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

gtaagtgtttttgacatttgtgcttggtggcttctactgatggttttgtgggactttgtagGAACGGAGCTCAAAAGCTTCTGGGTGTTTTGATCACGATTGGTGAAGCTGTCGCGTACGTTTTGTCTGGAATGTACGGCGACGTTCGTGATCTCGGAGCC

Basic information

species Selaginella moellendorffii
transcript EFJ15673
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ15673 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S114_48V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------------------gtaagtgtttttgacat----ttgtgcttggtggcttctactgatggttttgtgggactttgtagGAACGGAGCTCAAAAGCTTCTGGGTGTTTTGATCACGATTGGTGAAGCTGTCGCGTACGTTTTGTCTGGAATGTACGGCGACGTTCGTGATCTCGGAGCC
                                    ||  | ||| || |       |   | |     ||  || |  |   |||         || ||||| || ||||| ||||| || |||||||||||||| ||||| || || |||||||||||| |||| || ||||| ||||| |||||||||||||| || 
agttgccttatgcttttagaactatttatattacattacttatttgtgtcgcgatgataaacctttaaactcatatttgtaaatttcgaatgtcgtgaagGAATGGTGCTCAGAAGCTCCTTGGTGTTTTGATCACTATTGGAGAGGCAGTCGCGTACGTTCTGTCCGGCATGTATGGCGATGTTCGTGATCTCGGTGCT

upper sequence: EFJ15673 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: PP1S323_56V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------------------gtaagtgtttttgacatttgtgcttggtggctt---ctactgatggttttgtggg-actttgtagGAACGGAGCTCAAAAGCTTCTGGGTGTTTTGATCACGATTGGTGAAGCTGTCGCGTACGTTTTGTCTGGAATGTACGGCGACGTTCGTGATCTCGGAGCC
                                    | |||   | |   |  |  | |   ||| |    | | | ||     |||||  | |||||||||| || |||||||||||||| || || || |||||||||||||| || |||||||| ||  |||| || |||||||| ||||| ||||| ||||| || 
gtagtccttgaaagtaattatttgtctgttttgtaatcagttcctcttctagcttagttgactggttcaaccaattaatccacctgtggttaatttgtagGAATGGTGCTCAAAAGCTTCTCGGGGTGTTAATCACGATTGGTGAGGCAGTCGCGTATGTCCTGTCCGGCATGTACGGAGACGTCCGTGACCTCGGCGCT
















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|169067827|gb|FE473398.1|FE473398
EST:     TCGAAGATTATCGAGGTTGACAACAACGTGAGAGAAGACCGAGCTCTTGT                         GAACGGAGCTCAAAAGCTTCTGGGTGTTTTGATCACGATTGGTGAAGCTGT
genomic: TCGAAGATTATCGAGGTTGACAACAACGTGAGAGAAGACCGAGCTCTTGTgtaagtgttt ... gactttgtagGAACGGAGCTCAAAAGCTTCTGGGTGTTTTGATCACGATTGGTGAAGCTGT
EST: gi|169100434|gb|FE501322.1|FE501322
EST:     TCGAAGATTATCGAGGTTGACAACAACGTGAGAGAAGACCGAGCTCTTTT                         GAACGGAGCTCAAAAGCTTCTGGGTGTTTTGATCACGATTGGTGAAGCTGT
genomic: TCGAAGATTATCGAGGTTGACAACAACGTGAGAGAAGACCGAGCTCTTGTgtaagtgttt ... gactttgtagGAACGGAGCTCAAAAGCTTCTGGGTGTTTTGATCACGATTGGTGAAGCTGT
EST: gi|169043639|gb|FE452694.1|FE452694
EST:     TCGAAGATTATCGAGGTTGACAACAACGTGAGAGAAGACCGAGCTCTTGT                         GAACGGAGCTCAAAAGCTTCTGGGTGTTTTGATCACGATTGGTGAAGCTGT
genomic: TCGAAGATTATCGAGGTTGACAACAACGTGAGAGAAGACCGAGCTCTTGTgtaagtgttt ... gactttgtagGAACGGAGCTCAAAAGCTTCTGGGTGTTTTGATCACGATTGGTGAAGCTGT
EST: gi|70669535|gb|DN838112.1|DN838112
EST:     TCGAAGATTATCGAGGTTGACAACAACGTGAGAGAAGACCGAGCTCTTGT                         GAACGGAGCTCAAAAGCTTCTGGGTGTTTTGATCACGATTGGTGAAGCTGT
genomic: TCGAAGATTATCGAGGTTGACAACAACGTGAGAGAAGACCGAGCTCTTGTgtaagtgttt ... gactttgtagGAACGGAGCTCAAAAGCTTCTGGGTGTTTTGATCACGATTGGTGAAGCTGT
EST: gi|70669900|gb|DN838477.1|DN838477
EST:     TCGAAGATTATCGAGGTTGACAACAACGTGAGAGAAGACCGAGCTCTTGT                         GAACGGAGCTCAAAAGCTTCTGGGTGTTTTGATCACGATTGGTGAAGCTGT
genomic: TCGAAGATTATCGAGGTTGACAACAACGTGAGAGAAGACCGAGCTCTTGTgtaagtgttt ... gactttgtagGAACGGAGCTCAAAAGCTTCTGGGTGTTTTGATCACGATTGGTGAAGCTGT

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: 39

GAATTACTCCCATCGTTACTTCTGGTCTTGTGATGCAGCTCTTGGCTGGCTCGAAGATTATCGAGGTTGACAACAACGTGAGAGAAGACCGAGCTCTTGTgtaagtgttt ... gactttgtagGAACGGAGCTCAAAAGCTTCTGGGTGTTTTGATCACGATTGGTGAAGCTGTCGCGTACGTTTTGTCTGGAATGTACGGCGACGTTCGTGATCTCGGAGCC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttttgacatttgtgcttggtggcttctactgatggttttgtgggactttgtagGAACGGAGCTCAAAAGCTTCTGGGTGTTTTGATCACGATTGGTGAAGCTGTCGCGTACGTTTTGTCTGGAATGTACGGCGACGTTCGTGATCTCGGAGCC
                            tactgat  putative branch site (score: 39)