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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcgttggggtggtgtttttctagtactgttgtgctcatggctccttgtactctcagGTGAACAGCGGTGTGCTAGGAGTATGCTCGGCTTTCCTTTCTGGAGAGCCAGCGACAAAGCTCCGGTCCCAGGAGCTCCAGCAGCTGATTGCTGCATTGC

Basic information

species Selaginella moellendorffii
transcript EFJ04870
intron # 29
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|169032192|gb|FE439293.1|FE439293
EST:     TGCAGAGCTTACAAAGGATCCTTCAGGGCAGCGTTGCAGTACAG                         GTGAACAGCGGTGTGCTAGGAGTATGCTCGGCTTTCCTTTCTGGAGAGCCA
genomic: TGCAGAGCTTACAAAGGATCCTTCAGGGCAGCGTTGCAGTACAGgtaagcgttg ... gtactctcagGTGAACAGCGGTGTGCTAGGAGTATGCTCGGCTTTCCTTTCTGGAGAGCCA
EST: gi|169055148|gb|FE462387.1|FE462387
EST:     CTCGGCTGCAGAGCTTACAAAGGATCCTTCAGGGCAGCGTTGCAGTACAG                         GTGAACAGCGGTGTGCTAGGAGTATGCTCGGCTTTCCTTTCTGGAGAGCCA
genomic: CTCGGCTGCAGAGCTTACAAAGGATCCTTCAGGGCAGCGTTGCAGTACAGgtaagcgttg ... gtactctcagGTGAACAGCGGTGTGCTAGGAGTATGCTCGGCTTTCCTTTCTGGAGAGCCA
EST: gi|169027470|gb|FE433729.1|FE433729
EST:     CTCGGCTGCAGAGCTTACAAAGGATCCTTCAGGGCAGCGTTGCAGTACAG                         GTGAACAGCGGTGTGCTAGGAGTATGCTCGGCTTTCCTTTCTGGAGAGCCA
genomic: CTCGGCTGCAGAGCTTACAAAGGATCCTTCAGGGCAGCGTTGCAGTACAGgtaagcgttg ... gtactctcagGTGAACAGCGGTGTGCTAGGAGTATGCTCGGCTTTCCTTTCTGGAGAGCCA
EST: gi|169022808|gb|FE430212.1|FE430212
EST:     CTCGGCTGCAGAGCTTACAAAGGATCCTTCAGGGCAGCGTTGCAGTACAG                         GTGAACAGCGGTGTGCTAGGAGTATGCTCGGCTTTCCTTTCTGGAGAGCCA
genomic: CTCGGCTGCAGAGCTTACAAAGGATCCTTCAGGGCAGCGTTGCAGTACAGgtaagcgttg ... gtactctcagGTGAACAGCGGTGTGCTAGGAGTATGCTCGGCTTTCCTTTCTGGAGAGCCA
EST: gi|169116049|gb|FE517412.1|FE517412
EST:     CTCGGCTGCAGAGCTTACAAAGGATCCTTCAGGGCAGCGTTGCAGTACAG                         GTGAACAGCGGTGTGCTAGGAGTATGCTCGGCTTTCCTTTCTGGAGAGCCA
genomic: CTCGGCTGCAGAGCTTACAAAGGATCCTTCAGGGCAGCGTTGCAGTACAGgtaagcgttg ... gtactctcagGTGAACAGCGGTGTGCTAGGAGTATGCTCGGCTTTCCTTTCTGGAGAGCCA
EST: gi|169055149|gb|FE462388.1|FE462388
EST:     CTCGGCTGCAGAGCTTACAAAGGATCCTTCAGGGCAGCGTTGCAGTACAG                         GTGAACAGCGGTGTGCTAGGAGTATGCTCGGCTTTCCTTTCTGGAGAGCCA
genomic: CTCGGCTGCAGAGCTTACAAAGGATCCTTCAGGGCAGCGTTGCAGTACAGgtaagcgttg ... gtactctcagGTGAACAGCGGTGTGCTAGGAGTATGCTCGGCTTTCCTTTCTGGAGAGCCA
EST: gi|169096729|gb|FE499745.1|FE499745
EST:     CTCGGCTGCAGAGCTTACAAAGGATCCTTCAGGGCAGCGTTGCAGTACAG                         GTGAACAGCGGTGTGCTAGGAGTATGCTCGGCTTTCCTTTCTGGAGAGCCA
genomic: CTCGGCTGCAGAGCTTACAAAGGATCCTTCAGGGCAGCGTTGCAGTACAGgtaagcgttg ... gtactctcagGTGAACAGCGGTGTGCTAGGAGTATGCTCGGCTTTCCTTTCTGGAGAGCCA
EST: gi|169078389|gb|FE488264.1|FE488264
EST:     CTCGGCTGCAGAGCTTACAAAGGATCCTTCAGGGCAGCGTTGCAGTACAG                         GTGAACAGCGGTGTGCTAGGAGTATGCTCGGCTTTCCTTTCTGGAGAGCCA
genomic: CTCGGCTGCAGAGCTTACAAAGGATCCTTCAGGGCAGCGTTGCAGTACAGgtaagcgttg ... gtactctcagGTGAACAGCGGTGTGCTAGGAGTATGCTCGGCTTTCCTTTCTGGAGAGCCA
EST: gi|169022754|gb|FE429755.1|FE429755
EST:     CTCGGCTGCAGAGCTTACAAAGGATCCTTCAGGGCAGCGTTGCAGTACAG                         GTGAACAGCGGTGTGCTAGGAGTATGCTCGGCTTTCCTTTCTGGAGAGCCA
genomic: CTCGGCTGCAGAGCTTACAAAGGATCCTTCAGGGCAGCGTTGCAGTACAGgtaagcgttg ... gtactctcagGTGAACAGCGGTGTGCTAGGAGTATGCTCGGCTTTCCTTTCTGGAGAGCCA

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), 33 (downstream exon)
Score: 5

GTTGAGAAATGAACTCGAAGAGCCTCGCAACTCCGAGGGTGACCATCTCCCTCGGCTGCAGAGCTTACAAAGGATCCTTCAGGGCAGCGTTGCAGTACAGgtaagcgttg ... gtactctcagGTGAACAGCGGTGTGCTAGGAGTATGCTCGGCTTTCCTTTCTGGAGAGCCAGCGACAAAGCTCCGGTCCCAGGAGCTCCAGCAGCTGATTGCTGCATTGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgttggggtggtgtttttctagtactgttgtgctcatggctccttgtactctcagGTGAACAGCGGTGTGCTAGGAGTATGCTCGGCTTTCCTTTCTGGAGAGCCAGCGACAAAGCTCCGGTCCCAGGAGCTCCAGCAGCTGATTGCTGCATTGC
                                       ctccttgtactctc  CT-rich tract
             tttttcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcgttggggtggtgtttttctagtactgttgtgctcatggctccttgtactctcagGTGAACAGCGGTGTGCTAGGAGTATGCTCGGCTTTCCTTTCTGGAGAGCCAGCGACAAAGCTCCGGTCCCAGGAGCTCCAGCAGCTGATTGCTGCATTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC