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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCGTGCGACTGCTGCCAATGTTGATGAAGCTGTTCGAGAGCTTCCTGATGCAAACCAAgtcaggttccttctaacacatgattaatttcttgtttgtctctcgatgccaacgagaatttgtttcttattttcgtgtccag

Basic information

species Selaginella moellendorffii
transcript EFJ27458
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ27458 (Selaginella moellendorffii), 5'ss of exon 11
lower sequence: Vv03s0038g04210.t01 (Vitis vinifera), 5'ss of exon 10
GTTCGTGCGACTGCTGCCAATGTTGATGAAGCTGTTCGAGAGCTTCCTGATGCAAACCAAgtcaggt------tccttctaacacatgattaatttc---ttgtttgtctctcgatgccaacgagaatt-tgtttcttattttcgtgtccag--------
||    || ||||| |  ||||||||||||||||||||||| ||||||||||| |||   || ||||      |  || |      || || | ||    ||| |||      | || |   || |||  ||     |   |  ||| |           
GTCAAAGCTACTGCAGAAAATGTTGATGAAGCTGTTCGAGAACTTCCTGATGCCAACTTGgtaaggtactctttttttttgctttgtgtttgagtttggattgattgctaggaggtgtctttgaaaatcatgacctctccctctgtgactttgtactgtt
















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|169030320|gb|FE440045.1|FE440045
EST:     CTGCTGCCAATGTTGATGAAGCTGTTCGAGAGCTTCCTGATGCANACCAA                         ACACCCGACGACCTTTGGGCTAA-CACTCTAAAGTCGTCTATCCAAAGCCC
genomic: CTGCTGCCAATGTTGATGAAGCTGTTCGAGAGCTTCCTGATGCAAACCAAgtcaggttcc ... tcgtgtccagACACCCGACGACCTTTGGGCTAAACACTCTAAAGTCGTCTATCCAAAGCCC
EST: gi|169095351|gb|FE496742.1|FE496742
EST:     TGCTGCNCA-TGTTGATGAAGCTGTTCGAGAGCTTCCTGATGCAAACCAN                         ACACCCGACGACCTTTGGGCTAAACACTCTAAAGTCGTCTATCCAAAGCCC
genomic: TGCTGC-CAATGTTGATGAAGCTGTTCGAGAGCTTCCTGATGCAAACCAAgtcaggttcc ... tcgtgtccagACACCCGACGACCTTTGGGCTAAACACTCTAAAGTCGTCTATCCAAAGCCC
EST: gi|169080014|gb|FE487900.1|FE487900
EST:     CTGCTGCCAATGTTGATGAAGCTGTTCGAGAGCTTCCTGATGCAAACCAA                         ACACCCGACGACCTTTGNGCTAAACACTCTAAAGTCGTCTATCCAAAGCCC
genomic: CTGCTGCCAATGTTGATGAAGCTGTTCGAGAGCTTCCTGATGCAAACCAAgtcaggttcc ... tcgtgtccagACACCCGACGACCTTTGGGCTAAACACTCTAAAGTCGTCTATCCAAAGCCC
EST: gi|169063068|gb|FE471174.1|FE471174
EST:     CTGCTGCCAATGTTGATGAAGCTGTTCGAGAGCTTCCTGATGCAAACCAA                         ACACCTGACGACCTTTGGGCTAAACACTCTAAAGTCGTCTATCCAAAGCCC
genomic: CTGCTGCCAATGTTGATGAAGCTGTTCGAGAGCTTCCTGATGCAAACCAAgtcaggttcc ... tcgtgtccagACACCCGACGACCTTTGGGCTAAACACTCTAAAGTCGTCTATCCAAAGCCC
EST: gi|169020233|gb|FE430323.1|FE430323
EST:     CTGCTGCCAATGTTGATGAAGCTGTTCGAGAGCTTCCTGATGCAAACCAA                         G
genomic: CTGCTGCCAATGTTGATGAAGCTGTTCGAGAGCTTCCTGATGCAAACCAAgtcaggttcc ... tcgtgtccag-
EST: gi|169020233|gb|FE430323.1|FE430323
EST:     CTGCTGCCAATGTTGATGAAGCTGTTCGAGAGCTTCCTGATGCAAACCAA                         G
genomic: CTGCTGCCAATGTTGATGAAGCTGTTCGAGAGCTTCCTGATGCAAACCAAgtcaggttcc ... tcgtgtccag-
EST: gi|169020233|gb|FE430323.1|FE430323
EST:     CTGCTGCCAATGTTGATGAAGCTGTTCGAGAGCTTCCTGATGCAAACCAA                         G
genomic: CTGCTGCCAATGTTGATGAAGCTGTTCGAGAGCTTCCTGATGCAAACCAAgtcaggttcc ... tcgtgtccag-
EST: gi|169020233|gb|FE430323.1|FE430323
EST:     CTGCTGCCAATGTTGATGAAGCTGTTCGAGAGCTTCCTGATGCAAACCAA                         G
genomic: CTGCTGCCAATGTTGATGAAGCTGTTCGAGAGCTTCCTGATGCAAACCAAgtcaggttcc ... tcgtgtccag-
EST: gi|169108087|gb|FE511030.1|FE511030
EST:     CTGCTGCCAATGTTGATGAAGCTGTTCGAGAGCTTCCTGATGCAAACCAA                         ACACCCGACGACCTTTGGGCTAAACACTCTAAAGTCGTCTATCCAAAGCCC
genomic: CTGCTGCCAATGTTGATGAAGCTGTTCGAGAGCTTCCTGATGCAAACCAAgtcaggttcc ... tcgtgtccagACACCCGACGACCTTTGGGCTAAACACTCTAAAGTCGTCTATCCAAAGCCC
EST: gi|169030748|gb|FE440863.1|FE440863
EST:     TGCTGCCAATGTTGATGAAGCTGTTCGAGAGCTTCCTGATGNCAA-CCAA                         ACACCCGACGACCTTTGGGCTAAACACTCTANAGTCGTCTATCCAAAGCC
genomic: TGCTGCCAATGTTGATGAAGCTGTTCGAGAGCTTCCTGATG-CAAACCAAgtcaggttcc ... tcgtgtccagACACCCGACGACCTTTGGGCTAAACACTCTAAAGTCGTCTATCCAAAGCC

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: 32 (upstream exon), 31 (downstream exon)
Score: 9

GTTCGTGCGACTGCTGCCAATGTTGATGAAGCTGTTCGAGAGCTTCCTGATGCAAACCAAgtcaggttcc ... tcgtgtccagACACCCGACGACCTTTGGGCTAAACACTCTAAAGTCGTCTATCCAAAGCCCCATAAAGTCAACACCCCCGCTTGGGATGCCATTAAAAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCGTGCGACTGCTGCCAATGTTGATGAAGCTGTTCGAGAGCTTCCTGATGCAAACCAAgtcaggttccttctaacacatgattaatttcttgtttgtctctcgatgccaacgagaatttgtttcttattttcgtgtccag

- - - - -  TGCTGC
- - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - -  GAGCTT