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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctgcgtttttttttctttcgtgtgtatgacgacgtttttctttccagAAAATAGCTCTCTTCTTGTTGCGGAGCAGTGTACATGGGCTTTGGGAAACTTTGCCGGTGACAGCGAGGAGATAAGAAAAATACTTCTTGCTCAAGGATC

Basic information

species Selaginella moellendorffii
transcript EFJ22694
intron # 3
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|169074219|gb|FE481905.1|FE481905
EST:     GCAAGAAGATTTGCTAATGCCCGTTCCTCTTCTCATTGCTCATCTTGGAG                         AAAATAGCTCTCTTCTTGTTGCGGAGCAGTGTACATGGGCTTTGGGAAACT
genomic: GCAAGAAGATTTGCTAATGCCCGTTCCTCTTCTCATTGCTCATCTTGGAGgtatctgcgt ... ttctttccagAAAATAGCTCTCTTCTTGTTGCGGAGCAGTGTACATGGGCTTTGGGAAACT
EST: gi|169104835|gb|FE505404.1|FE505404
EST:     GCAAGAAGATTTGCTAATGCCCGTTCCTCTTCTCATTGCTCATCTTGGAG                         AAAATAGCTCTCTTCTTGTTGCGGAGCAGTGTGCATGGGCTCTGGGAAACT
genomic: GCAAGAAGATTTGCTAATGCCCGTTCCTCTTCTCATTGCTCATCTTGGAGgtatctgcgt ... ttctttccagAAAATAGCTCTCTTCTTGTTGCGGAGCAGTGTACATGGGCTTTGGGAAACT
EST: gi|169116224|gb|FE517171.1|FE517171
EST:     GCAAGAAGATTTGCTAATGCCCGTTCCTCTTCTCATTGCTCATCTTGGAG                         AAAATAGCTCTCTTCTTGTTGCGGAGCAGTGTACATGGGCTTTGGGAAACT
genomic: GCAAGAAGATTTGCTAATGCCCGTTCCTCTTCTCATTGCTCATCTTGGAGgtatctgcgt ... ttctttccagAAAATAGCTCTCTTCTTGTTGCGGAGCAGTGTACATGGGCTTTGGGAAACT

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

CTCGAAGCTGCTTGGTGTTTGACAAACATCGCTGTAGAGGATGTCCAGCAGCAAGAAGATTTGCTAATGCCCGTTCCTCTTCTCATTGCTCATCTTGGAGgtatctgcgt ... ttctttccagAAAATAGCTCTCTTCTTGTTGCGGAGCAGTGTACATGGGCTTTGGGAAACTTTGCCGGTGACAGCGAGGAGATAAGAAAAATACTTCTTGCTCAAGGATC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatctgcgtttttttttctttcgtgtgtatgacgacgtttttctttccagAAAATAGCTCTCTTCTTGTTGCGGAGCAGTGTACATGGGCTTTGGGAAACTTTGCCGGTGACAGCGAGGAGATAAGAAAAATACTTCTTGCTCAAGGATC
                                           cgtttttctttcc  CT-rich tract
             tttttttttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatctgcgtttttttttctttcgtgtgtatgacgacgtttttctttccagAAAATAGCTCTCTTCTTGTTGCGGAGCAGTGTACATGGGCTTTGGGAAACTTTGCCGGTGACAGCGAGGAGATAAGAAAAATACTTCTTGCTCAAGGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA