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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgactaccatttttcttctcctccagcccccagtttgatgatatctttttcttcttcttctttcagGGAGAGCGAAAAACGTACATTCTAGTGGTCCTTGCCGCATTTCTCATCCAACATGTCGAGGGTATATACTGGTGGTATCGTGCCGACGCTCTTTGGCGAC

Basic information

species Selaginella moellendorffii
transcript EFJ19091
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|169063899|gb|FE471254.1|FE471254
EST:     CTATTATGATCAAAGCGAATAGTCTTCTTCGTAAGCAGACGTCTCTAAGA                         GGAGAGCGAAAAACGTACATTCTAGTGGTCCTTGCCGCATTTCTCATCCAA
genomic: CTATTATGATCAAAGCGAATAGTCTTCTTCGTAAGCAGACGTCTCTAAGAgtaagtgact ... cttctttcagGGAGAGCGAAAAACGTACATTCTAGTGGTCCTTGCCGCATTTCTCATCCAA
EST: gi|169071910|gb|FE478158.1|FE478158
EST:     CTATTATGATCAAAGCGAATAGTCTTCTTCGTAAGCAGACGTCTCTAAGA                         GGAGAGCGAANAACGTACATTCTAGTGGTCCTTGCCGCATTTCTCATCCAA
genomic: CTATTATGATCAAAGCGAATAGTCTTCTTCGTAAGCAGACGTCTCTAAGAgtaagtgact ... cttctttcagGGAGAGCGAAAAACGTACATTCTAGTGGTCCTTGCCGCATTTCTCATCCAA
EST: gi|169101857|gb|FE504937.1|FE504937
EST:     CTATTATGATCAAAGCGAATAGTCTTCTTCGTAAGCAGACGTCTCTAAGA                         GGAGAGCGAAAAACGTACATTCTAGTGGTCCTTGCCGCATTTCTCATCCAA
genomic: CTATTATGATCAAAGCGAATAGTCTTCTTCGTAAGCAGACGTCTCTAAGAgtaagtgact ... cttctttcagGGAGAGCGAAAAACGTACATTCTAGTGGTCCTTGCCGCATTTCTCATCCAA
EST: gi|169110152|gb|FE513367.1|FE513367
EST:     CTATTATGATCAAAGCGAATAGTCTTCTTCGTAAGCAGACGTCTCTAAGA                         GGAGAGCGAAAAACGTACATTCTAGTGGTCCTTGCCGCATTTCTCATCCAA
genomic: CTATTATGATCAAAGCGAATAGTCTTCTTCGTAAGCAGACGTCTCTAAGAgtaagtgact ... cttctttcagGGAGAGCGAAAAACGTACATTCTAGTGGTCCTTGCCGCATTTCTCATCCAA
EST: gi|169060303|gb|FE467873.1|FE467873
EST:     CTATTATGATCAAAGCGAATAGTCTTCTTCGTAAGCAGACGTCTCTAAGA                         GGAGAGCGAAAAACGTACATTCTAGTGGTCCTTGCCGCATTTCTCATCCAA
genomic: CTATTATGATCAAAGCGAATAGTCTTCTTCGTAAGCAGACGTCTCTAAGAgtaagtgact ... cttctttcagGGAGAGCGAAAAACGTACATTCTAGTGGTCCTTGCCGCATTTCTCATCCAA
EST: gi|169036020|gb|FE446726.1|FE446726
EST:     CTATTATGATCAAAGCGAATAGTCTTCTTCGTAAGCAGACGTCTCTGAGA                         GGAGAGCGAAAAACGTACATTCTAGTGGTCCTTGCCGCATTTCTCATCCAA
genomic: CTATTATGATCAAAGCGAATAGTCTTCTTCGTAAGCAGACGTCTCTAAGAgtaagtgact ... cttctttcagGGAGAGCGAAAAACGTACATTCTAGTGGTCCTTGCCGCATTTCTCATCCAA
EST: gi|169100040|gb|FE502358.1|FE502358
EST:     CTATTATGATCAAAGCGAATAGTCTTCTTCGTAAGCAGACGTCTCTAAGA                         GGAGAGCGAAAAACGTACATTCTAGTGGTCCTTGCCGCATTTCTCATCCAA
genomic: CTATTATGATCAAAGCGAATAGTCTTCTTCGTAAGCAGACGTCTCTAAGAgtaagtgact ... cttctttcagGGAGAGCGAAAAACGTACATTCTAGTGGTCCTTGCCGCATTTCTCATCCAA
EST: gi|169113565|gb|FE514476.1|FE514476
EST:     CTATTATGATCAAAGCGAATAGTCTTCTTCGTAAGCAGACGTCTCTAAGA                         GGAGAGCGAAAAACGTACATTCTAGTGGTCCTTGCCGCATTTCTCCATCCA
genomic: CTATTATGATCAAAGCGAATAGTCTTCTTCGTAAGCAGACGTCTCTAAGAgtaagtgact ... cttctttcagGGAGAGCGAAAAACGTACATTCTAGTGGTCCTTGCCGCATTTCTC-ATCCA
EST: gi|169029063|gb|FE437566.1|FE437566
EST:     CTATTATGATCAAAGCGAATAGTCTTCTTCGTAAGCAGACGTCTCTAAGA                         GGAGAGCGAAAAACGTACATTCTAGTGGTCCTTGCCGCATTTCTCATCCAA
genomic: CTATTATGATCAAAGCGAATAGTCTTCTTCGTAAGCAGACGTCTCTAAGAgtaagtgact ... cttctttcagGGAGAGCGAAAAACGTACATTCTAGTGGTCCTTGCCGCATTTCTCATCCAA

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), 30 (downstream exon)
Score: 11

GTTTCCTTGTGACGCTTTGGATATCAGCTATTATGATCAAAGCGAATAGTCTTCTTCGTAAGCAGACGTCTCTAAGAgtaagtgact ... cttctttcagGGAGAGCGAAAAACGTACATTCTAGTGGTCCTTGCCGCATTTCTCATCCAACATGTCGAGGGTATATACTGGTGGTATCGTGCCGACGCTCTTTGGCGAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcttctcctccagcccccagtttgatgatatctttttcttcttcttctttcagGGAGAGCGAAAAACGTACATTCTAGTGGTCCTTGCCGCATTTCTCATCCAACATGTCGAGGGTATATACTGGTGGTATCGTGCCGACGCTCTTTGGCGAC
                     gtttgat  putative branch site (score: 11)
                           tgatatctttttcttc  CT-rich tract
                             atatcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgactaccatttttcttctcctccagcccccagtttgatgatatctttttcttcttcttctttcagGGAGAGCGAAAAACGTACATTCTAGTGGTCCTTGCCGCATTTCTCATCCAACATGTCGAGGGTATATACTGGTGGTATCGTGCCGACGCTCTTTGGCGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG