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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTTCGTCGTCGGTCGGGCCAGAGTACTATGTCAACATTCTTTCGTTCGTGGACAAGGACCAGCTTGAGCCCGGGTGTGCGATCCTCATGCACAATAAGgtactgtttcctgcttgctagcgtttgtttctactttgtttctcttcggcag

Basic information

species Selaginella moellendorffii
transcript EFJ20767
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ20767 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os07g49150.1 (Oryza sativa), 5'ss of exon 1
TGTTTCGTCGTCGGTCGGGCCAGAGTACTATGTCAACATTCTTTCGTTCGTGGACAAGGACCAGCTTGAGCCCGGGTGTGCGATCCTCATGCACAATAAGgtactgtttcctgcttgctagcgtttgtttctactttgtttctcttcggcag---------------------------------------------------
 || || || || ||||| || |||||||| |||  ||| || || ||||| |||||||||||||| |||||||| ||  | |||||||||||||| ||||||||  | |   |   | | || ||   ||  | | | |   ||||||                                                      
CGTCTCCTCCTCCGTCGGCCCCGAGTACTACGTCGGCATCCTCTCCTTCGTCGACAAGGACCAGCTCGAGCCCGGCTGCTCCATCCTCATGCACAACAAGgtactactgctcaccccccatcgctt---tccgcatcgatctacttcggttcatacacatactttaggccggcctcttccacataatcaaaagtattaagatc

upper sequence: EFJ20767 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: LOC_Os03g18690.1 (Oryza sativa), 5'ss of exon 1
TGTTTCGTCGTCGGTCGGGCCAGAGTACTATGTCAACATTCTTTCGTTCGTGGACAAGGACCAGCTTGAGCCCGGGTGTGCGATCCTCATGCACAATAAGgtactgtttcctgct-tgctagcgtttgtttctactttgtttctcttcggcag-----------------------------------------------
 || |||||||| |||||||| || ||||||||   |||  | || ||||| |||||||||||||| ||||| |||||||| || || ||||| || |||||| |  |   |    |     | |||  |  |   ||| |||  |  |   |                                               
CGTCTCGTCGTCCGTCGGGCCGGAATACTATGTTGGCATATTATCATTCGTCGACAAGGACCAGCTCGAGCCAGGGTGTGCCATTCTGATGCATAACAAGgtattaatgtgtataatttccccttttcctgatggattggttcagtgggattggaagcaccacactaacacatcagtagttcatggtttggtgattgggt

upper sequence: EFJ20767 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G056569_T01 (Zea mays), 5'ss of exon 1
TGTTTCGTCGTCGGTCGGGCCAGAGTACTATGTCAACATTCTTTCGTTCGTGGACAAGGACCAGCTTGAGCCCGGGTGTGCGATCCTCATGCACAATAAGgt--------actgtttcctgcttgctagcgtttgtttctactttgtttctcttcggcag----------------------------------------
 || || || || ||||| || ||||||||||||  ||| || || ||||| |||||||||||||| ||||| |||||  | |||||||||||||| |||||        |  |  ||  || | || |   |   |    |  |  ||  || |  | |                                        
CGTCTCCTCCTCCGTCGGACCCGAGTACTATGTCGGCATCCTCTCCTTCGTTGACAAGGACCAGCTCGAGCCGGGGTGCTCCATCCTCATGCACAACAAGgtttgtccggagcggatctagcatcctcgatctaaatgtctcactcctttcctcctaccgatctagtgctagctgctcactggctgaagggtgttcggta

upper sequence: EFJ20767 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G095593_T01 (Zea mays), 5'ss of exon 1
TGTTTCGTCGTCGGTCGGGCCAGAGTACTATGTCAACATTCTTTCGTTCGTGGACAAGGACCAGCTTGAGCCCGGGTGTGCGATCCTCATGCACAATAAGgtactgtttcctgcttgctagcg---tttgtttctactttgtttctcttcggcag-----------------------------------------------
 || || || || ||||| || ||||||||||||| ||| || || || || |||||||||||||| ||||| || ||  | ||||||||||||||||||||  |||||| | ||||| || |      | | ||||   |      |   |||                                                
CGTCTCCTCCTCTGTCGGACCCGAGTACTATGTCAGCATCCTCTCCTTTGTCGACAAGGACCAGCTCGAGCCGGGATGCTCCATCCTCATGCACAATAAGgt-ttgtttc-tacttgccagggacccgcgctactacccggagcggatctagcatcctcgatctaaatatctccctccgatctagtcgttggatgtgtagac

upper sequence: EFJ20767 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S4_277V6.1 (Physcomitrella patens), 5'ss of exon 1
TGTTTCGTCGTCGGTCGGGCCAGAGTACTATGTCAACATTCTTTCGTTCGTGGACAAGGACCAGCTTGAGCCCGGGTGTGCGATCCTCATGCACAATAAGgtactgtttcctgcttgctagcgtttgtttctactttgtttctcttcggcag--------------------------------------------------
 |||||||| || || ||||| ||||| ||||| |||||| | ||||||||||||||||| ||||| |||||||| || || |||||||||||||||||||||    ||||    |   ||   ||  |||  |||  || ||||||                                                       
CGTTTCGTCTTCCGTGGGGCCCGAGTATTATGTGAACATTTTGTCGTTCGTGGACAAGGATCAGCTCGAGCCCGGTTGCGCAATCCTCATGCACAATAAGgtatgccttcccaaatctaagaagtt--ttcagcttatttgctcttcaatttcttcattgccaaaccctaaactatgttctatcacacttgctagaatgtcc

upper sequence: EFJ20767 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S109_234V6.1 (Physcomitrella patens), 5'ss of exon 1
TGTTTCGTCGTCGGTCGGGCCAGAGTACTATGTCAACATTCTTTCGTTCGTGGACAAGGACCAGCTTGAGCCCGGGTGTGCGATCCTCATGCACAATAAGgtactgtttcctgcttgctagcgtttgtttctactttgtttctc-ttcggcag-----------------------------------------------
||| || ||||| || || || ||||| ||||| || ||| | ||||||||||||||||| ||||| ||||| || || || |||||||||||||| ||||| |  | | |||     || | ||  ||  |  |||    |||  | ||  |                                               
TGTGTCATCGTCCGTGGGTCCTGAGTATTATGTGAATATTTTATCGTTCGTGGACAAGGATCAGCTCGAGCCTGGTTGCGCAATCCTCATGCACAACAAGgtgcgatcttctgaggcttatcattgcttattttttttccactcgcttggttgtttcaacttattctctaggatagttggtagggtttcaatatgcgcaa

upper sequence: EFJ20767 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: PP1S12_207V6.1 (Physcomitrella patens), 5'ss of exon 1
TGTTTCGTCGTCGGTCGGGCCAGAGTACTATGTCAACATTCTTTCGTTCGTGGACAAGGACCAGCTTGAGCCCGGGTGTGCGATCCTCATGCACAATAAGgtactgtttcctgcttgctagcgtt-tgtttctactttgt-ttctcttcggcag----------------------------------------------
||| |||||||| || || || ||||| ||||| || ||| | |||||||| |||||||| ||||| ||||| || || || |||||||||||||| ||||| |  | |||||      ||| || |    ||| | ||  |||||||                                                    
TGTGTCGTCGTCCGTGGGTCCTGAGTATTATGTGAATATTTTGTCGTTCGTAGACAAGGATCAGCTGGAGCCTGGCTGCGCAATCCTCATGCACAACAAGgtgcgatctcctgaaattgagcattgttcaactattgtgcattctcttgcatgtttcaatatgatctttggcatggttatcatatgtccaggatgcacga

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|169060660|gb|FE467398.1|FE467398
EST:     TGGACAAGGACCAGCTTGAGCCCGGGTGTGCGATCCTCATGCACAATAAG                         GTTCTCTCCGTTGTTGGATTGTTGCAAGACGAAGTCGATCCTATGGTGTCG
genomic: TGGACAAGGACCAGCTTGAGCCCGGGTGTGCGATCCTCATGCACAATAAGgtactgtttc ... tcttcggcagGTTCTCTCCGTTGTTGGATTGTTGCAAGACGAAGTCGATCCTATGGTGTCG
EST: gi|169040853|gb|FE447904.1|FE447904
EST:     TGGACAAGGACCAGCTTGAGCCCGGGTGTGCGATCCTCATGCACAATAAG                         GTTCTCTCCGTTGTTGGATTGTTGCAAGACGAAGTCGATCCTATGGTGTCG
genomic: TGGACAAGGACCAGCTTGAGCCCGGGTGTGCGATCCTCATGCACAATAAGgtactgtttc ... tcttcggcagGTTCTCTCCGTTGTTGGATTGTTGCAAGACGAAGTCGATCCTATGGTGTCG
EST: gi|169034211|gb|FE445051.1|FE445051
EST:     TGGACAAGGACCAGCTTGAGCCCGGGTGTGCGATCCTCATGCACAATAAG                         GTTCTCTCCGTTGTTGGATTGTTGCAAGACGAAGTCGATCCTATGGTGTCG
genomic: TGGACAAGGACCAGCTTGAGCCCGGGTGTGCGATCCTCATGCACAATAAGgtactgtttc ... tcttcggcagGTTCTCTCCGTTGTTGGATTGTTGCAAGACGAAGTCGATCCTATGGTGTCG
EST: gi|169065782|gb|FE474372.1|FE474372
EST:     TGGACAAGGACCAGCTTGAGCCCGGGTGTGCGATCCTCATGCACAATAAG                         GTTCTCTCCGTTGTTGGATTGTTGCAAGACGAAGTCGATCCTATGGTGTCG
genomic: TGGACAAGGACCAGCTTGAGCCCGGGTGTGCGATCCTCATGCACAATAAGgtactgtttc ... tcttcggcagGTTCTCTCCGTTGTTGGATTGTTGCAAGACGAAGTCGATCCTATGGTGTCG

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), 35 (downstream exon)
Score: 22

TGTTTCGTCGTCGGTCGGGCCAGAGTACTATGTCAACATTCTTTCGTTCGTGGACAAGGACCAGCTTGAGCCCGGGTGTGCGATCCTCATGCACAATAAGgtactgtttc ... tcttcggcagGTTCTCTCCGTTGTTGGATTGTTGCAAGACGAAGTCGATCCTATGGTGTCGGTGATGAAAGTCGAAAAAGCTCCGCTAGAGTCTTATGCCGACATCGGGG




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