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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTACGTGCCTACAGTCTTTGATAACTTTAGTGCCAATGTTGTCGTGGATGGCAACACTGTGAATTTGGGTCTCTGGGACACCGCTGgtacgtttagctggaaaaactcggcttgttctaacgcaaacgcatgcttgctttttgtttctcgtaaatctcgcag

Basic information

species Selaginella moellendorffii
transcript EFJ16760
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ04304 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: LOC_Os02g58730.2 (Oryza sativa), 5'ss of exon 2
GACTACGTGCCTACAGTCTTTGATAACTTTAGTGCCAATGTTGTCGTGGATGGCAACACTGTGAATTTGGGTCTCTGGGACACCGCTGgt---acgtttagctggaaaaactcg--gcttgttctaacg--caaacgcatgcttgctttttgtttctcgtaaatctcgcag--------------------------
||||| || || || || ||||||||||| ||||| |||||||| || ||||| | ||||||||| |||||  | ||||| || || |||   || ||   ||      | | |  || ||    |||   |  |   |      | |||          |||      |                           
GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctactttcccctccttttaatggatgcatgcgtaaacctccttatatacatccacctttcacggtcatcaaaataaataaaaatttgacaaatttaacaggacaag

upper sequence: EFJ04304 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: LOC_Os02g58730.1 (Oryza sativa), 5'ss of exon 2
GACTACGTGCCTACAGTCTTTGATAACTTTAGTGCCAATGTTGTCGTGGATGGCAACACTGTGAATTTGGGTCTCTGGGACACCGCTGg---tacgtttagctggaaaaactcg--gcttgttctaacg--caaacgcatgcttgctttttgtttctcgtaaatctcgcag--------------------
||||| || || || || ||||||||||| ||||| |||||||| || ||||| | ||||||||| |||||  | ||||| || || ||   ||| ||   ||      | | |  || ||    |||   |  |   |      | |||          |||      |                     
GACTATGTTCCAACTGTTTTTGATAACTTCAGTGCAAATGTTGTGGTCGATGGGAGCACTGTGAACTTGGGGTTGTGGGATACAGCAGgttctactttcccctccttttaatggatgcatgcgtaaacctccttatatacatccacctttcacggtcatcaaaataaataaaaatttgacaaatttaacag

upper sequence: EFJ04304 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA11G11510.1 (Glycine max), 5'ss of exon 2
GACTACGTGCCTACAGTCTTTGATAACTTTAGTGCCAATGTTGTCGTGGATGGCAACACTGTGAATTTGGGTCTCTGGGACACCGCTGgtacgtttag------ctggaaaaactcggcttgttctaacgcaaacgcatgcttgctttttgtttctcgtaaatctcgcag
||||||||||| || |||||||| || || ||||| ||||| || |||||||| | |||||||||| | ||  | ||||| || ||||||| || |||      ||||  |   |       |  |         |  || ||  |  ||||||       ||  | |||
GACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTCGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatagtttttcctggttatctttcatccttcttgtgttttgtgagtgttttgtcattgttttcaacttatggcacag

upper sequence: EFJ04304 (Selaginella moellendorffii), 5'ss of exon 2
lower sequence: GLYMA12G03660.1 (Glycine max), 5'ss of exon 2
GACTACGTGCCTACAGTCTTTGATAACTTTAGTGCCAATGTTGTCGTGGATGGCAACACTGTGAATTTGGGTCTCTGGGACACCGCTGgtacgtttagctggaaaaactcggcttgttctaacgcaaacgcatgcttgctttt-tgtttctcgtaaatctcgcag
||||||||||| || |||||||| || || ||||| ||||| || |||||||| | |||||||||| | ||  | ||||| || ||||||| || ||| |             |  | ||            |  ||| |||  |||||       ||    |||
GACTACGTGCCAACTGTCTTTGACAATTTCAGTGCAAATGTAGTTGTGGATGGAAGCACTGTGAATCTTGGGTTGTGGGATACTGCTGgtaagtatagtttcccggttatctttcatccttcttgtgttttgtcattgttttgatgttttcaacttatgggacag

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|169038008|gb|FE445813.1|FE445813
EST:     TGTTGTCGTGGATGGCAACACTGTGAATTTGGGTCTCTGGGACACCGCTG                         GCCAGGAAGACTATAACATGCTGCGTCCATTGAGTTACCGAGGAGCCGACG
genomic: TGTTGTCGTGGATGGCAACACTGTGAATTTGGGTCTCTGGGACACCGCTGgtacgtttag ... aatctcgcagGCCAGGAAGACTATAACAGGCTGCGTCCATTGAGTTACCGAGGAGCCGATG
EST: gi|169075481|gb|FE482491.1|FE482491
EST:     TGTTGTCGTGGATGGCAACACTGTGAATTTGGGTCTCTGGGACACCGCTG                         GCCAGGAAGACTATAACAGGCTGCGTCCATTGAGTTACCGAGGAGCCGATG
genomic: TGTTGTCGTGGATGGCAACACTGTGAATTTGGGTCTCTGGGACACCGCTGgtacgtttag ... aatctcgcagGCCAGGAAGACTATAACAGGCTGCGTCCATTGAGTTACCGAGGAGCCGATG
EST: gi|169075482|gb|FE482492.1|FE482492
EST:     TGTTGTCGTGGATGGCAACACTGTGAATTTGGGTCTCTGGGACACCGCTG                         GCCAGGAAGACTATAACAGGCTGCGTCCATTGAGTTACCGAGGAGCCGATG
genomic: TGTTGTCGTGGATGGCAACACTGTGAATTTGGGTCTCTGGGACACCGCTGgtacgtttag ... aatctcgcagGCCAGGAAGACTATAACAGGCTGCGTCCATTGAGTTACCGAGGAGCCGATG
EST: gi|169110406|gb|FE512165.1|FE512165
EST:     TGTTGTCGTGGATGGCAACACTGTGAATTTGGGTCTCTGGGACACCGCTG                         GCCAGGAAGACTATAACAGGCTGCGTCCATTGAGTTACCGAGGAGCCGATG
genomic: TGTTGTCGTGGATGGCAACACTGTGAATTTGGGTCTCTGGGACACCGCTGgtacgtttag ... aatctcgcagGCCAGGAAGACTATAACAGGCTGCGTCCATTGAGTTACCGAGGAGCCGATG
EST: gi|169110405|gb|FE512164.1|FE512164
EST:     TGTTGTCGTGGATGGCAACACTGTGAATTTGGGTCTCTGGGACACCGCTG                         GCCAGGAAGACTATAACAGGCTGCGTCCATTGAGTTACCGAGGAGCCGATG
genomic: TGTTGTCGTGGATGGCAACACTGTGAATTTGGGTCTCTGGGACACCGCTGgtacgtttag ... aatctcgcagGCCAGGAAGACTATAACAGGCTGCGTCCATTGAGTTACCGAGGAGCCGATG

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), 35 (downstream exon)
Score: 13

GACTACGTGCCTACAGTCTTTGATAACTTTAGTGCCAATGTTGTCGTGGATGGCAACACTGTGAATTTGGGTCTCTGGGACACCGCTGgtacgtttag ... aatctcgcagGCCAGGAAGACTATAACAGGCTGCGTCCATTGAGTTACCGAGGAGCCGATGTTTTCCTTCTAGCTTTCTCACTTATAAGCCGAGCTAGCTATGAAAACAT




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