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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaactcgagtgttggcattctgccttaccttcttctcttttgttatttcagGTGTCTGTCGACGTCCCCGACGTGAAAGGAAGGACAGAAATTCTCAGAGTTCATGCTGGGAATAAGAAGTTTGACGGTGATGTGTCTTTGGACGTGATTG

Basic information

species Selaginella moellendorffii
transcript EFJ19987
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ19987 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: Vv12s0028g01600.t01 (Vitis vinifera), 3'ss of exon 2
----gtaactcgagtgt-tggcattctgccttaccttcttct--------------cttttgtta----ttt----cagGTGTCTGTCGACGTCCCCGACGTGAAAGGAAGGACAGAAATTCTCAGAGTTCATGCTGGGAATAAGAAGTTTGACGGTGATGTGTCTTTGGACGTGATTG
    | |    || | | | |  || ||||||| ||| |  |              |||  ||||    |||    |||||  |||| || || || ||  |    ||||||||||| ||  | |  ||||||||||| |||||||||||||| || ||||||||| | || || || |
gtaagcatagagaatatattgttttttgccttatcttttattataagtgggaaatacttacgttaaagctttggagcagGTAACTGTTGATGTTCCTGATATACGGGGAAGGACAGAGATCTTAAAGGTTCATGCTGGTAATAAGAAGTTTGATGGAGATGTGTCTCTTGATGTAATAG
















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|169044601|gb|FE451147.1|FE451147
EST:     CTGACATCCTTGATGCCGCATTGCTGAGGCCAGGAAGATTTGATCGACAG                         GTGTCTGTCGA
genomic: CTGACATCCTTGATGCCGCATTGCTGAGGCCAGGAAGATTTGATCGACAGgtaactcgag ... gttatttcagGTGTCTGTCGA
EST: gi|169101336|gb|FE501998.1|FE501998
EST:     CTGACATCCTTGATGCCGCATTGCTGAGGCCAGGAAGATTTGATCGACAG                         GTGTCTGTCGACGTCCCCGACGTGAAAGGAAGGACAGAAATTCTCAGAGTT
genomic: CTGACATCCTTGATGCCGCATTGCTGAGGCCAGGAAGATTTGATCGACAGgtaactcgag ... gttatttcagGTGTCTGTCGACGTCCCCGACGTGAAAGGAAGGACAGAAATTCTCAGAGTT
EST: gi|169115718|gb|FE517304.1|FE517304
EST:     CTGACATCCTTGATGCCGCATTGCTGAGGCCAGGAAGATTTGATCGACAG                         GTGTCTGTCGACGTCCCCGACGTGAAAGGAAG-ACAGAAATTCTCAGAGTT
genomic: CTGACATCCTTGATGCCGCATTGCTGAGGCCAGGAAGATTTGATCGACAGgtaactcgag ... gttatttcagGTGTCTGTCGACGTCCCCGACGTGAAAGGAAGGACAGAAATTCTCAGAGTT
EST: gi|169092756|gb|FE493698.1|FE493698
EST:     CTGACATCCTTGATGCCGCATTGCTGAGGCCAGGAAGATTTGATCGACAG                         GTGTCTGTCGACGTCCCCGACGTGAAAGGAAGGACAGAAATTCTCAGAGTT
genomic: CTGACATCCTTGATGCCGCATTGCTGAGGCCAGGAAGATTTGATCGACAGgtaactcgag ... gttatttcagGTGTCTGTCGACGTCCCCGACGTGAAAGGAAGGACAGAAATTCTCAGAGTT
EST: gi|169108621|gb|FE510797.1|FE510797
EST:     CTGACATCCTTGATGCCGCATTGCTGAGGCCAGGAAGATTTGATCGACAG                         GTGTCTGTCGACGTCCCCGACGTGAAAGGAAGGACAGAAATTCTCAGAGTT
genomic: CTGACATCCTTGATGCCGCATTGCTGAGGCCAGGAAGATTTGATCGACAGgtaactcgag ... gttatttcagGTGTCTGTCGACGTCCCCGACGTGAAAGGAAGGACAGAAATTCTCAGAGTT
EST: gi|169097740|gb|FE497467.1|FE497467
EST:     CTGACATCCTTGATGCCGCATTGCTGAGGCCAGGAAGATTTGATCGACAG                         GTGTCTGTCGACGTCCCCGACGTGAA
genomic: CTGACATCCTTGATGCCGCATTGCTGAGGCCAGGAAGATTTGATCGACAGgtaactcgag ... gttatttcagGTGTCTGTCGACGTCCCCGACGTGAA
EST: gi|169094549|gb|FE492434.1|FE492434
EST:     CTGACATCCTTGATGCCGCATTGCTGAGGCCAGGAAGATTTGATCGACAG                         GTGTCTGTCGACGTCCCCGACGTGAAAGGAAGGACAGAAATTCTC
genomic: CTGACATCCTTGATGCCGCATTGCTGAGGCCAGGAAGATTTGATCGACAGgtaactcgag ... gttatttcagGTGTCTGTCGACGTCCCCGACGTGAAAGGAAGGACAGAAATTCTC
EST: gi|169023480|gb|FE430078.1|FE430078
EST:     CTGACATCCTTGATGCCGCATTGCTGAGGCCAGGAAGATTTGATCGACAG                         GTGTCTGTCGACGTCCCCGACGTGAAAGGAAGGACAGAAATTCTCAGAGTT
genomic: CTGACATCCTTGATGCCGCATTGCTGAGGCCAGGAAGATTTGATCGACAGgtaactcgag ... gttatttcagGTGTCTGTCGACGTCCCCGACGTGAAAGGAAGGACAGAAATTCTCAGAGTT
EST: gi|169098459|gb|FE498515.1|FE498515
EST:     CTGACATCCTTGATGCCGCATTGCTGAGGCCAGGAAGATTTGATCGACAG                         GTGTCTGTCGACGTCCCCGACGTGAAAGGAAGGACAGAAATTCTCAGAGTT
genomic: CTGACATCCTTGATGCCGCATTGCTGAGGCCAGGAAGATTTGATCGACAGgtaactcgag ... gttatttcagGTGTCTGTCGACGTCCCCGACGTGAAAGGAAGGACAGAAATTCTCAGAGTT
EST: gi|169104527|gb|FE508127.1|FE508127
EST:     CTGACATCCTTGATGCCGCATTGCTGAGGCCAGGAAGATTTGATCGACAG                         GTGTCTGTCGACGTCCCCGACGTGAAAGGAAGGACAGAAATTCTCAGAGTT
genomic: CTGACATCCTTGATGCCGCATTGCTGAGGCCAGGAAGATTTGATCGACAGgtaactcgag ... gttatttcagGTGTCTGTCGACGTCCCCGACGTGAAAGGAAGGACAGAAATTCTCAGAGTT
EST: gi|169026505|gb|FE434779.1|FE434779
EST:     CTGACATCCTTGATGCCGCATTGCTGAGGCCAGGAAGATTTGATCGACAG                         GTGTCTGTCGACGTCCCCGACGTGAAAGGAAGGACAGAAATTCTCAGAGTT
genomic: CTGACATCCTTGATGCCGCATTGCTGAGGCCAGGAAGATTTGATCGACAGgtaactcgag ... gttatttcagGTGTCTGTCGACGTCCCCGACGTGAAAGGAAGGACAGAAATTCTCAGAGTT
EST: gi|169100282|gb|FE502951.1|FE502951
EST:     CTGACATCCTTGATGCCGCATTGCTGAGGCCAGGAAGATTTGATCGACAG                         GTGTCTGTCGACGTCCCCGACGTGAAAGGAAGGACAGAAATTCTCAGAGTT
genomic: CTGACATCCTTGATGCCGCATTGCTGAGGCCAGGAAGATTTGATCGACAGgtaactcgag ... gttatttcagGTGTCTGTCGACGTCCCCGACGTGAAAGGAAGGACAGAAATTCTCAGAGTT
EST: gi|169056846|gb|FE465423.1|FE465423
EST:     CTGACATCCTTGATGCCGCATTGCTGAGGCCAGGAAGATTTGATCGACAG                         GTGTCTGTCGACGTCCCCGACGTGAAAGGAAGGACAGAAATTCTCAGAGTT
genomic: CTGACATCCTTGATGCCGCATTGCTGAGGCCAGGAAGATTTGATCGACAGgtaactcgag ... gttatttcagGTGTCTGTCGACGTCCCCGACGTGAAAGGAAGGACAGAAATTCTCAGAGTT
EST: gi|169020911|gb|FE431989.1|FE431989
EST:     CTGACATCCTTGATGCCGCATTGCTGAGGCCAGGAAGATTTGATCGACAG                         GTGTCTGTCGACGTCCCCGACGTGAAAGGAAGGACAGAAATTCTCAGAGTT
genomic: CTGACATCCTTGATGCCGCATTGCTGAGGCCAGGAAGATTTGATCGACAGgtaactcgag ... gttatttcagGTGTCTGTCGACGTCCCCGACGTGAAAGGAAGGACAGAAATTCTCAGAGTT
EST: gi|169048292|gb|FE456266.1|FE456266
EST:     CTGACATCCTTGATGCCGCATTGCTGAGGCCAGGAAGATTTGATCGACAG                         GTGTCTGTCGACGTCCCCGACGTGAAAGGAAGGACAGAAATTCTCAGAGTT
genomic: CTGACATCCTTGATGCCGCATTGCTGAGGCCAGGAAGATTTGATCGACAGgtaactcgag ... gttatttcagGTGTCTGTCGACGTCCCCGACGTGAAAGGAAGGACAGAAATTCTCAGAGTT

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: 26

TGGATTCGAGGGCAACACAGGAGTAATAGTCGTTGCTGCTACAAACAGAGCTGACATCCTTGATGCCGCATTGCTGAGGCCAGGAAGATTTGATCGACAGgtaactcgag ... gttatttcagGTGTCTGTCGACGTCCCCGACGTGAAAGGAAGGACAGAAATTCTCAGAGTTCATGCTGGGAATAAGAAGTTTGACGGTGATGTGTCTTTGGACGTGATTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaactcgagtgttggcattctgccttaccttcttctcttttgttatttcagGTGTCTGTCGACGTCCCCGACGTGAAAGGAAGGACAGAAATTCTCAGAGTTCATGCTGGGAATAAGAAGTTTGACGGTGATGTGTCTTTGGACGTGATTG
                         gccttac  putative branch site (score: 26)
                   cattctgccttacctt  CT-rich tract
                                         ttttgttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaactcgagtgttggcattctgccttaccttcttctcttttgttatttcagGTGTCTGTCGACGTCCCCGACGTGAAAGGAAGGACAGAAATTCTCAGAGTTCATGCTGGGAATAAGAAGTTTGACGGTGATGTGTCTTTGGACGTGATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT