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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgagagctccccatttcaatctctcggctctcgcttgacctagctctcgatgtctagATGCGTGCATTGTCGGCGTGGCGAGGACGCCGATGGGCGGCTTGAGCGGATCTCTCTCCGCCCTGGCTGCTACCAAGCTCGGATCTATCGCGATCCAAG

Basic information

species Selaginella moellendorffii
transcript EFJ29932
intron # 1
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|169070973|gb|FE477364.1|FE477364
EST:     GGCGATCGACAGCGGCGCGCCTTCCGAGTCTTCGCCGATCGGGCCCAGGG                         ATGCGTGCATTGTCGGCGTGGCGAGGACGCCGATGGGCGGCTTGAGCGGAT
genomic: GGCGATCGACAGCAGCGCGCCTTCCGAGTCTTCGCCGATCGGGCCCAGGGgtgagtgaga ... cgatgtctagATGCGTGCATTGTCGGCGTGGCGAGGACGCCGATGGGCGGCTTGAGCGGAT
EST: gi|169108075|gb|FE513826.1|FE513826
EST:     GGCGATCGACAGCGGCGCGCCTTCCGAGTCTTCGCCGATCGGGCCCAGGG                         ATGCGTGCATTGTCGGCGTGGCGAGGACGCCGATGGGCGGCTTGAGCGGAT
genomic: GGCGATCGACAGCAGCGCGCCTTCCGAGTCTTCGCCGATCGGGCCCAGGGgtgagtgaga ... cgatgtctagATGCGTGCATTGTCGGCGTGGCGAGGACGCCGATGGGCGGCTTGAGCGGAT
EST: gi|169033460|gb|FE441804.1|FE441804
EST:     GGCGATCGACAGCAGCGCGCCTTCCGAGTCTTCGCCGATCGGGCCCAGGG                         ATGCGTGCATTGTCGGCGTGGCGAGGACGCCGATGGGCGGCTTGAGCGGAT
genomic: GGCGATCGACAGCAGCGCGCCTTCCGAGTCTTCGCCGATCGGGCCCAGGGgtgagtgaga ... cgatgtctagATGCGTGCATTGTCGGCGTGGCGAGGACGCCGATGGGCGGCTTGAGCGGAT
EST: gi|169081851|gb|FE487958.1|FE487958
EST:     GGCGATCGACAGCAGCGCGCCTTCCGAGTCTTCGCCGATCGGGCCCAGGG                         ATGCGTGCATTGTCGGCGTGGCGAGGACGCCGATGGGCGGCTTGAGCGGAT
genomic: GGCGATCGACAGCAGCGCGCCTTCCGAGTCTTCGCCGATCGGGCCCAGGGgtgagtgaga ... cgatgtctagATGCGTGCATTGTCGGCGTGGCGAGGACGCCGATGGGCGGCTTGAGCGGAT
EST: gi|169114964|gb|FE516329.1|FE516329
EST:     GGCGATCGACAGCGGCGCGCCTTCCGAGTCTTCGCCGATCGGGCCCAGGG                         ATGCGTGCATTGTCGGCGTGGCGAGGACGCCGATGGGCGGCTTGAGCGGAT
genomic: GGCGATCGACAGCAGCGCGCCTTCCGAGTCTTCGCCGATCGGGCCCAGGGgtgagtgaga ... cgatgtctagATGCGTGCATTGTCGGCGTGGCGAGGACGCCGATGGGCGGCTTGAGCGGAT
EST: gi|169041425|gb|FE448983.1|FE448983
EST:     GGCGATCGACAGCGGCGCGCCTTCCGAGTCTTCGCCGATCGGGCCCAGGG                         ATGCGTGCATTGTCGGCGTGGCGAGGACGCCGATGGGCGGCTTGAGCGGAT
genomic: GGCGATCGACAGCAGCGCGCCTTCCGAGTCTTCGCCGATCGGGCCCAGGGgtgagtgaga ... cgatgtctagATGCGTGCATTGTCGGCGTGGCGAGGACGCCGATGGGCGGCTTGAGCGGAT

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), 33 (downstream exon)
Score: 18

CCAGGGATTCTATTCTAGTGCCGTCTCGCCTTGCAGTGCAGATCAGCGATGGCGATCGACAGCAGCGCGCCTTCCGAGTCTTCGCCGATCGGGCCCAGGGgtgagtgaga ... cgatgtctagATGCGTGCATTGTCGGCGTGGCGAGGACGCCGATGGGCGGCTTGAGCGGATCTCTCTCCGCCCTGGCTGCTACCAAGCTCGGATCTATCGCGATCCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagctccccatttcaatctctcggctctcgcttgacctagctctcgatgtctagATGCGTGCATTGTCGGCGTGGCGAGGACGCCGATGGGCGGCTTGAGCGGATCTCTCTCCGCCCTGGCTGCTACCAAGCTCGGATCTATCGCGATCCAAG
                              gcttgac  putative branch site (score: 18)
                                         ctctc  putative PPT
          atttcaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgagagctccccatttcaatctctcggctctcgcttgacctagctctcgatgtctagATGCGTGCATTGTCGGCGTGGCGAGGACGCCGATGGGCGGCTTGAGCGGATCTCTCTCCGCCCTGGCTGCTACCAAGCTCGGATCTATCGCGATCCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT