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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttgtcctcgtttctttactccggctgccctcctcaaacactggatttgcagGAACTCGAGGAGAAGAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAGAAGGAATTACTCAAGCTGAGGCAAAAGGCGCTCACTGCTGCTGAAGAAA

Basic information

species Selaginella moellendorffii
transcript EFJ34798
intron # 4
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|169100109|gb|FE501868.1|FE501868
EST:     TGGGTCAGTTGTCCAAGGAAGTCGGGTGGCACCACCATGAGACGATCAAG                         GAACTCGAGGAGAAGAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAG
genomic: TGGGTCAGTTGTCCAAGGAAGTCGGGTGGCACCACCATGAGACGATCAAGgtgagttgtc ... ggatttgcagGAACTCGAGGAGAAGAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAG
EST: gi|169094936|gb|FE491644.1|FE491644
EST:     TGGGTCAGTTGTCCAAGGAAGTCGGGTGGCACCACCATGAGACGATCAAG                         GAACTCGAGGAGAAGAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAG
genomic: TGGGTCAGTTGTCCAAGGAAGTCGGGTGGCACCACCATGAGACGATCAAGgtgagttgtc ... ggatttgcagGAACTCGAGGAGAAGAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAG
EST: gi|169050490|gb|FE459597.1|FE459597
EST:     TGGGTCAGCTGTCCAAGGAAGTCGGGTGGCACCACCATGAGACAATCAAG                         GAACTCGAGGAGAAAAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAG
genomic: TGGGTCAGTTGTCCAAGGAAGTCGGGTGGCACCACCATGAGACGATCAAGgtgagttgtc ... ggatttgcagGAACTCGAGGAGAAGAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAG
EST: gi|169033363|gb|FE441755.1|FE441755
EST:     TGGGTCAGTTGTCCAAGGAAGTCGGGTGGCACCACCATGAGACGATCAAG                         GAACTCGAGGAGAAGAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAG
genomic: TGGGTCAGTTGTCCAAGGAAGTCGGGTGGCACCACCATGAGACGATCAAGgtgagttgtc ... ggatttgcagGAACTCGAGGAGAAGAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAG
EST: gi|169047185|gb|FE457266.1|FE457266
EST:     TGGGTCAGCTGTCCAAGGAAGTCGGGTGGCACCACCATGAGACAATCAAG                         GAACTCGAGGAGAAAAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAG
genomic: TGGGTCAGTTGTCCAAGGAAGTCGGGTGGCACCACCATGAGACGATCAAGgtgagttgtc ... ggatttgcagGAACTCGAGGAGAAGAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAG
EST: gi|169033364|gb|FE441756.1|FE441756
EST:     TGGGTCAGTTGTCCAAGGAAGTCGGGTGGCACCACCATGAGACGATCAAG                         GAACTCGAGGAGAAGAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAG
genomic: TGGGTCAGTTGTCCAAGGAAGTCGGGTGGCACCACCATGAGACGATCAAGgtgagttgtc ... ggatttgcagGAACTCGAGGAGAAGAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAG
EST: gi|169036055|gb|FE446761.1|FE446761
EST:     TGGGTCAGTTGTCCAAGGAAGTCGGGTGGCACCACCATGAGACGATCAAG                         GAACTCGAGGAGAAGAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAG
genomic: TGGGTCAGTTGTCCAAGGAAGTCGGGTGGCACCACCATGAGACGATCAAGgtgagttgtc ... ggatttgcagGAACTCGAGGAGAAGAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAG
EST: gi|169063743|gb|FE472473.1|FE472473
EST:     TGGGTCAGTTGTCCAAGGAAGTCGGGTGGCACCACCATGAGACGATCAAG                         GAACTCGAGGAGAAGAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAG
genomic: TGGGTCAGTTGTCCAAGGAAGTCGGGTGGCACCACCATGAGACGATCAAGgtgagttgtc ... ggatttgcagGAACTCGAGGAGAAGAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAG
EST: gi|169050489|gb|FE459596.1|FE459596
EST:     TGGGTCAGCTGTCCAAGGAAGTCGGGTGGCACCACCATGAGACAATCAAG                         GAACTCGAGGAGAAAAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAG
genomic: TGGGTCAGTTGTCCAAGGAAGTCGGGTGGCACCACCATGAGACGATCAAGgtgagttgtc ... ggatttgcagGAACTCGAGGAGAAGAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAG
EST: gi|169100110|gb|FE501869.1|FE501869
EST:     TGGGTCAGTTGTCCAAGGAAGTCGGGTGGCACCACCATGAGACGATCAAG                         GAACTCGAGGAGAAGAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAG
genomic: TGGGTCAGTTGTCCAAGGAAGTCGGGTGGCACCACCATGAGACGATCAAGgtgagttgtc ... ggatttgcagGAACTCGAGGAGAAGAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAG
EST: gi|169063744|gb|FE472474.1|FE472474
EST:     TGGGTCAGTTGTCCAAGGAAGTCGGGTGGCACCACCATGAGACGATCAAG                         GAACTCGAGGAGAAGAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAG
genomic: TGGGTCAGTTGTCCAAGGAAGTCGGGTGGCACCACCATGAGACGATCAAGgtgagttgtc ... ggatttgcagGAACTCGAGGAGAAGAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAG
EST: gi|169023345|gb|FE431867.1|FE431867
EST:     TGGGTCAGCTGTCCAAGGAAGTCGGGTGGCACCACCATGAGACAATCAAG                         GAACTCGAGGAGAAAAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAG
genomic: TGGGTCAGTTGTCCAAGGAAGTCGGGTGGCACCACCATGAGACGATCAAGgtgagttgtc ... ggatttgcagGAACTCGAGGAGAAGAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAG
EST: gi|169044733|gb|FE454074.1|FE454074
EST:     TGGGTCAGTTGTCCAAGGAAGTCGGGTGGCACCACCATGAGACGATCAAG                         GAACTCGAGGAGAAGAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAG
genomic: TGGGTCAGTTGTCCAAGGAAGTCGGGTGGCACCACCATGAGACGATCAAGgtgagttgtc ... ggatttgcagGAACTCGAGGAGAAGAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAG
EST: gi|169078892|gb|FE489664.1|FE489664
EST:     TGGGTCAGTTGTCCAAGGAAGTCGGGTGGCACCACCATGAGACGATCAAG                         GAACTCGAGGAGAAGAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAG
genomic: TGGGTCAGTTGTCCAAGGAAGTCGGGTGGCACCACCATGAGACGATCAAGgtgagttgtc ... ggatttgcagGAACTCGAGGAGAAGAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAG
EST: gi|169077600|gb|FE484862.1|FE484862
EST:     TGGGTCAGTTGTCCAAGGAAGTCGGGTGGCACCACCATGAGACGATCAAG                         GAACTCGAGGAGAAGAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAG
genomic: TGGGTCAGTTGTCCAAGGAAGTCGGGTGGCACCACCATGAGACGATCAAGgtgagttgtc ... ggatttgcagGAACTCGAGGAGAAGAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAG
EST: gi|169036054|gb|FE446760.1|FE446760
EST:     TGGGTCAGTTGTCCAAGGAAGTCGGGTGGCACCACCATGAGACGATCAAG                         GAACTCGAGGAGAAGAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAG
genomic: TGGGTCAGTTGTCCAAGGAAGTCGGGTGGCACCACCATGAGACGATCAAGgtgagttgtc ... ggatttgcagGAACTCGAGGAGAAGAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAG

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: 35 (upstream exon), 34 (downstream exon)
Score: 65

GGTCTTGCGGTTGAAACCCGGGCACAAGTTCTGTCTCCTGGGTCAGTTGTCCAAGGAAGTCGGGTGGCACCACCATGAGACGATCAAGgtgagttgtc ... ggatttgcagGAACTCGAGGAGAAGAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAGAAGGAATTACTCAAGCTGAGGCAAAAGGCGCTCACTGCTGCTGAAGAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgagttgtcctcgtttctttactccggctgccctcctcaaacactggatttgcagGAACTCGAGGAGAAGAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAGAAGGAATTACTCAAGCTGAGGCAAAAGGCGCTCACTGCTGCTGAAGAAA
             tttcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttgtcctcgtttctttactccggctgccctcctcaaacactggatttgcagGAACTCGAGGAGAAGAGGAAGGCGAAGGCTCTTGTGTTCTACCAGAAGAAGAAGGAATTACTCAAGCTGAGGCAAAAGGCGCTCACTGCTGCTGAAGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA