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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttatgatagtgttcgttctttcttgtaagcgtttaatttttttttttctcaacgatctctcacatggtgttttatcagGGCCTATTCTGCTGGAAGATTATCACTTGATCGAGAAGCTTGCTCAGTTTGACAGGGAACGCATTCCCGAGCGCGTCGTCCATGCGCGTGGAGCAAGTGC

Basic information

species Selaginella moellendorffii
transcript EFJ33688
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|169032372|gb|FE440929.1|FE440929
EST:     TGGCACTCCCGTCTGGAACAACAATTCCTCTTTGACAGTTGGGTCACGAG                         GGCCTATTCTGCTGGAAGATTATCACTTGATCGAGAAGCTTGCTCAGTTTG
genomic: TGGCACTCCCGTCTGGAACAACAATTCCTCTTTGACAGTTGGGTCACGAGgtacgttatg ... gttttatcagGGCCTATTCTGCTGGAAGATTATCACTTGATCGAGAAGCTTGCTCAGTTTG
EST: gi|169022284|gb|FE431243.1|FE431243
EST:     TGGCACTCCCGTCTGGAACAACAATTCCTCTTTGACAGTTGGGTCACGAG                         GGCCTATTCTGCTGGAAGATTATCACTTGATCGAGAAGCTTGCTCAGTTTG
genomic: TGGCACTCCCGTCTGGAACAACAATTCCTCTTTGACAGTTGGGTCACGAGgtacgttatg ... gttttatcagGGCCTATTCTGCTGGAAGATTATCACTTGATCGAGAAGCTTGCTCAGTTTG
EST: gi|169109507|gb|FE510292.1|FE510292
EST:     ACTCCCGTCTGGAACAACAATTCCTCTTTGACAGTTGGGTCACGAG                         GGCCTATTCTGCTGGAAGATTATCACTTGATCGAGAAGCTTGCTCAGTTTG
genomic: ACTCCCGTCTGGAACAACAATTCCTCTTTGACAGTTGGGTCACGAGgtacgttatg ... gttttatcagGGCCTATTCTGCTGGAAGATTATCACTTGATCGAGAAGCTTGCTCAGTTTG

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: 24 (upstream exon), 30 (downstream exon)
Score: 2

CACACTCCATCAAGCGCTTTCAATTCTTCTTTTTTCACCACAAACTCTGGCACTCCCGTCTGGAACAACAATTCCTCTTTGACAGTTGGGTCACGAGgtacgttatg ... gttttatcagGGCCTATTCTGCTGGAAGATTATCACTTGATCGAGAAGCTTGCTCAGTTTGACAGGGAACGCATTCCCGAGCGCGTCGTCCATGCGCGTGGAGCAAGTGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtaagcgtttaatttttttttttctcaacgatctctcacatggtgttttatcagGGCCTATTCTGCTGGAAGATTATCACTTGATCGAGAAGCTTGCTCAGTTTGACAGGGAACGCATTCCCGAGCGCGTCGTCCATGCGCGTGGAGCAAGTGC
                                 ctctcac  putative branch site (score: 2)
                                              ttttatc  putative PPT
        tttaattttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgttatgatagtgttcgttctttcttgtaagcgtttaatttttttttttctcaacgatctctcacatggtgttttatcagGGCCTATTCTGCTGGAAGATTATCACTTGATCGAGAAGCTTGCTCAGTTTGACAGGGAACGCATTCCCGAGCGCGTCGTCCATGCGCGTGGAGCAAGTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG