Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCCGGAATTCTATGCGGCGTGCACTGTCGGGGGGATTCTTAGCTGCGGCCTCACTCACACGGCCGTGACGCCTTTGGACATGGTCAAGTGTAATATGCAGgtaagctcgattttctggtttaaagcgtgtggctgatgaatggattctttgctcag

Basic information

species Selaginella moellendorffii
transcript EFJ31006
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ31006 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G015401_T01 (Zea mays), 5'ss of exon 1
GCCGGAATTCTATGCGGCGTGCACTGTCGGGGGGATTCTTAGCTGCGGCCTCACTCACACGGCCGTGACGCCTTTGGACATGGTCAAGTGTAATATGCAGgtaagc---tcgattttctggtttaaagcgtgtggctgatgaatggattctttgctcag-------------------------------------------
|||||  |||||||| || ||||||| ||| || ||    |||||||| ||||| |||| |||||| |||||| | ||| | |||||||| ||||||||||| |||   | |       | | |   ||   ||  || |  |  |  ||  |  |  |                                           
GCCGGCCTTCTATGCCGCCTGCACTGCCGGAGGAATCGCCAGCTGCGGGCTCACCCACATGGCCGTCACGCCTCTCGACCTCGTCAAGTGCAATATGCAGgtgagcgggtagcaccctagatctgtcgcccctg--tgctccacaggatccattttgggaagattcactgattctaatggaacatggccagagtcaaagtca

upper sequence: EFJ31006 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GRMZM2G152827_T01 (Zea mays), 5'ss of exon 1
GCCGGAATTCTATGCGGCGTGCACTGTCGGGGGGATTCTTAGCTGCGGCCTCACTCACACGGCCGTGACGCCTTTGGACATGGTCAAGTGTAATATGCAGgtaagctcg-attttctggtttaaagcgtgtggctgatgaatggattctttgctcag-------------------------------------------
|||||  |||||||| || ||||||| ||| || ||    |||||||| ||||| |||| |||||| |||||| | ||| | |||||||| ||||||||||| |||  | |    |     |    ||    | || |  |  |  ||| |  |  |                                           
GCCGGCCTTCTATGCCGCCTGCACTGCCGGAGGAATCGCCAGCTGCGGGCTCACCCACATGGCCGTCACGCCTCTCGACCTCGTCAAGTGCAATATGCAGgtgagcgggtagcaccctagatctgtcgccccggtgctccacaggatctattttgggaaggttcactggttctaatggaacatggccagagtcaaagtca

upper sequence: EFJ31006 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA16G05450.1 (Glycine max), 5'ss of exon 1
GCCGGAATTCTATGCGGCGTGCACTGTCGGGGGGATTCTTAGCTGCGGCCTCACTCACACGGCCGTGACGCCTTTGGACATGGTCAAGTGTAATATGCAGgtaagctcgattt-----tctggtttaaagcgtgtggctg-----atgaatggattctttgctcag----------------------------------
 || |  ||||| || || ||||| | ||| || || || ||||| ||||||||||||| |||||| || ||| | ||| | ||||||||||||||||||||   |||  | |     |||   |  |    | |   |      ||  ||  ||   | | || |                                  
CCCTGCCTTCTACGCCGCCTGCACCGCCGGTGGAATCCTCAGCTGTGGCCTCACTCACATGGCCGTCACTCCTCTTGACCTAGTCAAGTGTAATATGCAGgttctctctctctctctctctctctctatatatatatatatatatatatatatatatatcgatctgtcttattgtgcttagatttaactctgtttttgtt

upper sequence: EFJ31006 (Selaginella moellendorffii), 5'ss of exon 1
lower sequence: GLYMA19G27380.1 (Glycine max), 5'ss of exon 1
GCCGGAATTCTATGCGGCGTGCACTGTCGGGGGGATTCTTAGCTGCGGCCTCACTCACACGGCCGTGACGCCTTTGGACATGGTCAAGTGTAATATGCAGgtaagctcgattttctggtttaaagcgtgtggctgatgaatggat-tctttgctcag-------------------------------------------
 || |  ||||| || || ||||| | ||| || || || ||||| ||||||||||||| | |||| || ||| | ||| | ||||||||||||||||||||   |||  | |     | |    |         ||  ||  || | | |    |                                            
CCCCGCCTTCTACGCCGCCTGCACCGCCGGTGGAATCCTCAGCTGTGGCCTCACTCACATGACCGTCACTCCTCTTGACCTAGTCAAGTGTAATATGCAGgtcctctctctctctctctctctctctctctctctatatatatatatatatatatatatatatatatatatatatatatatatatatatatcgatctgac

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|169045764|gb|FE451191.1|FE451191
EST:     TCACTCACACGGCCGTGACGCCTTTGGACATGGTCAAGTGTAATATGCAG                         ATCGATCCCGCCAAGTATAGATCTATCGGCAGTGGATTTGGGGTTTTGTAC
genomic: TCACTCACACGGCCGTGACGCCTTTGGACATGGTCAAGTGTAATATGCAGgtaagctcga ... ctttgctcagATCGATCCCGCCAAGTATAGATCTATCGGCAGTGGATTTGGGGTTTTGTAC
EST: gi|169115023|gb|FE516388.1|FE516388
EST:     TCACTCACACGGCCGTGACGCCTTTGGACATGGTCAAGTGTAATATGCAG                         ATCGATCCCGCCAAGTATAGATCTATCGGCAGTGGATTTGGGGTTTTGTAC
genomic: TCACTCACACGGCCGTGACGCCTTTGGACATGGTCAAGTGTAATATGCAGgtaagctcga ... ctttgctcagATCGATCCCGCCAAGTATAGATCTATCGGCAGTGGATTTGGGGTTTTGTAC
EST: gi|169050329|gb|FE457551.1|FE457551
EST:     TCACTCACACGGCCGTGACGCCTTTGGACATGGTCAAGTGTAATATGCAG                         ATCGATCCCGCCAAGTATAGATCTATCGGCAGTGGATTTGGGGTTTTGTAC
genomic: TCACTCACACGGCCGTGACGCCTTTGGACATGGTCAAGTGTAATATGCAGgtaagctcga ... ctttgctcagATCGATCCCGCCAAGTATAGATCTATCGGCAGTGGATTTGGGGTTTTGTAC
EST: gi|169099377|gb|FE500993.1|FE500993
EST:     TCACTCACACGGCCGTGACGCCTTTGGACATGGTCAAGTGTAATATGCAG                         ATCGATCCCGCCAAGTATAGATCTATCGGCAGTGGATTTGGGGTTTTGTAC
genomic: TCACTCACACGGCCGTGACGCCTTTGGACATGGTCAAGTGTAATATGCAGgtaagctcga ... ctttgctcagATCGATCCCGCCAAGTATAGATCTATCGGCAGTGGATTTGGGGTTTTGTAC

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: 36

GCCGGAATTCTATGCGGCGTGCACTGTCGGGGGGATTCTTAGCTGCGGCCTCACTCACACGGCCGTGACGCCTTTGGACATGGTCAAGTGTAATATGCAGgtaagctcga ... ctttgctcagATCGATCCCGCCAAGTATAGATCTATCGGCAGTGGATTTGGGGTTTTGTACAAGGAGGCTGGCCCCAAAGGTTTGTTCAAGGGATGGGTTCCGACGCTGT




<











<


<