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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtagcgatacttttctttttttttttgctcttgtccttttgggtcttgacttgttcttatcaacagGAAAGGAGACTACTTCCGTTATCTCGCGGAGTTCAAGACCGGTAACGAAAGAAAGGAGGCGGCCGATCAATCATTCAAGGCTTACCAG

Basic information

species Selaginella moellendorffii
transcript EFJ35972
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|169037539|gb|FE446280.1|FE446280
EST:     CTAGTCCCCGCATCTAGCACCGGCGAGTCTACGGTGTTTTATTACAAGAT                         GAAAGGAGACTACTTCCGTTATCTCGCGGAGTTCAAGACCGGTAACGAAAG
genomic: CTAGTCCCCGCATCTAGCACCGGGGAGTCTACGGTGTTCTATTACAAGATgtgagtagcg ... ttatcaacagGAAAGGAGACTACTTCCGTTATCTCGCGGAGTTCAAGACCGGTAACGAAAG
EST: gi|169043569|gb|FE452663.1|FE452663
EST:     CTAGTCCCCGCATCTAGCACCGGCGAGTCTACAGTGTTTTATTACCAGAT                         GAAAGGAGACTACTTCCGTTATCTCGCGGAGTTCAAGACCGGTAACGAAAG
genomic: CTAGTCCCCGCATCTAGCACCGGGGAGTCTACGGTGTTCTATTACAAGATgtgagtagcg ... ttatcaacagGAAAGGAGACTACTTCCGTTATCTCGCGGAGTTCAAGACCGGTAACGAAAG
EST: gi|169096262|gb|FE497848.1|FE497848
EST:     CTAGTCCCCGCATCTAGCACCGGCGAGTCTACGGTGTTTTATTACAAGAT                         GAAAGGAGACTACTTCCGTTATCTCGCGGAGTTCAAGACCGGTAACGAAAG
genomic: CTAGTCCCCGCATCTAGCACCGGGGAGTCTACGGTGTTCTATTACAAGATgtgagtagcg ... ttatcaacagGAAAGGAGACTACTTCCGTTATCTCGCGGAGTTCAAGACCGGTAACGAAAG
EST: gi|169034332|gb|FE443105.1|FE443105
EST:     CTAGTCCCCGCATCTAGCACCGGCGAGTCTACGGTGTTTTATTACAAGAT                         GAAAGGAGACTACTTCCGTTATCTCGCGGAGTTCAAGACCGGTAACGAAAG
genomic: CTAGTCCCCGCATCTAGCACCGGGGAGTCTACGGTGTTCTATTACAAGATgtgagtagcg ... ttatcaacagGAAAGGAGACTACTTCCGTTATCTCGCGGAGTTCAAGACCGGTAACGAAAG
EST: gi|169034593|gb|FE446473.1|FE446473
EST:     CTAGTCCCCGCATCTAGCACCGGGGAGTCTACGGTGTTCTATTACAAGAT                         GAAAGGAGACTACTTCCGTTATCTCGCGGAGTTCAAGACCGGTAACGAAAG
genomic: CTAGTCCCCGCATCTAGCACCGGGGAGTCTACGGTGTTCTATTACAAGATgtgagtagcg ... ttatcaacagGAAAGGAGACTACTTCCGTTATCTCGCGGAGTTCAAGACCGGTAACGAAAG
EST: gi|169051570|gb|FE458453.1|FE458453
EST:     CTAGTCCCCGCATCTAGCACCGGGGAGTCTACGGTGTTCTATTACAAGAT                         GAAAGGAGACTACTTCCGTTATCTCGCGGAGTTCAAGACCGGTAACGAAAG
genomic: CTAGTCCCCGCATCTAGCACCGGGGAGTCTACGGTGTTCTATTACAAGATgtgagtagcg ... ttatcaacagGAAAGGAGACTACTTCCGTTATCTCGCGGAGTTCAAGACCGGTAACGAAAG
EST: gi|169111479|gb|FE510339.1|FE510339
EST:     CTAGTCCCCGCATCTAGCACCGGGGAGTCTACGGTGTTCTATTACAAGAT                         GAAAGGAGACTACTTCCGTTATCTCGCGGAGTTCAAGACCGGTAACGAAAG
genomic: CTAGTCCCCGCATCTAGCACCGGGGAGTCTACGGTGTTCTATTACAAGATgtgagtagcg ... ttatcaacagGAAAGGAGACTACTTCCGTTATCTCGCGGAGTTCAAGACCGGTAACGAAAG

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), 35 (downstream exon)
Score: 35

ACGAGCTCTCCACGATTTGCAATGACATTCTCACCATCATCGACGAGCATCTAGTCCCCGCATCTAGCACCGGGGAGTCTACGGTGTTCTATTACAAGATgtgagtagcg ... ttatcaacagGAAAGGAGACTACTTCCGTTATCTCGCGGAGTTCAAGACCGGTAACGAAAGAAAGGAGGCGGCCGATCAATCATTCAAGGCTTACCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctttttttttttgctcttgtccttttgggtcttgacttgttcttatcaacagGAAAGGAGACTACTTCCGTTATCTCGCGGAGTTCAAGACCGGTAACGAAAGAAAGGAGGCGGCCGATCAATCATTCAAGGCTTACCAG
                                tcttgac  putative branch site (score: 35)
                                      cttgttctt  CT-rich tract
     tttttttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtagcgatacttttctttttttttttgctcttgtccttttgggtcttgacttgttcttatcaacagGAAAGGAGACTACTTCCGTTATCTCGCGGAGTTCAAGACCGGTAACGAAAGAAAGGAGGCGGCCGATCAATCATTCAAGGCTTACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG