Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttcgcgttctctggtgctttggagactcttgatagtttttcttttctttccttccttagCCTCACGAAGTTCCGCTCAACCAACACACTCTCAAGCTTCTCAAATCCTGGACATGGCAATTCGTGATCATTCGTCCGGTGCTATCCATCCTCATGATCT

Basic information

species Selaginella moellendorffii
transcript EFJ04796
intron # 2
splice site 3'
intron type U2

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|169109775|gb|FE511846.1|FE511846
EST:     AGATCAAGGGCCGGAAAATTCACAATTCTTTTCCAATGACGCTGTTCTTG                         CCTCACGAAGTTCCGCTCAACCAACACACTCTTAAGCTTCTCAAATCCTGG
genomic: AGATCAAGGGCCGGAAAATTCACAATTCTTTTCCAATGACGCTGTTCTTGgtatgttcgc ... ccttccttagCCTCACGAAGTTCCGCTCAACCAACACACTCTCAAGCTTCTCAAATCCTGG
EST: gi|169107369|gb|FE508290.1|FE508290
EST:     AGATCAAGGGCCGGAAAATTCACAATTCTTTTCCAATGACGCTGTTCTTG                         CCTCACGAAGTTCCGCTCAACCAACACACTCTCAAGCTTCTCAAATCCTGG
genomic: AGATCAAGGGCCGGAAAATTCACAATTCTTTTCCAATGACGCTGTTCTTGgtatgttcgc ... ccttccttagCCTCACGAAGTTCCGCTCAACCAACACACTCTCAAGCTTCTCAAATCCTGG
EST: gi|169107370|gb|FE508291.1|FE508291
EST:     AGATCAAGGGCCGGAAAATTCACAATTCTTTTCCAATGACGCTGTTCTTG                         CCTCACGAAGTTCCGCTCAACCAACACACTCTCAAGCTTCTCAAATCCTGG
genomic: AGATCAAGGGCCGGAAAATTCACAATTCTTTTCCAATGACGCTGTTCTTGgtatgttcgc ... ccttccttagCCTCACGAAGTTCCGCTCAACCAACACACTCTCAAGCTTCTCAAATCCTGG
EST: gi|169045407|gb|FE452264.1|FE452264
EST:     TCCAATGACGCTGTTCTTG                         CCTCACGAAGTTCCGCTCAACCAACACACTCTCAAGCTTCTCAAATCCTGG
genomic: TCCAATGACGCTGTTCTTGgtatgttcgc ... ccttccttagCCTCACGAAGTTCCGCTCAACCAACACACTCTCAAGCTTCTCAAATCCTGG
EST: gi|169109774|gb|FE511845.1|FE511845
EST:     AGATCAAGGGCCGGAAAATTCACAATTCTTTTCCAATGACGCTGTTCTTG                         CCTCACGAAGTTCCGCTCAACCAACACACTCTTAAGCTTCTCAAATCCTGG
genomic: AGATCAAGGGCCGGAAAATTCACAATTCTTTTCCAATGACGCTGTTCTTGgtatgttcgc ... ccttccttagCCTCACGAAGTTCCGCTCAACCAACACACTCTCAAGCTTCTCAAATCCTGG
EST: gi|169045408|gb|FE452265.1|FE452265
EST:     AGATCAAGGGCCGGAAAATTCACAATTCTTTTCCAATGACGCTGTTCTTG                         CCTCACGAAGTTCCGCTCAACCAACACACTCTCAAGCTTCTCAAATCCTGG
genomic: AGATCAAGGGCCGGAAAATTCACAATTCTTTTCCAATGACGCTGTTCTTGgtatgttcgc ... ccttccttagCCTCACGAAGTTCCGCTCAACCAACACACTCTCAAGCTTCTCAAATCCTGG
EST: gi|169072441|gb|FE483837.1|FE483837
EST:     AGATCAAGGGCCGGAAAATTCACAATTCTTTTCCAATGACGCTGTTCTTG                         CCTCACGAAGTTCCGCTCAACCAACACACTCTTAAGCTTCTCAAATCCTGG
genomic: AGATCAAGGGCCGGAAAATTCACAATTCTTTTCCAATGACGCTGTTCTTGgtatgttcgc ... ccttccttagCCTCACGAAGTTCCGCTCAACCAACACACTCTCAAGCTTCTCAAATCCTGG

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: 20 (upstream exon), 26 (downstream exon)
Score: 3

CATGTATAGCTACATGGGGATCTCGATGAGCAACAATGTGATTCCCGACGAGATCAAGGGCCGGAAAATTCACAATTCTTTTCCAATGACGCTGTTCTTGgtatgttcgc ... ccttccttagCCTCACGAAGTTCCGCTCAACCAACACACTCTCAAGCTTCTCAAATCCTGGACATGGCAATTCGTGATCATTCGTCCGGTGCTATCCATCCTCATGATCT




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgttctctggtgctttggagactcttgatagtttttcttttctttccttccttagCCTCACGAAGTTCCGCTCAACCAACACACTCTCAAGCTTCTCAAATCCTGGACATGGCAATTCGTGATCATTCGTCCGGTGCTATCCATCCTCATGATCT
                      tcttgat  putative branch site (score: 3)
                     ctcttgatagtttttc  CT-rich tract
                           atagtttttctttt  TA-rich tract