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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGGGCGCTGAATCTCATGGCCGACGTCGCCCAGGAGGAGGCGTCAAACAAGATGAACTCCCGGAACATCGCAATGGTTTTTGCTCCCAACATGACTCAGgtacgttcctctttcatttggttcttggtttttgttttgttttctgtaatgtatttccttttgctgtcccag

Basic information

species Selaginella moellendorffii
transcript EFJ12967
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ12967 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: LOC_Os02g45600.1 (Oryza sativa), 5'ss of exon 4
CTGGGCGCTGAATCTCATGGCCGACGTCGCCCAGGAGGAGGCGTCAAACAAGATGAACTCCCGGAACATCGCAATGGTTTTTGCTCCCAACATGACTCAGgt-acgttcctctttcatttggttct-tggtttttgttttgttttctgtaatgtatttccttttgctgtcccag--------------------------
 |||||  | ||||| ||||| || || |   |  | ||    |  || ||||||||| | || ||||| || ||||||||||| || |||||||||||||| |   ||    |  |||||| | | |   |||| | ||| | |||  |   | |    |||  | | |  |                           
TTGGGCCATCAATCTGATGGCAGATGTTGTGGAACATGAAAACTACAATAAGATGAACGCTCGCAACATTGCTATGGTTTTTGCACCAAACATGACTCAGgttattctcaaaatctatttggctttatttattttttcttgctatctacagaatttgctatttcacagactaatcatgtaacataccatctcttttatag

upper sequence: EFJ12967 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: LOC_Os12g34840.1 (Oryza sativa), 5'ss of exon 4
CTGGGCGCTGAATCTCATGGCCGACGTCGCCCAGGAGGAGGCGTCAAACAAGATGAACTCCCGGAACATCGCAATGGTTTTTGCTCCCAACATGACTCAGgtacgttcc---tctttcattt----ggttcttggtttttgttttgtt--ttctgtaatgtatttccttttgctgtcccag--------------------------------------
 |||||  |  | || ||||| ||||| | | | ||||||| |   |||||||||||  |  ||||||| || ||||| ||||| ||||||||||||||||||   |||   ||| | ||||    ||   |  | |  |   | | |  ||||  | |   || |||      |  || |                                      
TTGGGCTGTTGAACTGATGGCTGACGTTGTCGAAGAGGAGGAGCTGAACAAGATGAATGCTAGGAACATAGCCATGGTGTTTGCCCCCAACATGACTCAGgtaatctccatttctgtaattttgcaggggatcaggtgatacgtaggtgattcttcagtactttccctacaaaagaacctgactgaggtttgctcttttgtttttgggttctatgctag

upper sequence: EFJ12967 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: GRMZM2G114192_T01 (Zea mays), 5'ss of exon 4
CTGGGCGCTGAATCTCATGGCCGACGTCGCCCAGGAGGAGGCGTCAAACAAGATGAACTCCCGGAACATCGCAATGGTTTTTGCTCCCAACATGACTCAGgtacgtt----cctctttcatttggttcttggtttttgttttgttttctgtaatgtatttccttttgctgtcccag-----------------
||||||  | ||||| |||||||| || |   || | ||    |  |||||||||||| ||||||||||||| ||||||||||| ||||| |||||||||||    |    |   | | | |  ||  |  | || |     |||   | | ||   |   | |  |||   || |                 
CTGGGCAATTAATCTGATGGCCGATGTTGTAGAGCAAGAAAACTACAACAAGATGAACGCCCGGAACATCGCGATGGTTTTTGCGCCCAATATGACTCAGgttaactgacacgcgtcttactatgtcttcagattatacaaggttca-tattatacctacacatacgctaatcctggtgcatttctcttccag

upper sequence: EFJ12967 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: GLYMA10G02720.1 (Glycine max), 5'ss of exon 3
CTGGGCGCTGAATCTCATGGCCGACGTCGCCCAGGAGGAGGCGTCAAACAAGATGAACTCCCGGAACATCGCAATGGTTTTTGCTCCCAACATGACTCAGgtacgttcctctttcatttggttcttggtttttgttttgttttct--gtaatgtatttccttttgctgtcccag--------------------------
||||||  |  |||||||||| || || |   | |||||||  |  ||||| |||||  |  | || || ||||||||||||||||| ||||||||||||||| | ||   |     |||| | ||    ||     ||||| ||   |  | |||||   |||| ||                                
CTGGGCTATTGATCTCATGGCTGATGTTGTAGAAGAGGAGGAATTTAACAAAATGAATGCTAGAAATATTGCAATGGTTTTTGCTCCAAACATGACTCAGgtatgctcacatacacattggatgttaaaattgtcagtgtttgcttaatgttctatttgtatttgttggtttttatgtgaaattttttttattaaaagga

upper sequence: EFJ12967 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: GLYMA03G35480.1 (Glycine max), 5'ss of exon 4
CTGGGCGCTGAATCTCATGGCCGACGTCGCCCAGGAGGAGGCGTCAAACAAGATGAACTCCCGGAACATCGCAATGGTTTTTGCTCCCAACATGACTCAGgtacgt-----tcctctttcatt-tggttcttggtttttgttttgttttctgtaatg-tatttccttttgctgtcccag---------------------
 |||||  | ||  | ||||| || || || ||   |||    |  |||||||||||  | || || || ||||||||||||||||| ||||||||||| ||| |      || | ||  ||| |   | | |  |   |||||| | |  |      | |||  | |||   ||  |                      
TTGGGCAATAAACTTAATGGCAGATGTTGCTCAAATGGAAAACTTGAACAAGATGAATGCACGCAATATTGCAATGGTTTTTGCTCCAAACATGACTCAAgtaagagtaaatcattttctattgtaaatgtagtatacagttttgctcttagccccaatttttgttattgaattcgtaaaagtcaacctcatcttattgg

upper sequence: EFJ12967 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: GLYMA02G17070.1 (Glycine max), 5'ss of exon 3
CTGGGCGCTGAATCTCATGGCCGACGTCGCCCAGGAGGAGGCGTCAAACAAGATGAACTCCCGGAACATCGCAATGGTTTTTGCTCCCAACATGACTCAGgtacgttcctctttcat-----ttggttcttggtttttgttttgttttctgtaatgtatttccttttgctgtcccag------------------------
||||||  |  |||||||||| || || |   | |||||||     ||||| |||||  |  | || || |||||||||||||| || |||||||||||||||   ||   |    |     ||   | ||  | || || | |||| ||  | |||  |||  ||||   |    |                        
CTGGGCTATTGATCTCATGGCTGATGTTGTAGAAGAGGAGGAACTTAACAAAATGAATGCAAGAAATATTGCAATGGTTTTTGCACCAAACATGACTCAGgtatcctcacatactgtacacattttctgttaatattagtatagtttgctcca-tgttcttctatttgtatttgttgtttttttttttttgtaaaaatact

upper sequence: EFJ12967 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: AT3G11490.1 (Arabidopsis thaliana), 5'ss of exon 4
CTGGGCGCTGAATCTCATGGCCGACGTCGCCCAGGAGGAGGCGTCAAACAAGATGAACTCCCGGAACATCGCAATGGTTTTTGCTCCCAACATGACTCAGgtacgttcctctttcatttggttcttggtttttgttttgt-tttctgtaatgtatttccttttgctgtcccag------
 |||||  | ||||| ||||| || || |   ||  |||       |||||||||||  | || ||||| |||||||||||||| || ||||||||||||||| |||    ||| | |   |   |     ||||||  | | |  ||| | |  |   |         | |       
TTGGGCTATCAATCTAATGGCTGATGTTGTTGAGATGGAACAACTTAACAAGATGAATGCTCGAAACATTGCAATGGTTTTTGCACCTAACATGACTCAGgtaagttt---tttgaatgaatctctaaagattgtttgatgtgttcgtattttggtaaatgacatcagtcaaattgcag

upper sequence: EFJ12967 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: Vv15s0048g02830.t01 (Vitis vinifera), 5'ss of exon 5
CTGGGCGCTGAATCTCATGGCCGACGTCGCCCAGGAGGAGGCGTCA-AACAAGATGAACTCCCGGAACATCGCAATGGTTTTTGCTCCCAACATGACTCAGgtacgtt--cctctttcatttggttcttggttttt---gttttgttttctgtaatgtatttccttttgctgtcccag-----------------------
|||| |  | ||| | ||| | || || |  ||| | ||  | ||| |||||||||||  | || ||||| |||||||||||||| || ||||||||||||||   ||  | | | |  ||  ||  ||   ||||   ||| || |   | |   |||| | |  ||| | ||| |                        
CTGGACCATCAATTTGATGACAGATGTAGTGCAGCATGAA-CATCACAACAAGATGAATGCACGCAACATTGCAATGGTTTTTGCACCTAACATGACTCAGgttgcttaacatatcttgttctgtcgttttgttttaaggttctgctacatatggggtatctacagttggtatccaatgtgctagcctcactagctgactt

upper sequence: EFJ12967 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: PP1S256_73V6.1 (Physcomitrella patens), 5'ss of exon 6
CTGGGCGCTGAATCTCATGGCCGACGTCGCCCAGGAGGAGGCGTCAAACAAGATGAACTCCCGGAACATCGCAATGGTTTTTGCTCCCAACATGACTCAGgtacgttcctct-----ttcatttggttcttggtttttgttttg-------ttttctgtaatgtatttccttttgct--gtcccag-----------------------------------------------------------
 |||||  | ||||| ||||| || || |  || |||||  |||  |||||||||||| | |  ||||| |||||||| |||||||| |||||||| |||||||||   |||          |  | |  |||  ||| || ||       | | |   ||   ||   | || ||    |  |                                                             
TTGGGCTGTCAATCTGATGGCTGATGTAGTTCAAGAGGAAACGTTCAACAAGATGAACGCTCACAACATTGCAATGGTATTTGCTCCTAACATGACCCAGgtacgtcattctgaacccctcctcagatgctgggctttattctgaacataatctgcccaaaaaaatcgtccttcgcctcatttcgaaacaaaaattccagttcgacattatttatttatttcttctccgacctttgtatttgcag

upper sequence: EFJ12967 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: PP1S107_15V6.1 (Physcomitrella patens), 5'ss of exon 5
CTGGGCGCTGAATCTCATGGCCGACGTCGCCCAGGAGGAGGCGTCAAACAAGATGAACTCCCGGAACATCGCAATGGTTTTTGCTCCCAACATGACTCAGgtacgt--tcctctttcatttggttcttggtttttgttttgtttt----ctgtaa-tgtatttccttttgctgtcccag------------------------------------------------------------------------------------------------------------------
||||||  | || |||||||| || || |   ||  |||| | |  |||||||||||  | || ||||| || |||||||||||||| |||||||| ||||||       |   |||  | |  ||||  ||||     |  |||    ||  || ||| |  | | |||    ||  |                                                                                                                  
CTGGGCCATCAACCTCATGGCGGATGTGGTGGAGCTGGAGTCTTACAACAAGATGAATGCTCGCAACATTGCTATGGTTTTTGCTCCGAACATGACACAGgtatagagcacctcttcggtggtctctttcttttgaaactagtttagagctaaaactgtgtagcgtgttgtctcccgtgttttctcatgatctttgcacattatttcagcctcgaaggtcgtttgttgttagttggtgttcgatctgttgacgaaggtcatctctttgataatttgagtttcttgccctgcag

upper sequence: EFJ12967 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: PP1S13_243V6.1 (Physcomitrella patens), 5'ss of exon 4
CTGGGCGCTGAATCTCATGGCCGACGTCGCCCAGGAGGAGGCGTCAAACAAGATGAACTCCCGGAACATCGCAATGGTTTTTGCTCCCAACATGACTCAGgtacgttcctctttcatttggttcttggtttttg---ttttgttttctgtaatgtatttccttttgctgtcccag-------------------------------------------------------
||||||  | ||| | ||||| || || | ||| || || |     |||||||||||| | || || || |||||||| |||||||| || |||||||||||| || | ||||  |  |    ||||| |  ||    ||   |  |  | | |  |||  |||  || | |                                                          
CTGGGCTGTCAATTTGATGGCTGATGTAGTCCAAGACGAAGTAGTCAACAAGATGAACGCTCGCAATATTGCAATGGTCTTTGCTCCTAATATGACTCAGgtaagt-catcttcgacctcccccttggatgctggcacttgaataccatttacgatttttttttcactcttcacctcattttggaacgctaactgaagcctaacacctgtttcgacctctatatctgcag

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: 34 (upstream exon), 35 (downstream exon)
Score: 27

CTGGGCGCTGAATCTCATGGCCGACGTCGCCCAGGAGGAGGCGTCAAACAAGATGAACTCCCGGAACATCGCAATGGTTTTTGCTCCCAACATGACTCAGgtacgttcct ... gctgtcccagATGGCGGATCCACTAACAGCACTCATGCACGCTGTACAAGTGATGAACATTCTAAAGACGCTGATTGTGAGGACGCTACGGGACAGGCAAGAGGCTGTG




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