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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGTATAGCTACATGGGGATCTCGATGAGCAACAATGTGATTCCCGACGAGATCAAGGGCCGGAAAATTCACAATTCTTTTCCAATGACGCTGTTCTTGgtatgttcgcgttctctggtgctttggagactcttgatagtttttcttttctttccttccttag

Basic information

species Selaginella moellendorffii
transcript EFJ04796
intron # 2
splice site 5'
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




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGTATAGCTACATGGGGATCTCGATGAGCAACAATGTGATTCCCGACGAGATCAAGGGCCGGAAAATTCACAATTCTTTTCCAATGACGCTGTTCTTGgtatgttcgcgttctctggtgctttggagactcttgatagtttttcttttctttccttccttag

- - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT