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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttcgctgactatttttcattggattccatctctaacatgactttcactttgtcagGTTGATGCAAAGGGCGGTGCTGCAAAAAAGCTTTTCGACCTTGCCTATCGACGACGCCTGGCAGCTATTGAAGGCAGCTGGTTTGGTGCGTGGGGATTGG

Basic information

species Selaginella moellendorffii
transcript EFJ26722
intron # 5
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|169062087|gb|FE469679.1|FE469679
EST:     CTGCAGTCCCTGCAATTCTTGATCGTATCCGAGATGGAGTCAGAAAAACG                         GTTGATGCAAAGGGCGGTGCTGCCAAAAAGCTTTTCGACCTTGCCTATCGA
genomic: CTGCAGTCCCTGCAATTCTTGATCGTATCCGAGATGGTGTCAGAAAAACGgttcgctgac ... actttgtcagGTTGATGCAAAGGGCGGTGCTGCAAAAAAGCTTTTCGACCTTGCCTATCGA
EST: gi|169102590|gb|FE508569.1|FE508569
EST:     CTGCAGTCCCTGCAATTCTTGATCGTATCCGAGATGGAGTCAGAAAAACG                         GTTGATGCAAAGGGCGGTGCTGCCAAAAAGCTTTTCGACCTTGCCTATCGA
genomic: CTGCAGTCCCTGCAATTCTTGATCGTATCCGAGATGGTGTCAGAAAAACGgttcgctgac ... actttgtcagGTTGATGCAAAGGGCGGTGCTGCAAAAAAGCTTTTCGACCTTGCCTATCGA
EST: gi|169020953|gb|FE429340.1|FE429340
EST:     CTGCAGTCCCTGCAATTCTTGATCGTATCCGAGATGGTGTCAGAAAAACG                         GTTGATGCAAAGGGCGGTGCTGCNNNNNNNGCTTTTCGACCTTGCCTATCG
genomic: CTGCAGTCCCTGCAATTCTTGATCGTATCCGAGATGGTGTCAGAAAAACGgttcgctgac ... actttgtcagGTTGATGCAAAGGGCGGTGCTGC-AAAAAAGCTTTTCGACCTTGCCTATCG
EST: gi|169081833|gb|FE487446.1|FE487446
EST:     CTGCAGTCCCTGCAATTCTTGATCGTATCCGAGATGGAGTCAGAAAAACG                         GTTGATGCANAGGGCGGTGCTGCCAAANAGCTTTTCGACCTTGCCTATCGA
genomic: CTGCAGTCCCTGCAATTCTTGATCGTATCCGAGATGGTGTCAGAAAAACGgttcgctgac ... actttgtcagGTTGATGCAAAGGGCGGTGCTGCAAAAAAGCTTTTCGACCTTGCCTATCGA
EST: gi|169113591|gb|FE514502.1|FE514502
EST:     CTGCAGTCCCTGCAATTCTTGATCGTATCCGAGATGGTGTCAGAAAAACG                         GTTGATGCAAAGGGCGGTGCTGCNNNNNNNNGCTTTTCGACCTTGCCTATC
genomic: CTGCAGTCCCTGCAATTCTTGATCGTATCCGAGATGGTGTCAGAAAAACGgttcgctgac ... actttgtcagGTTGATGCAAAGGGCGGTGCTGC--AAAAAAGCTTTTCGACCTTGCCTATC
EST: gi|169088888|gb|FE492866.1|FE492866
EST:     CTGCAGTCCCTGCAATTCTTGATCGTATCCGAGATGGAGTCAGAAAAACG                         GTTGATGCAAAGGGCGGTGCTGCCAAAAAGCTTTTCGACCTTGCCTATCGA
genomic: CTGCAGTCCCTGCAATTCTTGATCGTATCCGAGATGGTGTCAGAAAAACGgttcgctgac ... actttgtcagGTTGATGCAAAGGGCGGTGCTGCAAAAAAGCTTTTCGACCTTGCCTATCGA

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: 33 (upstream exon), 34 (downstream exon)
Score: 12

AAAGAAGGGAACAAAGGGTGATGTAAGCGTGTTAAGGCCGACGCTGATGACTGCAGTCCCTGCAATTCTTGATCGTATCCGAGATGGTGTCAGAAAAACGgttcgctgac ... actttgtcagGTTGATGCAAAGGGCGGTGCTGCAAAAAAGCTTTTCGACCTTGCCTATCGACGACGCCTGGCAGCTATTGAAGGCAGCTGGTTTGGTGCGTGGGGATTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgctgactatttttcattggattccatctctaacatgactttcactttgtcagGTTGATGCAAAGGGCGGTGCTGCAAAAAAGCTTTTCGACCTTGCCTATCGACGACGCCTGGCAGCTATTGAAGGCAGCTGGTTTGGTGCGTGGGGATTGG
                             ctctaac  putative branch site (score: 12)
                                        ctttcacttt  putative PPT
         tatttttcatt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttcgctgactatttttcattggattccatctctaacatgactttcactttgtcagGTTGATGCAAAGGGCGGTGCTGCAAAAAAGCTTTTCGACCTTGCCTATCGACGACGCCTGGCAGCTATTGAAGGCAGCTGGTTTGGTGCGTGGGGATTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG