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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACTCGGTGGAGCATCACACACAGGTGAAGATCAAGAAGCGAGGCTCGGACACCAAGTACCTGGCCAACGTTCTTGCCATTGGAACCGAGTGTGACATTGgtgagtttccaagcttttatggtgtttatgacttctttttgtttgcttctttgttctatcag

Basic information

species Selaginella moellendorffii
transcript EFJ16952
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ16952 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os02g50880.1 (Oryza sativa), 5'ss of exon 1
CACTCGGTGGAGCATCACACACAGGTGAAGATCAAGAAGCGAGGCTCGGACACCAAGTACCTGGCCAACGTTCTTGCCATTGGAACCGAGTGTGACATTGgtgagtttccaagcttttatggtgtt-tatgacttctttttgtttgcttctttgttctatcag--------------------------------------
||||| ||||||||  |||| ||||| ||| | |||||||| ||||| |||||||||||||||||||  || || |||||||| || ||||| |||||||||  | || |   ||| | || ||     ||  || || ||   | ||   |||||  |   |                                      
CACTCCGTGGAGCACTACACCCAGGTCAAGCTTAAGAAGCGCGGCTCCGACACCAAGTACCTGGCCACGGTCCTCGCCATTGGGACGGAGTGCGACATTGgtatgatttccc-cttctctgctgcaacctgcattgttctttccttctcaattgttgcaattgtagtacttatccaatgcttcctaagattgctccaatag

upper sequence: EFJ16952 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os06g12780.1 (Oryza sativa), 5'ss of exon 1
CACTCGGTGGAGCATCACACACAGGTGAAGATCAAGAAGCGAGGCTCGGACACCAAGTACCTGGCCAACGTTCTTGCCATTGGAACCGAGTGTGACATTGgtgagttt---ccaagcttttatggtgtt--------tatg-acttctttttg----tttgcttctttgttctatcag----------------------
||||| || |||||  |||| ||||| ||| | |||||| | || ||||| ||||| ||||| |||| |||||| || ||||| ||||||||||||||||||  || |   |||  ||  |  |   ||        |||| |||  ||||||    |  |  || |||   | |  |                      
CACTCCGTCGAGCACTACACCCAGGTCAAGCTTAAGAAGAGGGGATCGGATACCAAATACCTTGCCACCGTTCTCGCTATTGGCACCGAGTGTGACATTGgtatgtatagcccacactcgtgcgactttactaggactatggactagtttttggcaatcggaatccttgcaatgtttggtaaaatggcaatgtcctgtga

upper sequence: EFJ16952 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G165969_T01 (Zea mays), 5'ss of exon 2
CACTCGGTGGAGCATCACACACAGGTGAAGATCAAGAAGCGAGGCTCGGACACCAAGTACCTGGCCAACGTTCTTGCCATTGGAACCGAGTGTGACATTGgtgagtttccaagcttttatggtgtttatgacttctttttgtttgctt-ctttgttctatcag-------------------------------------
|||||||| |||||| |||| ||||| ||| |||||||||| |||||||||||||||||||| || |  || |||||||| || ||||||||||||||||||  |  ||       |       |||    ||      | ||  | | | |||| || | ||                                     
CACTCGGTTGAGCATTACACCCAGGTCAAGCTCAAGAAGCGTGGCTCGGACACCAAGTACCTTGCGACTGTCCTTGCCATAGGCACCGAGTGTGACATTGgtatgcatcactagactcgcctcattttaacctgtgaaatattgacataccttgtactgtgagctagttgtagttgtacttgcaatgagctaaactttgt

upper sequence: EFJ16952 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: AC212112.4_FGT002 (Zea mays), 5'ss of exon 1
CACTCGGTGGAGCATCACACACAGGTGAAGATCAAGAAGCGAGGCTCGGACACCAAGTACCTGGCCAACGTTCTTGCCATTGGAACCGAGTGTGACATTGgtgag-------tttccaagctt-ttatggtgtttatgacttctttttg---tttgcttctttgttctatcag---------------------------
||||| ||||||||  | || ||||| ||| | |||||||| ||||| |||||||||||||| |||| ||| || ||||| || || ||||| |||||||||| |       |  |||  | |   |  || |  ||   || ||| |     ||  || ||| |  | | |                            
CACTCCGTGGAGCACTATACCCAGGTTAAGCTTAAGAAGCGCGGCTCCGACACCAAGTACCTTGCCACCGTCCTGGCCATCGGCACAGAGTGCGACATTGgtgcgcccgctctccccatccctgccactgtctccattgtttatttcttactcttagttttttttcttcttattgtgatgttgggtttgtccattgtagt

upper sequence: EFJ16952 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G015959_T01 (Zea mays), 5'ss of exon 1
CACTCGGTGGAGCATCACACACAGGTGAAGATCAAGAAGCGAGGCTCGGACACCAAGTACCTGGCCAACGTTCTTGCCATTGGAACCGAGTGTGACATTGgtgagt------ttccaagcttttatggtgtttatg------acttctttttgtttgcttctttgttctatcag--------------------------
 |||| ||||||||  | || ||||| ||| | |||||||| ||||| |||||||||||||| |||| ||| || ||||| || || ||||| |||||||||| |       | || | |  |     ||| |         | |||||  | || | || ||| ||||    |                          
TACTCCGTGGAGCACTATACCCAGGTTAAGCTTAAGAAGCGCGGCTCCGACACCAAGTACCTTGCCACCGTCCTGGCCATCGGCACAGAGTGCGACATTGgtgcgcccactgtccccatccctgccactgtctccattgtttatttcttactcttagtttttttcttcttattgtgatgttgggtttgtccattgtagtc

upper sequence: EFJ16952 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G144501_T02 (Zea mays), 5'ss of exon 1
CACTCGGTGGAGCATCACACACAGGTGAAGATCAAGAAGCGAGGCTCGGACACCAAGTACCTGGCCAACGTTCTTGCCATTGGAACCGAGTGTGACATTGgtgagt------ttccaagcttt--------tatggtgtttatgacttctttttgtttgcttctttgtt-ctatcag-----------------------
||||| ||||||||  | || ||||| ||| | |||||||| ||||| |||||||||||||| |||| ||| || ||||| || || ||||| || ||||||| |       |||| | |  |        |    |||||||  |||  | | |||   ||  || ||  |||                          
CACTCCGTGGAGCACTATACCCAGGTTAAGCTTAAGAAGCGCGGCTCTGACACCAAGTACCTTGCCACCGTCCTGGCCATCGGCACAGAGTGCGATATTGgtgcgcccgctcttcccatccctgccctgcctccattgtttatttcttactatcgttaattttcttattgttatgtaaccatgaaaatcagatgcataat

upper sequence: EFJ16952 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM5G887390_T01 (Zea mays), 5'ss of exon 1
CACTCGGTGGAGCATCACACACAGGTGAAGATCAAGAAGCGAGGCTCGGACACCAAGTACCTGGCCAACGTTCTTGCCATTGGAACCGAGTGTGACATTGgtgag-------tttccaagctt-ttatggtgtttatgacttcttttt---gtttgcttctttgttctatcag----------------------------------------------------------------------
||||| ||||||||  | || ||||| ||| | |||||||| || || |||||||||||||| |||| ||| || ||||| || || ||||| |||||||||| |       |  |||  | |   |  || |  ||   || ||| |     ||  || ||| |  | | |                                                                       
CACTCCGTGGAGCACTATACCCAGGTTAAGCTTAAGAAGCGCGGTTCCGACACCAAGTACCTTGCCACCGTCCTAGCCATCGGCACAGAGTGCGACATTGgtgcgcccgctctccccatccctgccactgtctccattgtttatttcttactcttagttttttttcttcttattgtgatgttgggtttgtccattgtagtcgtgaaaatcggatgcatagtaatttctttattgttttcttag

upper sequence: EFJ16952 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA05G01930.1 (Glycine max), 5'ss of exon 1
CACTCGGTGGAGCATCACACACAGGTGAAGATCAAGAAGCGAGGCTCGGACACCAAGTACCTGGCCAACGTTCTTGCCATTGGAACCGAGTGTGACATTGgtgagtttccaagcttttatggtgtttatgacttctttttgtttgcttctttgttctatcag----------------------------------------
|| ||||| || ||  | |||||||| ||| ||||||| || ||||| || ||||||||| ||||||  || || |||||||||||||| |||||||||||| |    | |     || |  | | | |   ||   |||  |  |     || |  |  ||                                        
CATTCGGTAGAACACTATACACAGGTCAAGCTCAAGAAACGTGGCTCTGATACCAAGTACTTGGCCACTGTGCTCGCCATTGGAACCGAATGTGACATTGgtaa-caactatctccttgtcatttatttactttgaatttaat-acaaggatgatagagtagtagaaatttagaatcattagacaataacagtgaataagtg

upper sequence: EFJ16952 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA01G16820.1 (Glycine max), 5'ss of exon 1
CACTCGGTGGAGCATCACACACAGGTGAAGATCAAGAAGCGAGGCTCGGACACCAAGTACCTGGCCAACGTTCTTGCCATTGGAACCGAGTGTGACATTGgtg----agtttc---------caagctttt-----------atggtgtttatgacttctttttgtttgcttct--ttgttctatcag------------
|| || || |||||||||||||| || ||  ||||||| || ||||| || ||||| ||| |||||| ||| || ||||| || ||||||||||| || |||     | ||||          |  ||| |           ||||  |||||||     |  | |||| |  |  || || | |  |            
CATTCTGTTGAGCATCACACACAAGTCAAACTCAAGAAACGCGGCTCTGATACCAAATACTTGGCCACCGTCCTCGCCATCGGGACCGAGTGTGATATCGgtatttcaatttcactttatattatccttcttcattttagggatggaatttatgagacagtactttttgttcttaattattttgttggtgcctttctatc

upper sequence: EFJ16952 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA17G09970.1 (Glycine max), 5'ss of exon 1
CACTCGGTGGAGCATCACACACAGGTGAAGATCAAGAAGCGAGGCTCGGACACCAAGTACCTGGCCAACGTTCTTGCCATTGGAACCGAGTGTGACATTGgtgagtttccaagcttttatggtgtttatgacttctttttgtttgcttctttgttctatcag--------------------------------------------
|| || ||||| ||  |||| ||||| ||| ||||||| || || || || ||||||||| ||||||  || || |||||||||||||| ||||| |||||| |     ||| |   ||   |  || | | || |||   ||   ||   |        |                                             
CATTCCGTGGAACACTACACGCAGGTCAAGCTCAAGAAACGTGGTTCTGATACCAAGTACTTGGCCACTGTGCTCGCCATTGGAACCGAATGTGATATTGgtaa-----caaacaacta-actccttgtcatttatttactttgaatttcatacaacgagaatagatgtatagaaatgtagaatcataagacaataacggtgaata

upper sequence: EFJ16952 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S1_203V6.1 (Physcomitrella patens), 5'ss of exon 2
CACTCGGTGGAGCATCACACACAGGTGAAGATCAAGAAGCGAGGCTCGGACACCAAGTACCTGGCCAACGTTCTTGCCATTGGAACCGAGTGTGACATTGgtgagtttccaagct-tttatggtgtttatgacttctttttgtttgcttctttgttctatcag---------------------------------------
|| ||||||||||| || || || |||||| | ||||| || |||||||| ||||||||||||||||  |||||||| ||||| ||||| || ||||| ||| |||||      | | || |   | ||  |        | || || | |  |   || |||                                       
CATTCGGTGGAGCACCATACGCAAGTGAAGGTAAAGAAACGTGGCTCGGATACCAAGTACCTGGCCACGGTTCTTGCGATTGGTACCGAATGCGACATAGgtcagtttttgccttctctacgagctctacaatgaaccaattttggcatgt--gaaatagcagtcgtacctatgttgtgcacatcatgatgaacgcgtgttg

upper sequence: EFJ16952 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S176_87V6.1 (Physcomitrella patens), 5'ss of exon 2
CACTCGGTGGAGCATCACACACAGGTGAAGATCAAGAAGCGAGGCTCGGACACCAAGTACCTGGCCAACGTTCTTGCCATTGGAACCGAGTGTGACATTGgtgagtt----tccaagcttttatggtgtttatgacttctttttgtttgcttctttgttctatcag----------------------------------
||||| |||||||| || || ||||||||| | ||||| || || ||||| || |||||| ||||||  || ||||| ||||||||||| || || || ||| ||||     |||     | |  ||||    |    |   |    | |      || |   | |                                  
CACTCAGTGGAGCACCATACGCAGGTGAAGGTGAAGAAACGGGGATCGGATACAAAGTACTTGGCCACAGTGCTTGCGATTGGAACCGAATGCGATATAGgtcagttgctgcccagtgcatgagcgtgtgcgaggggccgagtacggtacgaggacgtgcaggcggtcatgcggtctccgcaatacgagctgagtgtgac

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: 31 (upstream exon), 33 (downstream exon)
Score: 10

CACTCGGTGGAGCATCACACACAGGTGAAGATCAAGAAGCGAGGCTCGGACACCAAGTACCTGGCCAACGTTCTTGCCATTGGAACCGAGTGTGACATTGgtgagtttcc ... gttctatcagCGATGCTGTCTGTAAATGACGAAGAGTTTTGGGAGGGTATCACACCCGTGACATTTGGAAGCTTACCGAGGCTCCAGGACGCTGTGACCGTCGTTGGCTA




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