Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTCGTGAGGCAAGCTGCTTCTAAAACCAACGATTTGGCTGGGGATGGGACGACGACTTCCTTGATCCTGGCACAAGGATTGATTGCCGAAGGCGTCAAGgtttttttcgtttttttgttcttccagattcattaagccttctgcttggctgtag

Basic information

species Selaginella moellendorffii
transcript EFJ16507
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ16507 (Selaginella moellendorffii), 5'ss of exon 3
lower sequence: Vv09s0002g03930.t01 (Vitis vinifera), 5'ss of exon 3
ACTCGTGAGGCAAGCTGCTTCTAAAACCAACGATTTGGCTGGGGATGGGACGACGACTTCCTTGATCCTGGCACAAGGATTGATTGCCGAAGGCGTCAAGgtttttttcgttttt-----ttgttcttc--cagattcattaagccttctgcttggctgtag--------------------------------------
  | ||||| ||||||||||| |||||||| ||||||||||| |||||||| || |||||  |  | ||||| ||||| |||||| | ||||| || ||||||| |   | ||||     ||| | |||   ||   ||  ||      ||  ||  ||                                         
GTTGGTGAGACAAGCTGCTTCAAAAACCAATGATTTGGCTGGTGATGGGACAACTACTTCTGTTGTTCTGGCTCAAGGCTTGATTACTGAAGGTGTTAAGgtttgtaaaggttttgtcacttgcttttctttaggaacacaaattagcgtgaatgcttgggccgatgcttgtaatacttacatggcactgattcgttcag
















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|169056613|gb|FE463851.1|FE463851
EST:     CGACGACTTCCTTGATCCTGGCACAAGGATTGATTGCCGAAGGCGTCAAG                         GTTGTGGCTGCTGGCTCGAATCCTATTCAAATCACGAGGGGAATTGACAAA
genomic: CGACGACTTCCTTGATCCTGGCACAAGGATTGATTGCCGAAGGCGTCAAGgtttttttcg ... ttggctgtagGTTGTGGCTGCTGGCTCGAATCCTATTCAAATCACGAGGGGAATTGACAAA
EST: gi|169052991|gb|FE460706.1|FE460706
EST:     CGACGACTTCCTTGATCCTGGCACAAGGATTGATTGCCGAAGGCGTCAAG                         GTTGTGGCTGCTGGCTCGAATCCTATTCAAATCACGAGGGGAATTGACAAA
genomic: CGACGACTTCCTTGATCCTGGCACAAGGATTGATTGCCGAAGGCGTCAAGgtttttttcg ... ttggctgtagGTTGTGGCTGCTGGCTCGAATCCTATTCAAATCACGAGGGGAATTGACAAA
EST: gi|169088898|gb|FE494423.1|FE494423
EST:     GACGACTTCCTTGATCCTGCGCACAAGGATTGATTGCCGAAGGCGTCAAG                         GTTGTGGCTGCTGGCTCGAATCCTATTCAAATCACGAGGGGAATTGACAAA
genomic: GACGACTTCCTTGATCCTG-GCACAAGGATTGATTGCCGAAGGCGTCAAGgtttttttcg ... ttggctgtagGTTGTGGCTGCTGGCTCGAATCCTATTCAAATCACGAGGGGAATTGACAAA
EST: gi|169076091|gb|FE484393.1|FE484393
EST:     CGACGACTTCCTTGATCCTGGCACAAGGATTGATTGCCGAAGGCGTCAAG                         GTTGTGGCTGCTGGCTCGAATCCTATTCAAATCACGAGGGGAATTGACAAA
genomic: CGACGACTTCCTTGATCCTGGCACAAGGATTGATTGCCGAAGGCGTCAAGgtttttttcg ... ttggctgtagGTTGTGGCTGCTGGCTCGAATCCTATTCAAATCACGAGGGGAATTGACAAA
EST: gi|169082802|gb|FE486257.1|FE486257
EST:     CGACGACTTCCTTGATCCTGGCACAAGGATTGATTGCCGAAGGCGTCAAG                         GTTGTGGCTGCTGGCTCGAATCCTATTCAAATCACGAGGGGAATTGACAAA
genomic: CGACGACTTCCTTGATCCTGGCACAAGGATTGATTGCCGAAGGCGTCAAGgtttttttcg ... ttggctgtagGTTGTGGCTGCTGGCTCGAATCCTATTCAAATCACGAGGGGAATTGACAAA

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: 32 (upstream exon), 35 (downstream exon)
Score: 37

ACTCGTGAGGCAAGCTGCTTCTAAAACCAACGATTTGGCTGGGGATGGGACGACGACTTCCTTGATCCTGGCACAAGGATTGATTGCCGAAGGCGTCAAGgtttttttcg ... ttggctgtagGTTGTGGCTGCTGGCTCGAATCCTATTCAAATCACGAGGGGAATTGACAAAACCATCGCAGCTCTGGTGAAGGAGCTGAAGGAGATTTCGAAAGAG




<











<


<