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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACTTTCTGCCTTTCAATCCTGTGGACAAGAGGACAGCACTCACCTACATTGACTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAGgttcgaacaacctagtattctcttttgctttctgatttggctaaagctatgtttgcttgtgaag

Basic information

species Selaginella moellendorffii
transcript EFJ18860
intron # 10
splice site 5'
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|169021094|gb|FE430703.1|FE430703
EST:     TTGACTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAG                         ATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
genomic: TTGACTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAGgttcgaacaa ... gcttgtgaagATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
EST: gi|169116091|gb|FE517454.1|FE517454
EST:     TTGACTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAG                         ATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
genomic: TTGACTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAGgttcgaacaa ... gcttgtgaagATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
EST: gi|169028222|gb|FE432188.1|FE432188
EST:     TTGACTCCGATGGAAAGTGGCACAGAACAAGTAAAGGAGCTCCTGAGCAG                         ATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
genomic: TTGACTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAGgttcgaacaa ... gcttgtgaagATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
EST: gi|169074592|gb|FE480874.1|FE480874
EST:     TTGACTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAG                         ATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
genomic: TTGACTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAGgttcgaacaa ... gcttgtgaagATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
EST: gi|169114143|gb|FE516822.1|FE516822
EST:     TTGACTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAG                         ATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
genomic: TTGACTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAGgttcgaacaa ... gcttgtgaagATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
EST: gi|169107442|gb|FE508311.1|FE508311
EST:     CTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAG                         ATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
genomic: CTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAGgttcgaacaa ... gcttgtgaagATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
EST: gi|169027081|gb|FE435615.1|FE435615
EST:     TTGACTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAG                         ATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
genomic: TTGACTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAGgttcgaacaa ... gcttgtgaagATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
EST: gi|169026011|gb|FE434454.1|FE434454
EST:     TTGACTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAG                         ATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
genomic: TTGACTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAGgttcgaacaa ... gcttgtgaagATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
EST: gi|169096134|gb|FE500294.1|FE500294
EST:     TTGACTCCGATGGAAAGTGGCACAGAACAAGTAAAGGAGCTCCTGAGCAG                         ATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
genomic: TTGACTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAGgttcgaacaa ... gcttgtgaagATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
EST: gi|169081472|gb|FE487733.1|FE487733
EST:     TTGACTCCGATGGAAAGTGGCACAGAACAAGTAAAGGAGCTCCTGAGCAG                         ATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
genomic: TTGACTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAGgttcgaacaa ... gcttgtgaagATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
EST: gi|169110944|gb|FE509856.1|FE509856
EST:     TTGACTCCGATGGAAAGTGGCACAGAACAAGTAAAGGAGCTCCTGAGCAG                         ATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
genomic: TTGACTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAGgttcgaacaa ... gcttgtgaagATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
EST: gi|169022707|gb|FE429734.1|FE429734
EST:     TTGACTCCGATGGAAAGTGGCACAGAACAAGTAAAGGAGCTCCTGAGCAG                         ATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
genomic: TTGACTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAGgttcgaacaa ... gcttgtgaagATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
EST: gi|169023502|gb|FE431920.1|FE431920
EST:     TTGACTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAG                         ATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
genomic: TTGACTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAGgttcgaacaa ... gcttgtgaagATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
EST: gi|169027227|gb|FE436125.1|FE436125
EST:     TTGACTCCGATGGAAAGTGGCACAGAACAAGTAAAGGAGCTCCTGAGCAG                         ATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
genomic: TTGACTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAGgttcgaacaa ... gcttgtgaagATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
EST: gi|169052201|gb|FE461411.1|FE461411
EST:     TTGACTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAG                         ATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
genomic: TTGACTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAGgttcgaacaa ... gcttgtgaagATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
EST: gi|169083022|gb|FE488544.1|FE488544
EST:     TTGACTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAG                         ATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
genomic: TTGACTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAGgttcgaacaa ... gcttgtgaagATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
EST: gi|169029737|gb|FE438344.1|FE438344
EST:     TGACTCCGATGGAAAGTGGCACAGAACAAGTAAAGGAGCTCCTGAGCAG                         ATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
genomic: TGACTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAGgttcgaacaa ... gcttgtgaagATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
EST: gi|169082644|gb|FE486203.1|FE486203
EST:     TTGACTCCGATGGAAAGTGGCACAGAACAAGTAAAGGAGCTCCTGAGCAG                         ATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
genomic: TTGACTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAGgttcgaacaa ... gcttgtgaagATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
EST: gi|169028953|gb|FE438626.1|FE438626
EST:     TTGACTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAG                         ATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
genomic: TTGACTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAGgttcgaacaa ... gcttgtgaagATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
EST: gi|169044104|gb|FE452106.1|FE452106
EST:     TTGACTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAG                         ATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC
genomic: TTGACTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAGgttcgaacaa ... gcttgtgaagATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCC

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: 34 (upstream exon), 35 (downstream exon)
Score: 78

GCACTTTCTGCCTTTCAATCCTGTGGACAAGAGGACAGCACTCACCTACATTGACTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAGgttcgaacaa ... gcttgtgaagATTCTCGCCTTGGCTCACAATAAGTCCGAAATAGCAGACAAGGTTCACTCCATCATCGACAAGTTCGCTGAGCGAGGGCTTCGTTCTCTTGCCGTTGCCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCACTTTCTGCCTTTCAATCCTGTGGACAAGAGGACAGCACTCACCTACATTGACTCCGATGGAAAATGGCACAGAGCAAGTAAAGGAGCTCCTGAGCAGgttcgaacaacctagtattctcttttgctttctgatttggctaaagctatgtttgcttgtgaag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG