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

gcaaggccttgagcgcgatatcttgaatgtatattcttttttgctatggactaacaacaggctaaaacatctcttctgtggttctaactgggtgatattacctgttgtttcagGCTGGAAGAATGGACGTGGTGTGGGGAGAGACCGCGGGGATGAAGGGACAGATCTGGGTGCTGTATCCCCTGCTCTTCATTCTCCAG

Basic information

species Selaginella moellendorffii
transcript EFJ12166
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ12166 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: LOC_Os08g05660.1 (Oryza sativa), 3'ss of exon 7
------------------------------------------------------------------------------------gcaaggccttgagcgcgatatcttgaatgtatattcttttttgctatggactaacaacaggctaaaacatctcttctgtggttctaactgggtgatattacctgttgtttcagGCTGGAAGAATGGACGTGGTGTGGGGAGAGACCGCGGGGATGAAGGGACAGATCTGGGTGCTGTATCCCCTGCTCTTCATTCTCCAG
                                                                                      | ||| ||    ||   || | |  | |||   |||   ||  | |  |     |    ||  |   |       ||  || |   |   ||| |||  || || |   ||||| ||||||||||||| |||||||||||||| || ||  |  | || ||  | | | | || |  ||  | |||||  |  | |||
gtaacatatttttctgatcaaaaaacaaactgatactctatgttcctgctgttccaaagaactttctggtatctatttgcttttttatggcatttcaagcatcatgt-ggctatatgcacttacctgtga-gatcatgtcatttccttcattttagtccaagtaattttgcataactga-attttcttttttggtagGCTAGAAGAATGGACGTTGTGTGGGGAGAGACTGCTGGTGTTGAAGGTCAATTGTTGCTACTATGCCCTGTCCTCTTTCTGTTGCAG
















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|169056974|gb|FE466201.1|FE466201
EST:     AGAATCGATATCAGCGACAGCGCTTGTACACACGAATCGCTCTTGGAAAG                         GCTGGAAGAATGGACGTGGTGTGGGGAGAGACCGCGGGGATGAAGGGACAG
genomic: AGAATCGATACCAGCGACAGCGCTTGTACACACGAATCGCTCTTGGAAAGgcaaggcctt ... gttgtttcagGCTGGAAGAATGGACGTGGTGTGGGGAGAGACCGCGGGGATGAAGGGACAG
EST: gi|169056973|gb|FE466200.1|FE466200
EST:     AGAATCGATATCAGCGACAGCGCTTGTACACACGAATCGCTCTTGGAAAG                         GCTGGAAGAATGGACGTGGTGTGGGGAGAGACCGCGGGGATGAAGGGACAG
genomic: AGAATCGATACCAGCGACAGCGCTTGTACACACGAATCGCTCTTGGAAAGgcaaggcctt ... gttgtttcagGCTGGAAGAATGGACGTGGTGTGGGGAGAGACCGCGGGGATGAAGGGACAG
EST: gi|169064281|gb|FE471844.1|FE471844
EST:     AGAATCGATATCAGCGACAGCGCTTGTACACACGAATCGCTCTTGGAAAG                         GCTGGAAGAATGGACGTGGTGTGGGGAGAGACCGCGGGGATGAAGGGACAG
genomic: AGAATCGATACCAGCGACAGCGCTTGTACACACGAATCGCTCTTGGAAAGgcaaggcctt ... gttgtttcagGCTGGAAGAATGGACGTGGTGTGGGGAGAGACCGCGGGGATGAAGGGACAG
EST: gi|169020374|gb|FE431621.1|FE431621
EST:     AGAATCGATATCAGCGACAGCGCTTGTACACACGAATCGCTCTTGGAAAG                         GCTGGAAGAATGGACGTGGTGTGGGGAGAGACCGCGGGGATGAAGGGACAG
genomic: AGAATCGATACCAGCGACAGCGCTTGTACACACGAATCGCTCTTGGAAAGgcaaggcctt ... gttgtttcagGCTGGAAGAATGGACGTGGTGTGGGGAGAGACCGCGGGGATGAAGGGACAG
EST: gi|169031683|gb|FE437484.1|FE437484
EST:     AGAATCGATATCAGCGACAGCGCTTGTACACACGAATCGCTCTTGGAAAG                         GCTGGAAGAATGGACGTGGTGTGGGGAGAGACCGCGGGGATGAAGGGACAG
genomic: AGAATCGATACCAGCGACAGCGCTTGTACACACGAATCGCTCTTGGAAAGgcaaggcctt ... gttgtttcagGCTGGAAGAATGGACGTGGTGTGGGGAGAGACCGCGGGGATGAAGGGACAG
EST: gi|169053303|gb|FE462578.1|FE462578
EST:     AGAATCGATATCAGCGACAGCGCTTGTACACACGAATCGCTCTTGGAAAG                         GCTGGAAGAATGGACGTGGTGTGGGGAGAGACCGCGGGGATGAAGGGACAG
genomic: AGAATCGATACCAGCGACAGCGCTTGTACACACGAATCGCTCTTGGAAAGgcaaggcctt ... gttgtttcagGCTGGAAGAATGGACGTGGTGTGGGGAGAGACCGCGGGGATGAAGGGACAG

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: 17

GAGACACTTTTTGTCTTGGGCAGCCATGCAGGGAGTCTCGATGCTACTGCAGAATCGATACCAGCGACAGCGCTTGTACACACGAATCGCTCTTGGAAAGgcaaggcctt ... gttgtttcagGCTGGAAGAATGGACGTGGTGTGGGGAGAGACCGCGGGGATGAAGGGACAGATCTGGGTGCTGTATCCCCTGCTCTTCATTCTCCAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggctaaaacatctcttctgtggttctaactgggtgatattacctgttgtttcagGCTGGAAGAATGGACGTGGTGTGGGGAGAGACCGCGGGGATGAAGGGACAGATCTGGGTGCTGTATCCCCTGCTCTTCATTCTCCAG
                       ttctaac  putative branch site (score: 17)
                                              ttgtttc  putative PPT
                                  tgatatta  TA-rich tract