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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttacatgttttgcttttcttttattttgttcatgctgacgtctgagctttctgctttcagGCTACGAAAGAGCTTGGTGGAGAGAATTACGTGTTCTGGGGTGGCCGGGAAGGATATCAGTCTCTCTTGAACACAGACCTTGAGAGGGAGCTCAATCACC

Basic information

species Selaginella moellendorffii
transcript EFJ07670
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ07670 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: GLYMA17G07380.1 (Glycine max), 3'ss of exon 9
---------------------gtatgttacatgttttgcttttcttttattttgttcatgctgacgtctgagctttctgc-tttcagGCTACGAAAGAGCTTGGTGGAGAGAATTACGTGTTCTGGGGTGGCCGGGAAGGATATCAGTCTCTCTTGAACACAGACCTTGAGAGGGAGCTCAATCACC
                     ||| || | | | ||   | |  |||||      |  | ||   | ||||  |   |   || ||||  ||  |  |  | || ||||| ||||| || ||||||||||| || ||||| ||||| ||||| |||||||||||  | ||| | ||||| |||||  
gtactgttgtgtatgcatgtagta-gtaagaaggttcattgtatttttaaaaccattgttcttttg-ctgatttgaatatattgcagGTGACACATTATTTGGGGGGAGAAAATTATGTTTTCTGGGGTGGTCGTGAAGGTTATCAATCTCTTTTGAACACAGATATGGAGCGAGAGCTTAATCATT
















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|169101012|gb|FE500925.1|FE500925
EST:     ACGCTAGGATTTATGCTTATGCAGCCGCTCAAGTCAAGAAGGCTATGGAG                         GCTACGAAAGAGCTTGGTGGGGAGAATTACGTGTTCTGGGGTGGC
genomic: ACGCTAGGATTTATGCTTATGCAGCCGCTCAAGTCAAGAAGGCTATGGAGgtatgttaca ... ctgctttcagGCTACGAAAGAGCTTGGTGGAGAGAATTACGTGTTCTGGGGTGGC
EST: gi|169115654|gb|FE517864.1|FE517864
EST:     ACGCTAGGATTTATGCTTATGCAGCCGCTCAAGTCAAGAAGGCTATGGAG                         GCTACGAAAGAGCTTGGTGGAGAGAATTACGTGTTCTGGGGTGGCCGGGAA
genomic: ACGCTAGGATTTATGCTTATGCAGCCGCTCAAGTCAAGAAGGCTATGGAGgtatgttaca ... ctgctttcagGCTACGAAAGAGCTTGGTGGAGAGAATTACGTGTTCTGGGGTGGCCGGGAA
EST: gi|169047634|gb|FE454802.1|FE454802
EST:     ACGCTAGGATTTATGCTTATGCAGCCGCTCAAGTCAAGAAGGCTATGGAG                         GCTACGAAAGAGCTTGGTGGAGAGAATTACGTGTTCTGGGGTGGCCGGGAA
genomic: ACGCTAGGATTTATGCTTATGCAGCCGCTCAAGTCAAGAAGGCTATGGAGgtatgttaca ... ctgctttcagGCTACGAAAGAGCTTGGTGGAGAGAATTACGTGTTCTGGGGTGGCCGGGAA
EST: gi|169053271|gb|FE462546.1|FE462546
EST:     ACGCTAGGATTTATGCTTATGCAGCCGCTCAAGTCAAGAAGGCTATGGAG                         GCTACGAAAGAGCTTGGTGGGGAGAATTACGTGTTCTGGGGTGGCCGGGAA
genomic: ACGCTAGGATTTATGCTTATGCAGCCGCTCAAGTCAAGAAGGCTATGGAGgtatgttaca ... ctgctttcagGCTACGAAAGAGCTTGGTGGAGAGAATTACGTGTTCTGGGGTGGCCGGGAA

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), 20 (downstream exon)
Score: 12

TCCCGACGCTAGGATTTATGCTTATGCAGCCGCTCAAGTCAAGAAGGCTATGGAGgtatgttaca ... ctgctttcagGCTACGAAAGAGCTTGGTGGAGAGAATTACGTGTTCTGGGGTGGCCGGGAAGGATATCAGTCTCTCTTGAACACAGACCTTGAGAGGGAGCTCAATCACC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgttttgcttttcttttattttgttcatgctgacgtctgagctttctgctttcagGCTACGAAAGAGCTTGGTGGAGAGAATTACGTGTTCTGGGGTGGCCGGGAAGGATATCAGTCTCTCTTGAACACAGACCTTGAGAGGGAGCTCAATCACC
                           tgctgac  putative branch site (score: 12)
                                         ctttctgctttc  putative PPT
        ttttcttttattttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgttacatgttttgcttttcttttattttgttcatgctgacgtctgagctttctgctttcagGCTACGAAAGAGCTTGGTGGAGAGAATTACGTGTTCTGGGGTGGCCGGGAAGGATATCAGTCTCTCTTGAACACAGACCTTGAGAGGGAGCTCAATCACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA