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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgcgttatctatctcttccttgtatccaatacctgacttctttgactcgcagGTAAGTGACAAGATGGACCCCAACGAGCTGGTCAAGCTCATCGACATCCTGAATCCTCAAAACAAGCCCGGTAGGCTGACTGTCGTTGTCCGCATGGGAG

Basic information

species Selaginella moellendorffii
transcript EFJ08096
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ08096 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA02G37080.2 (Glycine max), 3'ss of exon 3
--------------------------------gtacgcgttatctatctcttccttgtatccaatacc-----tgacttctttg-actcgcagGTAAGTGACAAGATGGACCCCAACGAGCTGGTCAAGCTCATCGACATCCTGAATCCTCAAAACAAGCCCGGTAGGCTGACTGTCGTTGTCCGCATGGGAG
| | | | | || || | ||| ||| || || || | | ||||||||||||||||||||| || || ||||| || || ||||| || ||| |||||||||||||||| | || || | ||||| | | |||||||
gttcgtacatgattaattgttatcattcttaagcatttgattttcatgcattggctttattgaattttgattatgtttttcatgcattggcagGTAAGTGACAAGATGGATCCAAATGAGCTAGTTAAACTCATTGAGATCTTGAATCCTCAAAACAAAGCAGGAAGAATTACTGTGATCACGAGGATGGGAG

upper sequence: EFJ08096 (Selaginella moellendorffii), 3'ss of exon 3
lower sequence: GLYMA14G35370.1 (Glycine max), 3'ss of exon 3
----------------------------------------------------------gtacgcgttatctatct-cttccttgtatccaatacctgacttctttg-actcgcagGTAAGTGACAAGATGGACCCCAACGAGCTGGTCAAGCTCATCGACATCCTGAATCCTCAAAACAAGCCCGGTAGGCTGACTGTCGTTGTCCGCATGGGAG
||| | | | || | | | ||| | || || | || | | ||||||||||||||||||||| || || ||||| || | ||||| || ||| ||||||| |||||||| || || || | ||||| || | |||||||
gtttggacttgattaattgttatcattcttaaagtatttgattttcattccttggcgtgtaagaggctttaatttgcattattgaagttttgttatgttttttatgcattggcagGTAAGTGACAAGATGGATCCAAATGAGCTTGTTAGACTCATTGAGATCTTGAATCCCCAAAACAAACCAGGGAGAATAACTGTGATTACGAGGATGGGAG
















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|169072295|gb|FE480220.1|FE480220
EST:     AGCACACA-TGNAGTTCCTCCGAGGAGTAGCAAATCCCATTGGTGTTAAG                         GTAAGTGACAAGATGGACCCCAACGAGCTGGTCAAGCTCATCGACATCCTG
genomic: AGCACACATTG-AGTTCCTCCGAGGAGTAGCAAATCCCATTGGTGTTAAGgtacgcgtta ... tgactcgcagGTAAGTGACAAGATGGACCCCAACGAGCTGGTCAAGCTCATCGACATCCTG
EST: gi|169075832|gb|FE482803.1|FE482803
EST:     GAGCACACATTGAGTTCCTCCGAGGAGTAGCAAATCCCATTGGTGTTAAG                         GTAAGTGACAAGATGGACCCCAACGAGCTGGTCAAGCTCATCGACATCCTG
genomic: GAGCACACATTGAGTTCCTCCGAGGAGTAGCAAATCCCATTGGTGTTAAGgtacgcgtta ... tgactcgcagGTAAGTGACAAGATGGACCCCAACGAGCTGGTCAAGCTCATCGACATCCTG
EST: gi|169113101|gb|FE514957.1|FE514957
EST:     GAGCACACATTGAGTTCCTCCGAGGAGTAGCAAATCCCATTGGTGTTAAG                         GTAAGTGACAAGATGGACCCCAACGAGCTGGTCAAGCTCATCGACATCCTG
genomic: GAGCACACATTGAGTTCCTCCGAGGAGTAGCAAATCCCATTGGTGTTAAGgtacgcgtta ... tgactcgcagGTAAGTGACAAGATGGACCCCAACGAGCTGGTCAAGCTCATCGACATCCTG

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: 34

CTGCTCGGCACATATGTTGTGGATTGGAGAGCGCACGCGACAACTCGACGGAGCACACATTGAGTTCCTCCGAGGAGTAGCAAATCCCATTGGTGTTAAGgtacgcgtta ... tgactcgcagGTAAGTGACAAGATGGACCCCAACGAGCTGGTCAAGCTCATCGACATCCTGAATCCTCAAAACAAGCCCGGTAGGCTGACTGTCGTTGTCCGCATGGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacgcgttatctatctcttccttgtatccaatacctgacttctttgactcgcagGTAAGTGACAAGATGGACCCCAACGAGCTGGTCAAGCTCATCGACATCCTGAATCCTCAAAACAAGCCCGGTAGGCTGACTGTCGTTGTCCGCATGGGAG
                                       cttcttt  CT-rich tract
 ttatctat  TA-rich tract