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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTGgttcgtcaaaaaaaaatctgtgtttgatttgaggatgaatcaatctctcatctctggctgcttcgtcacgcag

Basic information

species Selaginella moellendorffii
transcript EFJ11645
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ11645 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: LOC_Os02g02840.1 (Oryza sativa), 5'ss of exon 2
GATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTGgttcgtcaaaaaaaaatctgtgtttgatttgaggatgaatcaatctctcatctctggctgcttcgtcacgcag--------------
||||| ||||| || || ||||| |||||||| ||||| || || || ||||| ||||| |||||||| ||||| ||||||||||| |||               |||   |  | ||  | |||  |   | |||  |  |  | |  |  ||    |                
GATTATGTTCCGACGGTGTTTGACAACTTCAGTGCCAACGTCGTGGTTGATGGTAACACCGTCAACCTCGGGCTATGGGACACTGCAGgtaatctggttgcg---ctgctatctaattctgcatgc-ttgttttcttctaccaagttattaagtttttccttcggaataccacag

upper sequence: EFJ11645 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: LOC_Os02g58730.2 (Oryza sativa), 5'ss of exon 2
GATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTGgttcgtcaaaaaaaaatctgtgtttgatttgaggatgaatcaatctct-catctctggctgcttcg-tcacgcag----------------------------------
|| || ||||| |||||||||||||||||||| || ||||| || |||||||| | |||||| ||| | ||| | ||||| || || |||||  |           | |  | |||    |  | || |    | |  |  ||   ||    || |||   |                                   
GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctactttcccctccttttaatggatgcatgcgtaaacctccttatatacatccacctttcacggtcatcaaaataaataaaaatttgacaaatttaacaggacaag

upper sequence: EFJ11645 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: LOC_Os02g58730.1 (Oryza sativa), 5'ss of exon 2
GATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTGgttcgtcaaaaaaaaatctgtgtttgatttgaggatgaatcaatctct-catctctggctgcttcg-tcacgcag----------------------------
|| || ||||| |||||||||||||||||||| || ||||| || |||||||| | |||||| ||| | ||| | ||||| || || |||||  |           | |  | |||    |  | || |    | |  |  ||   ||    || |||   |                             
GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctactttcccctccttttaatggatgcatgcgtaaacctccttatatacatccacctttcacggtcatcaaaataaataaaaatttgacaaatttaacag

upper sequence: EFJ11645 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM5G846811_T01 (Zea mays), 5'ss of exon 2
GATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTGgttcgtcaaaaaaaaatctgtgtttgatttgaggatgaatcaatctct---catctctggctgcttcgtcacgcag---------------------------------
|| || ||||| || || |||||||||||||| ||||| || || || ||||| || ||||||||||| || |||||||||||||| |||  | | |   |   | | |  ||  ||||| | |    |   || |   ||| ||    | | | ||    ||                                  
GACTATGTTCCGACAGTGTTTGATAACTTCAGTGCCAACGTTGTGGTTGATGGTAATACTGTCAACCTCGGCCTCTGGGACACTGCAGgt--gaccagctatcctattttgttactttgatgcttttcccccctttgtgcatatcctttttccttgtttatcaaaatggttgaacttcatctttgcaactgccgcag

upper sequence: EFJ11645 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GRMZM5G803949_T02 (Zea mays), 5'ss of exon 2
GATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTGgttcgtcaaaaaaaaatctgtgtttgatttgaggatgaatcaatctctcatctctggctgcttcgtcacgcag------------------------------------------------------
|| || ||||| || || ||||| |||||||| || || || || || ||||| |||||||||||||| || |||||||||||||| |||     |          | |||    |      |   || |  || |  | |     | ||| |      |                                                       
GACTATGTTCCGACGGTGTTTGACAACTTCAGTGCTAACGTTGTGGTTGATGGTAACACTGTCAACCTCGGCCTCTGGGACACTGCAGgtg-actagccgtgctgttctgtcctgtcctgctacttatgatgctttttttttcctttcctttgcgcgatatcctttttctttgttcatcaaaatggttgagcttccatctttgcaactgtaatag

upper sequence: EFJ11645 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA01G36880.1 (Glycine max), 5'ss of exon 3
GATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTGgttcgtcaaaaaaaaatctgtgtttgatttgaggatgaatcaatctctcatctctggctgcttcgtcacgcag-------
||||| || || ||||||||||| || |||||||| |||||||||||| |||| | || ||| || || ||  | ||||| |||||||||    |      |    ||| | ||   ||  |  |  |  |  | |  |||     |  |  || ||           
GATTATGTGCCGACTGTTTTTGACAATTTCAGCGCAAATGTGGTTGTCAATGGGAGCATTGTGAATCTGGGTTTGTGGGATACTGCTGgtaatgctgcgtgattattgtttctgtgatgttggagcttggaagttttctctggatttattgtgttacttgtggaacag

upper sequence: EFJ11645 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: AT4G35020.3 (Arabidopsis thaliana), 5'ss of exon 4
GATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTGgttcgtcaaaaaaaaatctgtgtttgatttgaggatgaatcaatctc--------tcatctctggct---gcttcgtcacgcag
||||| || || ||||| || ||||| ||||| ||||||||| |||| |||||||||||| ||||| | ||  | ||||| ||||| ||   ||    |       | | ||||  ||  | ||       |||         |||| | ||  |    ||| || |  |||
GATTATGTGCCAACTGTGTTCGATAATTTCAGTGCCAATGTGATTGTTGATGGCAACACTATCAACTTGGGATTGTGGGATACTGCAGgcaagttgttaccttggatttttttgtcttttgaatttcctcctcttccagagagtcatttgtgtttttgacttggtgaaacag

upper sequence: EFJ11645 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: Vv10s0003g00570.t01 (Vitis vinifera), 5'ss of exon 2
GATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTGgttcgtcaaaaaaaaatctgtg--tttgatttgaggatgaatcaatctctcatctctggctgcttcgtcacgcag-------------------------------
||||| |||||||| ||||| || |||||||| || || |||||||| ||||| | ||| ||||||||||| || ||||||||||| |||  ||| || | |  |   |   || || ||  | | |   |    |    |  |       |  |    |  |                               
GATTATGTTCCCACAGTTTTCGACAACTTCAGTGCTAACGTGGTTGTGGATGGTAGCACAGTCAACCTTGGCCTATGGGACACTGCAGgtgagtccaatacagctgcataatttggacttctgcaagttccttcttgcagtggccatgaaatgagctctggggtacgtacttagaatatttttgggcattacag

upper sequence: EFJ11645 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: Vv04s0023g03860.t01 (Vitis vinifera), 5'ss of exon 3
GATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTGgttcgtcaaaaaaaaatctgtgtttgatttgaggatgaatcaatctctcat-ctctggctgcttcgtcacgcag---------------------
||||| || || |||||||| || || ||||| || |||||||||||| ||||   |||||| ||||||||| | ||||| |||||||||  |    | |   |  ||| |    |||     | ||| | |  |  |   | ||  |  ||  |  | | |                     
GATTATGTGCCAACTGTTTTCGACAATTTCAGTGCAAATGTGGTTGTCAATGGGGCCACTGTTAACCTTGGGTTGTGGGATACTGCTGgta-gcttcacagtcacttgtttccttttttgttttcaattactaacaaacattttgattattttatggctctgaatttgttctctttggaacag

upper sequence: EFJ11645 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: Vv18s0001g14670.t01 (Vitis vinifera), 5'ss of exon 2
GATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTGgttcgtcaaaaaaaaatctgtgtttgatttgaggatga----atcaatctc-tcatctctggctgcttcgtcacgcag---------------
||||| || || ||||||||||| || ||||| || ||||||||||| ||||| | |||||||||  | ||| | ||||| |||||||||   ||  |  || |||  |  | |||||   |||      |||| | || |||| ||| | |  |   | ||                   
GATTATGTGCCAACTGTTTTTGACAATTTCAGTGCAAATGTGGTTGTTGATGGGAGCACTGTCAATTTAGGGTTGTGGGATACTGCTGgta-atcttatgaacatcctt-ctggatttcttgattcttttatcagtttcctcatttcttgtttttaattgactatattcgattttgaacag

upper sequence: EFJ11645 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: PP1S165_55V6.1 (Physcomitrella patens), 5'ss of exon 2
GATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTGgttcgtcaaaaaa-aaatctgtgtttg------atttgaggatgaatcaatctc-tcatctctggctgcttcgtcacgcag--------------------
||||||||||| || |||||||||||||||||||| ||||| ||||||||||| |||||||| |||||||| || ||||| || || |||  |  | ||   || |  |||||        ||||        || | |  | |  | | ||||     | || |||||                    
GATTACGTTCCTACCGTTTTTGATAACTTCAGCGCGAATGTCGTTGTCGATGGAAACACTGTAAACCTTGGACTATGGGATACAGCAGgtaagagataacttaagttggtgttcttttggcatttcgcagctgattactagcgttttgtatggcaagggcatc-cgcagtgaccgaccaataattcaat

upper sequence: EFJ11645 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: PP1S51_114V6.1 (Physcomitrella patens), 5'ss of exon 2
GATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTGgt------tcgtcaaaaaaaaatctgtgtttgat--ttgaggatgaatcaatctctcatctctggct---gcttcgtcacgcag----------------
||||||||||| || || ||||| ||||||||||| ||||| || |||||||| || || |||||||| ||| | ||||| || || |||      |  |   |    || || |  |  ||  || |     | || |  ||  |||    ||    |  | |   || ||                
GATTACGTTCCTACCGTGTTTGACAACTTCAGCGCAAATGTAGTGGTCGATGGAAATACCGTCAACCTCGGGTTATGGGATACAGCAGgtgagagatgatttgacgccaagctcttctctatcgttcatatctactcgagttccaatcgacagcgctggtattgatgcgtagtgcttccgaatggaaa

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|169057946|gb|FE465544.1|FE465544
EST:     TGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTG                         GTCAAGAAGATTACAACCGCTTGAGGCCCCTCAGCTATAGAGGAGCCGATG
genomic: TGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTGgttcgtcaaa ... cgtcacgcagGTCAAGAAGATTACAACCGCTTGAGGCCCCTCAGCTATAGAGGAGCCGATG
EST: gi|169057947|gb|FE465545.1|FE465545
EST:     TGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTG                         GTCAAGAAGATTACAACCGCTTGAGGCCCCTCAGCTATAGAGGAGCCGATG
genomic: TGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTGgttcgtcaaa ... cgtcacgcagGTCAAGAAGATTACAACCGCTTGAGGCCCCTCAGCTATAGAGGAGCCGATG
EST: gi|169034528|gb|FE444575.1|FE444575
EST:     TGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTG                         GTCAAGAAGATTACAACCGCTTGAGGCCCCTCAGCTATAGAGGAGCCGATG
genomic: TGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTGgttcgtcaaa ... cgtcacgcagGTCAAGAAGATTACAACCGCTTGAGGCCCCTCAGCTATAGAGGAGCCGATG
EST: gi|169037117|gb|FE444402.1|FE444402
EST:     TGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTTTGGGACACTGCTG                         GTCAAGAAGATTACACCCGCTTGAGGCCCCTCAGCTATAGAGGAGCCGATG
genomic: TGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTGgttcgtcaaa ... cgtcacgcagGTCAAGAAGATTACAACCGCTTGAGGCCCCTCAGCTATAGAGGAGCCGATG

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: 29

GATTACGTTCCCACTGTTTTTGATAACTTCAGCGCCAATGTGGTTGTCGATGGCAACACTGTCAACCTTGGGCTCTGGGACACTGCTGgttcgtcaaa ... cgtcacgcagGTCAAGAAGATTACAACCGCTTGAGGCCCCTCAGCTATAGAGGAGCCGATGTTTTCCTCTTGGCCTTTTCCCTTATCAGCAGGGCCAGCTATGAAAACAT




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