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'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   		30  
 5'  3'   		31  
 5'  3'   		32  
 5'  3'   		33  
 5'  3'   		34  
 5'  3'   		35  
 5'  3'   		36  
 5'  3'   		37  
 5'  3'   		38  
 5'  3'   		39  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactatttctcggtgctgctagctttgtgtgagaccaatactactgttcagATCGACGTTTTTCCGGTTTGGGAAGCATGGGGTTACGCACTACTTCGGATAGAACATTATGCGCAAGCCAGGCTAAAGTTCAA

Basic information

species Selaginella moellendorffii
transcript EFJ21919
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ21919 (Selaginella moellendorffii), 3'ss of exon 24
lower sequence: PP1S109_57V6.1 (Physcomitrella patens), 3'ss of exon 27
-------------------------------------------------------------gtaactatttctcggtgctgctagctttgtgtgagaccaa---tactactgttcagATCGACGTTTTTCCGGTTTGGGAAGCATGGGGTTACGCACTACTTCGGATAGAACATTATGCGCAAGCCAGGCTAAAGTTCAA
                                                               ||||||||   |      |    |   | |  ||||||   | | |   | |||||  |    |  |  ||||||||||||||||||||||| || ||||| || || || || || ||||| ||| ||||||||||
gtacatagcactttaccatggagtggaagtatgaggaaattatttgatagctattatcgccaaaactattttctgtcttcacataatgaatatttgaccaacctttcaatgatacagATTAATCCGTGCCTAGTTTGGGAAGCATGGGGTTACGCGCTCCTTCGTATTGAGCACTACGCTCAAGCAAGGGTAAAGTTCAA
















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|169095259|gb|FE499367.1|FE499367
EST:     TCCAGGAGGAGCGATATGGTATGGCCGTATACACATGCACGAAATGCAAG                         ATCGACGTTTTTCCGGTTTGNGAAGCATGGGGTTACGCACTACTTCGGATA
genomic: TCCAGGAGGAGCGATATGGTATGGCCGTATACACATGCACGAAATGCAAGgtaactattt ... tactgttcagATCGACGTTTTTCCGGTTTGGGAAGCATGGGGTTACGCACTACTTCGGATA
EST: gi|169115117|gb|FE516690.1|FE516690
EST:     TCCAGGAGGAGCGATATGGTATGGCCGTATACACATGCACGAAATGCAAG                         ATCGACGTTTTTCCGGTTTGGGAAGCATGGGGTTACGCACTACTTCGGATA
genomic: TCCAGGAGGAGCGATATGGTATGGCCGTATACACATGCACGAAATGCAAGgtaactattt ... tactgttcagATCGACGTTTTTCCGGTTTGGGAAGCATGGGGTTACGCACTACTTCGGATA
EST: gi|169046678|gb|FE455420.1|FE455420
EST:     TCCAGGAGGAGCGATATGGTATGGCCGTATACACATGCACGAAATGCAAG                         ATCGACGTTTTTCCGGTTTGGGAAGCATGGGGTTACGCACTACTTCGGATA
genomic: TCCAGGAGGAGCGATATGGTATGGCCGTATACACATGCACGAAATGCAAGgtaactattt ... tactgttcagATCGACGTTTTTCCGGTTTGGGAAGCATGGGGTTACGCACTACTTCGGATA
EST: gi|169055737|gb|FE466668.1|FE466668
EST:     ATGGTATGGCCGTATACACATGCACGAAATGCAAG                         ATCGACGTTTTTCCGGTTTGGGAAGCATGGGGTTACGCACTACTTCGGATA
genomic: ATGGTATGGCCGTATACACATGCACGAAATGCAAGgtaactattt ... tactgttcagATCGACGTTTTTCCGGTTTGGGAAGCATGGGGTTACGCACTACTTCGGATA
EST: gi|169076901|gb|FE485294.1|FE485294
EST:     TCCAGGAGGAGCGATATGGTATGGCCGTATACACATGCACGAAATGCAAG                         ATCGACGTTTTTCCGGTTTGGGAAGCATGGGGTTACGCACTACTTCGGATA
genomic: TCCAGGAGGAGCGATATGGTATGGCCGTATACACATGCACGAAATGCAAGgtaactattt ... tactgttcagATCGACGTTTTTCCGGTTTGGGAAGCATGGGGTTACGCACTACTTCGGATA

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: 32 (upstream exon), 32 (downstream exon)
Score: 9

AGGCGATGTGGCAGACGAAACCTCGGCGCTTCTCCTTCGTGACCGTTTGATCCAGGAGGAGCGATATGGTATGGCCGTATACACATGCACGAAATGCAAGgtaactattt ... tactgttcagATCGACGTTTTTCCGGTTTGGGAAGCATGGGGTTACGCACTACTTCGGATAGAACATTATGCGCAAGCCAGGCTAAAGTTCAA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaactatttctcggtgctgctagctttgtgtgagaccaatactactgttcagATCGACGTTTTTCCGGTTTGGGAAGCATGGGGTTACGCACTACTTCGGATAGAACATTATGCGCAAGCCAGGCTAAAGTTCAA
        actattt  TA-rich tract