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'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTTATGCCGCAGAAGTCTTGGTTGCCTTGGAGTATCTTCATTGCCTGGgtgtgtttataaaccgtgctgccttgctgcatacttactaaattcgttgatagtgcag

Basic information

species Selaginella moellendorffii
transcript EFJ07343
intron # 17
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ07343 (Selaginella moellendorffii), 5'ss of exon 17
lower sequence: GLYMA12G07890.2 (Glycine max), 5'ss of exon 18
ATTTTATGCCGCAGAAGTCTTGGTTGCCTTGGAGTATCTTCATTGCCTGGgtgtgtttataaaccgtgctgccttgctgcatacttactaaattcgttg-atagtgcag--------------------------------------------
|||||||||||| |||||  | ||||| ||||||||||||||||| |  |||  ||| | ||  | |    ||      |||  | || | |||  ||| | | ||                                               
ATTTTATGCCGCTGAAGTAGTTGTTGCGTTGGAGTATCTTCATTGTCAAGgtaggttca-aattcat--cacccatacacatggtaacaatattttttggacaatgagtgtgttaccttttaatttgtgaacttcttttcaactttggaagtg
















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|169033080|gb|FE441412.1|FE441412
EST:     ATTTTATGCCGCAGAAGTCTTGGTTGCCTTGGAGTATCTTCATTGCCTGG                         GCGTTGTCTATCGAGATCTCAAACCGGAAAACGTTCTAGTCCAAGCGAACG
genomic: ATTTTATGCCGCAGAAGTCTTGGTTGCCTTGGAGTATCTTCATTGCCTGGgtgtgtttat ... gatagtgcagGCGTTGTCTATCGAGATCTCAAACCGGAAAACGTTCTAGTCCAAGCGAACG
EST: gi|169113824|gb|FE515372.1|FE515372
EST:     -TTTTATGCCGCAGAAGTCTTGGTTGCCTTGGAGTATCTTCATTGCCTGG                         GCGTTGTCTATCGAGATCTCAAACCGGGAAACGTTCTAGTCCAAGCGAACG
genomic: ATTTTATGCCGCAGAAGTCTTGGTTGCCTTGGAGTATCTTCATTGCCTGGgtgtgtttat ... gatagtgcagGCGTTGTCTATCGAGATCTCAAACCGGAAAACGTTCTAGTCCAAGCGAACG
EST: gi|169057926|gb|FE465524.1|FE465524
EST:     ATTTTATGCCGCAGAAGTCTTGGTTGCCTTGGAGTATCTTCATTGCCTGG                         GCGTTGTCTATCGAGATCTCAAACCGGAAAACGTTCTAGTCCAAGCGAACG
genomic: ATTTTATGCCGCAGAAGTCTTGGTTGCCTTGGAGTATCTTCATTGCCTGGgtgtgtttat ... gatagtgcagGCGTTGTCTATCGAGATCTCAAACCGGAAAACGTTCTAGTCCAAGCGAACG
EST: gi|169113823|gb|FE515371.1|FE515371
EST:     -TTTTATGCCGCAGAAGTCTTGGTTGCCTTGGAGTATCTTCATTGCCTGG                         GCGTTGTCTATCGAGATCTCAAACCGGAAAACGTTCTAGTCCAAGCGAACG
genomic: ATTTTATGCCGCAGAAGTCTTGGTTGCCTTGGAGTATCTTCATTGCCTGGgtgtgtttat ... gatagtgcagGCGTTGTCTATCGAGATCTCAAACCGGAAAACGTTCTAGTCCAAGCGAACG
EST: gi|169052749|gb|FE461166.1|FE461166
EST:     AGTATCTTCATNGCCTGG                         GCGTTGTCTATCGAGATCTCAAACCGGAAAACGTTCTAGTCCAAGCGAACG
genomic: AGTATCTTCATTGCCTGGgtgtgtttat ... gatagtgcagGCGTTGTCTATCGAGATCTCAAACCGGAAAACGTTCTAGTCCAAGCGAACG
EST: gi|169115293|gb|FE517009.1|FE517009
EST:     ATTTTATGCCGCAGAAGTCTTGGTTGCCTTGGAGTATCTTCATTGCCTGG                         GCGTTGTCTATCGAGATCTCAAACCGGAAAACGTTCTAGTCCAAGCGAACG
genomic: ATTTTATGCCGCAGAAGTCTTGGTTGCCTTGGAGTATCTTCATTGCCTGGgtgtgtttat ... gatagtgcagGCGTTGTCTATCGAGATCTCAAACCGGAAAACGTTCTAGTCCAAGCGAACG
EST: gi|169046222|gb|FE456381.1|FE456381
EST:     TGGTTGCCTTGGAGTATCTTCATNGCCTGG                         GCGTTGTCTATCGAGATCTCAAACCGGAAAACGTTCTAGTCCAAGCGAACG
genomic: TGGTTGCCTTGGAGTATCTTCATTGCCTGGgtgtgtttat ... gatagtgcagGCGTTGTCTATCGAGATCTCAAACCGGAAAACGTTCTAGTCCAAGCGAACG
EST: gi|169033081|gb|FE441413.1|FE441413
EST:     ATTTTATGCCGCAGAAGTCTTGGTTGCCTTGGAGTATCTTCATTGCCTGG                         GCGTTGTCTATCGAGATCTCAAACCGGANAACGTTCTAGTCCAAGCGAACG
genomic: ATTTTATGCCGCAGAAGTCTTGGTTGCCTTGGAGTATCTTCATTGCCTGGgtgtgtttat ... gatagtgcagGCGTTGTCTATCGAGATCTCAAACCGGAAAACGTTCTAGTCCAAGCGAACG
EST: gi|169024980|gb|FE433813.1|FE433813
EST:     AGTATCTTCATTGCCTGG                         GCGTTGTCTATCGAGATCTCAAACCGGAAAACGTTCTAGTCCAAGCGAACG
genomic: AGTATCTTCATTGCCTGGgtgtgtttat ... gatagtgcagGCGTTGTCTATCGAGATCTCAAACCGGAAAACGTTCTAGTCCAAGCGAACG
EST: gi|169024981|gb|FE433814.1|FE433814
EST:     ATTTTATGCCGCAGAAGTCTTGGTTGCCTTGGAGTATCTTCATTGCCTGG                         GCGTTGTCTATCGAGATCTCAAACCGGAAAACGTTCTAGTCCAAGCGAACG
genomic: ATTTTATGCCGCAGAAGTCTTGGTTGCCTTGGAGTATCTTCATTGCCTGGgtgtgtttat ... gatagtgcagGCGTTGTCTATCGAGATCTCAAACCGGAAAACGTTCTAGTCCAAGCGAACG
EST: gi|169024987|gb|FE434639.1|FE434639
EST:     GCCTTGGAGTATCTTCATTGCCTGG                         GCGTTGTCTATCGAGATCTCAAACCGGAAAACGTTCTAGTCCAAGCGAACG
genomic: GCCTTGGAGTATCTTCATTGCCTGGgtgtgtttat ... gatagtgcagGCGTTGTCTATCGAGATCTCAAACCGGAAAACGTTCTAGTCCAAGCGAACG

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: 15

ATTTTATGCCGCAGAAGTCTTGGTTGCCTTGGAGTATCTTCATTGCCTGGgtgtgtttat ... gatagtgcagGCGTTGTCTATCGAGATCTCAAACCGGAAAACGTTCTAGTCCAAGCGAACGGACATTTGTGTTTGACGGACTTTGATCTTTCTTTGCTATCTACAACAAA




<











<


<









Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTTATGCCGCAGAAGTCTTGGTTGCCTTGGAGTATCTTCATTGCCTGGgtgtgtttataaaccgtgctgccttgctgcatacttactaaattcgttgatagtgcag

- - - - - - AGAAGT
- - - - - - - - - - - - - - TTGGAG