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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcttgtccattatcgctgcaacttgatggcaaacggagaaagccttgcagAGCCCTCACGCCCGCTGAGATTGACGACTATTTGGCGGAAGTAGAGTAATTGGATCGAGAATCGGGACTGTTTTAAGCCCTCTGTTCAAGGTACTTATTG

Basic information

species Selaginella moellendorffii
transcript EFJ19637
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ19637 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: GLYMA08G17810.2 (Glycine max), 3'ss of exon 10
---------------------------------------------gtatcttg-tccattatcgctgcaacttgatggcaa-acggagaaagccttgcagAGCCCTCACGCCCGCTGAGATTGACGACTATTTGGCGGAAGTAGAGTAATTGG--ATCGAGAA-TCGGGACTGTTTTAAGCCCTCTGTTCAAGGTACTTATTG
                                              ||| | | |   ||| |   |  | || ||   |  | |   |     |||||| |   | || || ||||| ||||||||||||||||| |||||||| ||||  |  ||  |||| ||  |  |   | |||   | ||||  |   | ||    
aaattctaaaccaatctagacttcaaacttcaaagccatccttatatatttagattgtttaactgggtgatttaataatagcatgttaatgatgttgcagGGTATTGACACCAGCTGAAATTGACGACTATTTGGCTGAAGTAGAATAATCTGCAATGAAGAACTCTTGTGTTCCTGAAGTTGTTTGTTTCA--CAGTTGGG-
















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|169115599|gb|FE517809.1|FE517809
EST:     TCCGGGAAGAATATCGAGATTGGCATCGTGGGGTCGGACCAAAAGTTCAG                         AGCCCTCACGCCCGCTGAGATTGACGACTATTTGGCGGAAGTAGAGTAATT
genomic: TCCGGGAAGAATATCGAGATTGGCATCGTGGGGTCGGACCAAAAGTTCAGgtatcttgtc ... agccttgcagAGCCCTCACGCCCGCTGAGATTGACGACTATTTGGCGGAAGTAGAGTAATT
EST: gi|169109748|gb|FE511819.1|FE511819
EST:     TCCGGGAAGAATATCGAGATTGGCATCGTGGGGTCGGACCAAAAGTTCAG                         AGCCCTCACGCCCGCTGAGATTGACGACTATCTGGCGGAAGTAGAGTAATT
genomic: TCCGGGAAGAATATCGAGATTGGCATCGTGGGGTCGGACCAAAAGTTCAGgtatcttgtc ... agccttgcagAGCCCTCACGCCCGCTGAGATTGACGACTATTTGGCGGAAGTAGAGTAATT
EST: gi|169108705|gb|FE510504.1|FE510504
EST:     TCCGGGAAGAATATCGAGATTGGCATCGTGGGGTCGGACCAAAAGTTCAG                         AGCCCTCACGCCCGCTGAGATTGACGACTATTTGGCGGAAGTAGAGTAATT
genomic: TCCGGGAAGAATATCGAGATTGGCATCGTGGGGTCGGACCAAAAGTTCAGgtatcttgtc ... agccttgcagAGCCCTCACGCCCGCTGAGATTGACGACTATTTGGCGGAAGTAGAGTAATT
EST: gi|169115598|gb|FE517808.1|FE517808
EST:     TCCGGGAAGAATATCGAGATTGGCATCGTGGGGTCGGACCAAAAGTTCAG                         AGCCCTCACGCCCGCTGAGATTGACGACTATTTGGCGGAAGTAGAGTAATT
genomic: TCCGGGAAGAATATCGAGATTGGCATCGTGGGGTCGGACCAAAAGTTCAGgtatcttgtc ... agccttgcagAGCCCTCACGCCCGCTGAGATTGACGACTATTTGGCGGAAGTAGAGTAATT

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), 30 (downstream exon)
Score: 26

TTTCGAGGGGCAAATTTCCGGGAAGAATATCGAGATTGGCATCGTGGGGTCGGACCAAAAGTTCAGgtatcttgtc ... agccttgcagAGCCCTCACGCCCGCTGAGATTGACGACTATTTGGCGGAAGTAGAGTAATTGGATCGAGAATCGGGACTGTTTTAAGCCCTCTGTTCAAGGTACTTATTG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatcttgtccattatcgctgcaacttgatggcaaacggagaaagccttgcagAGCCCTCACGCCCGCTGAGATTGACGACTATTTGGCGGAAGTAGAGTAATTGGATCGAGAATCGGGACTGTTTTAAGCCCTCTGTTCAAGGTACTTATTG
                         acttgat  putative branch site (score: 26)
               attat  TA-rich tract