||||||| || || ||||||||||| ||||||||||||||||||||| | ||||| || || || |||||||| || | || || ||| | | || ||| | | | | |||||| ||
TGATGCGCGACTTCAAGCGCCTGCAGCATGATCCTCCGGCCGGCATCAGCGGCGCCCCGCAGGACAACAACATCATGTTGTGGAATGCTGTCATATTCGGgtacccaaactcctccccgattttcgttctgcatgctcaattgtgtcggtatgaatgcgaaattcgtggggcgcggagatttgcatggcggtgtcggttt

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: 81

TGATGCGAGACTTCAAGCGCCTCCAACACGATCCTCCCGCGGGAATCAGCGGCGCGCCGCAGGACAACAACATCATGCTCTGGAACGCGGTGATCTTCGGgtaggaatgt ... cgtgttgcagGCCGGATGACACTCCCTGGGATGGAG




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