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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatttttgtttctcgatagttggttttgtttctaaactccattttcagATATCTGTGCCACACCATGATTCCGACAAGCTCGACCGAGCGTCTGCCGAGAAGATGACTCTGATTGAG

Basic information

species Selaginella moellendorffii
transcript EFJ12424
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|169061551|gb|FE469338.1|FE469338
EST:     TCCTGTCATTCACTGTGCTAGACAAGCATATCTGGTTTCGAAACTACCAA                         ATATCTGTGCCACACCATGATTCAGACAAGCTCGACCGAGCGTCTGCCGAG
genomic: TTCTGTCATTCACTGTGCTAGACAAGCATATCTGGTTTCGAAACTACCAAgtaatttttg ... ccattttcagATATCTGTGCCACACCATGATTCCGACAAGCTCGACCGAGCGTCTGCCGAG
EST: gi|169049031|gb|FE456109.1|FE456109
EST:     TCCTGTCATTCACTGTGCTAGACAAGCATATCTGGTTTCGAAACTACCAA                         ATATCTGTGCCACACCATGATTCAGACAAGCTCGACCGAGCGTCTGCCGAG
genomic: TTCTGTCATTCACTGTGCTAGACAAGCATATCTGGTTTCGAAACTACCAAgtaatttttg ... ccattttcagATATCTGTGCCACACCATGATTCCGACAAGCTCGACCGAGCGTCTGCCGAG
EST: gi|169060063|gb|FE468673.1|FE468673
EST:     TCCTGTCATTCACTGTGCTAGACAAGCATATCTGGTTTCGAAACTACCAA                         ATATCTGTGCCACACCATGATTCAGACAAGCTCGACCGAGCGTCTGCCGAG
genomic: TTCTGTCATTCACTGTGCTAGACAAGCATATCTGGTTTCGAAACTACCAAgtaatttttg ... ccattttcagATATCTGTGCCACACCATGATTCCGACAAGCTCGACCGAGCGTCTGCCGAG
EST: gi|169049030|gb|FE456108.1|FE456108
EST:     TCCTGTCATTCACTGTGCTAGACAAGCATATCTGGTTTCGAAACTACCAA                         ATATTTGTGCCACACCATGATTCAGACAAGCTCGACCGAGCGTCTGCCGAG
genomic: TTCTGTCATTCACTGTGCTAGACAAGCATATCTGGTTTCGAAACTACCAAgtaatttttg ... ccattttcagATATCTGTGCCACACCATGATTCCGACAAGCTCGACCGAGCGTCTGCCGAG
EST: gi|169071863|gb|FE477617.1|FE477617
EST:     TCCTGTCATTCACTGTGCTAGACAAGCATATCTGGTTTCGAAACTACCAA                         ATATCTGTGCCACACCATGATTCAGACAAGCTCGACCGAGCGTCTGCCGAG
genomic: TTCTGTCATTCACTGTGCTAGACAAGCATATCTGGTTTCGAAACTACCAAgtaatttttg ... ccattttcagATATCTGTGCCACACCATGATTCCGACAAGCTCGACCGAGCGTCTGCCGAG
EST: gi|169060062|gb|FE468672.1|FE468672
EST:     TCCTGTCATTCACTGTGCTAGACAAGCATATCTGGTTTCGAAACTACCAA                         ATATCTGTGCCACACCATGATTCAGACAAGCTCGACCGAGCGTCTGCCGAG
genomic: TTCTGTCATTCACTGTGCTAGACAAGCATATCTGGTTTCGAAACTACCAAgtaatttttg ... ccattttcagATATCTGTGCCACACCATGATTCCGACAAGCTCGACCGAGCGTCTGCCGAG
EST: gi|169099356|gb|FE502129.1|FE502129
EST:     TCCTGTCATTCACTGTGCTAGACAAGCATATCTGGTTTCGAAACTACCAA                         ATATCTGTGCCACACCATGATTCAGACAAGCTCGACCGAGCGTCTGCCGAG
genomic: TTCTGTCATTCACTGTGCTAGACAAGCATATCTGGTTTCGAAACTACCAAgtaatttttg ... ccattttcagATATCTGTGCCACACCATGATTCCGACAAGCTCGACCGAGCGTCTGCCGAG
EST: gi|169071864|gb|FE477618.1|FE477618
EST:     TCCTGTCATTCACTGTGCTAGACAAGCATATCTGGTTTCGAAACTACCAA                         ATATCTGTGCCACACCATGATTCAGACAAGCTCGACCGAGCGTCTGCCGAG
genomic: TTCTGTCATTCACTGTGCTAGACAAGCATATCTGGTTTCGAAACTACCAAgtaatttttg ... ccattttcagATATCTGTGCCACACCATGATTCCGACAAGCTCGACCGAGCGTCTGCCGAG
EST: gi|169053952|gb|FE461251.1|FE461251
EST:     TCCTGTCATTCACTGTGCTAGACAAGCATATCTGGTTTCGAAACTACCAA                         ATATCTGTGCCACACCATGATTCAGACAAGCTCGACCGAGCGTCTGCCGAG
genomic: TTCTGTCATTCACTGTGCTAGACAAGCATATCTGGTTTCGAAACTACCAAgtaatttttg ... ccattttcagATATCTGTGCCACACCATGATTCCGACAAGCTCGACCGAGCGTCTGCCGAG
EST: gi|169099357|gb|FE502130.1|FE502130
EST:     TCCTGTCATTCACTGTGCTAGACAAGCATATCTGGTTTCGAAACTACCAA                         ATATCTGTGCCACACCATGATTCAGACAAGCTCGACCGAGCGTCTGCCGAG
genomic: TTCTGTCATTCACTGTGCTAGACAAGCATATCTGGTTTCGAAACTACCAAgtaatttttg ... ccattttcagATATCTGTGCCACACCATGATTCCGACAAGCTCGACCGAGCGTCTGCCGAG

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: 32 (upstream exon), 35 (downstream exon)
Score: 8

CTTTGGTACTCCTAAAGACCACAGGAAGAGCAAGCCTTTCTTTGATCACGTTCTGTCATTCACTGTGCTAGACAAGCATATCTGGTTTCGAAACTACCAAgtaatttttg ... ccattttcagATATCTGTGCCACACCATGATTCCGACAAGCTCGACCGAGCGTCTGCCGAGAAGATGACTCTGATTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaatttttgtttctcgatagttggttttgtttctaaactccattttcagATATCTGTGCCACACCATGATTCCGACAAGCTCGACCGAGCGTCTGCCGAGAAGATGACTCTGATTGAG
                                    ttctaaa  putative branch site (score: 8)
                                           ctccattttc  CT-rich tract
      taatttttgtttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatttttgtttctcgatagttggttttgtttctaaactccattttcagATATCTGTGCCACACCATGATTCCGACAAGCTCGACCGAGCGTCTGCCGAGAAGATGACTCTGATTGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG