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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTTACAATCACTTCTTCTGGATTTACCCGGACTCTTGTTCTTCACGACGTACACTTTGCTAGTACTCTTCTGGGCTGAGATTTATCACCAGgtaaatctaggctagagatcttgattgcttgggtgattgatagtctctttccttgcggaatcttggattttgtccag

Basic information

species Selaginella moellendorffii
transcript EFJ23006
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ23006 (Selaginella moellendorffii), 5'ss of exon 4
lower sequence: GRMZM2G171469_T02 (Zea mays), 5'ss of exon 4
ATTTTACAATCACTTCTTCTGGATTTACCCGGACTCTTGTTCTTCACGACGTACACTTTGCTAGTACTCTTCTGGGCTGAGATTTATCACCAGgt-aaatctaggctagagatcttgattgcttgggtgattgatagtctct---ttccttgcggaatcttggattttgtccag
||  | |||    | ||| | ||||| || || ||   |||||||||||| ||| || ||||||| ||||||||||||||||||||  | ||||| |  | |  | |  | |  ||  |  | ||| |   |||  |   ||    || |||  | ||  ||   |||| | ||
ATACTTCAACACGTGCTTATTGATTTGCCGGGCCTAGCGTTCTTCACGACCTACGCTCTGCTAGTGCTCTTCTGGGCTGAGATTTACTATCAGgttaggtttcagttcaacagttttttgacatggttctgtgaatgctgctgtgctcattgttgtatgctgatgtttg-ctag
















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|169049297|gb|FE458221.1|FE458221
EST:     TCACGACGTACACTTTGCTAGTACTCTTCTGGGCTGAGATTTATCACCAG                         GCTCGGAGCCTTCCGACGGATAACCTGAGACCAACCTTTGTGGTGATCAAT
genomic: TCACGACGTACACTTTGCTAGTACTCTTCTGGGCTGAGATTTATCACCAGgtaaatctag ... ttttgtccagGCTCGGAGCCTTCCGACGGATAACCTGAGACCAACCTTTGTGGTGATCAAT
EST: gi|169049298|gb|FE458222.1|FE458222
EST:     TCACGACGTACACTTTGCTAGTACTCTTCTGGGCTGAGATTTATCACCAG                         GCTCGGAGCCTTCCGACGGATAACCTGAGACCAACCTTTGTGGTGATCAAT
genomic: TCACGACGTACACTTTGCTAGTACTCTTCTGGGCTGAGATTTATCACCAGgtaaatctag ... ttttgtccagGCTCGGAGCCTTCCGACGGATAACCTGAGACCAACCTTTGTGGTGATCAAT
EST: gi|169087157|gb|FE493104.1|FE493104
EST:     TCACGACGTATACTTTGCTAGTACTCTTCTGGGCTGAGATTTATCACCAG                         GCTCGGAGCCTTCCGACGGATAACCTGAGACCAACCTTTGTGGTGATCAAT
genomic: TCACGACGTACACTTTGCTAGTACTCTTCTGGGCTGAGATTTATCACCAGgtaaatctag ... ttttgtccagGCTCGGAGCCTTCCGACGGATAACCTGAGACCAACCTTTGTGGTGATCAAT
EST: gi|169087158|gb|FE493105.1|FE493105
EST:     TCACGACGTATACTTTGCTAGTACTCTTCTGGGCTGAGATTTATCACCAG                         GCTCGGAGCCTTCCGACGGATAACCTGAGACCAACCTTTGTGGTGATCAAT
genomic: TCACGACGTACACTTTGCTAGTACTCTTCTGGGCTGAGATTTATCACCAGgtaaatctag ... ttttgtccagGCTCGGAGCCTTCCGACGGATAACCTGAGACCAACCTTTGTGGTGATCAAT

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: 23

ATTTTACAATCACTTCTTCTGGATTTACCCGGACTCTTGTTCTTCACGACGTACACTTTGCTAGTACTCTTCTGGGCTGAGATTTATCACCAGgtaaatctag ... ttttgtccagGCTCGGAGCCTTCCGACGGATAACCTGAGACCAACCTTTGTGGTGATCAATACCATCATCTACACAATCCAG




<











<


<