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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatagtttgttttggtttctcttaagtgcttaacgtcgtgtttccagCCTTCATTGTCCAGATTAGAAGTTTGGATGATCATAAGCCTTTGCCTGGAGTTACTGTTGCTGATATTGGTGTAAAGTTTGGAAATGCTGGTTACAACAC

Basic information

species Selaginella moellendorffii
transcript EFJ35164
intron # 5
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|169062876|gb|FE472886.1|FE472886
EST:     TCTAGTGTATGCTCGACTGATCACCGACAATCACGACTACGGGATACACG                         CCTTCATTGTCCAGATTAGAAGTTTGGATGATCATAAGCCTTTGCCTGGAG
genomic: TCTAGTGTATGCTCGACTGATCACCGACAATCACGACTACGGGATCCACGgtatagtttg ... gtgtttccagCCTTCATTGTCCAGATTAGAAGTTTGGATGATCATAAGCCTTTGCCTGGAG
EST: gi|169063685|gb|FE471791.1|FE471791
EST:     TCTAGTGTATGCTCGACTGATCACCGACAATCACGACTACGGGATCCACG                         CCTTCATTGTCCAGATTAGAAGTTTGGATGATCATAAGCCTTTGCCTGGAG
genomic: TCTAGTGTATGCTCGACTGATCACCGACAATCACGACTACGGGATCCACGgtatagtttg ... gtgtttccagCCTTCATTGTCCAGATTAGAAGTTTGGATGATCATAAGCCTTTGCCTGGAG
EST: gi|169023125|gb|FE429177.1|FE429177
EST:     TCTAGTGTATGCTCGACTGATCACCGACAATCACGACTACGGGATACACG                         CCTTCATTGTCCAGATTAGAAGTTTGGATGATCATAAGCCTTTGCCTGGAG
genomic: TCTAGTGTATGCTCGACTGATCACCGACAATCACGACTACGGGATCCACGgtatagtttg ... gtgtttccagCCTTCATTGTCCAGATTAGAAGTTTGGATGATCATAAGCCTTTGCCTGGAG
EST: gi|169024575|gb|FE435683.1|FE435683
EST:     TCTAGTGTATGCTCGACTGATCACCGACAATCACGACTACGGGATACACG                         CCTTCATTGTCCAGATTAGAAGTTTGGATGATCATAAGCCTTTGCCTGGAG
genomic: TCTAGTGTATGCTCGACTGATCACCGACAATCACGACTACGGGATCCACGgtatagtttg ... gtgtttccagCCTTCATTGTCCAGATTAGAAGTTTGGATGATCATAAGCCTTTGCCTGGAG
EST: gi|169099715|gb|FE503112.1|FE503112
EST:     TCTAGTGTATGCTCGACTGATCACCGACAATCACGACTACGGGATACACG                         CCTTCATTGTCCAGATTAGAAGTTTGGATGATCATAAGCCTTTGCCTGGAG
genomic: TCTAGTGTATGCTCGACTGATCACCGACAATCACGACTACGGGATCCACGgtatagtttg ... gtgtttccagCCTTCATTGTCCAGATTAGAAGTTTGGATGATCATAAGCCTTTGCCTGGAG
EST: gi|169025869|gb|FE433168.1|FE433168
EST:     TCTAGTGTATGCTCGACTGATCACCGACAATCACGACTACGGGATACACG                         CCTTCATTGTCCAGATTAGAAGTTTGGATGATCATAAGCCTTTGCCTGGAG
genomic: TCTAGTGTATGCTCGACTGATCACCGACAATCACGACTACGGGATCCACGgtatagtttg ... gtgtttccagCCTTCATTGTCCAGATTAGAAGTTTGGATGATCATAAGCCTTTGCCTGGAG
EST: gi|169037439|gb|FE443333.1|FE443333
EST:     TCTAGTGTATGCTCGACTGATCACCGACAATCACGACTACGGGATCCACG                         CCTTCATTGTCCAGATTAGAAGTTTGGATGATCATAAGCCTTTGCCTGGAG
genomic: TCTAGTGTATGCTCGACTGATCACCGACAATCACGACTACGGGATCCACGgtatagtttg ... gtgtttccagCCTTCATTGTCCAGATTAGAAGTTTGGATGATCATAAGCCTTTGCCTGGAG

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: 22 (upstream exon), 34 (downstream exon)
Score: 4

TGGTGGCCTGGTGGTCTAGGCAAAGCCTCTACACACGCTCTAGTGTATGCTCGACTGATCACCGACAATCACGACTACGGGATCCACGgtatagtttg ... gtgtttccagCCTTCATTGTCCAGATTAGAAGTTTGGATGATCATAAGCCTTTGCCTGGAGTTACTGTTGCTGATATTGGTGTAAAGTTTGGAAATGCTGGTTACAACAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtatagtttgttttggtttctcttaagtgcttaacgtcgtgtttccagCCTTCATTGTCCAGATTAGAAGTTTGGATGATCATAAGCCTTTGCCTGGAGTTACTGTTGCTGATATTGGTGTAAAGTTTGGAAATGCTGGTTACAACAC
                                   gcttaac  putative branch site (score: 4)
                                              tgtttcc  putative PPT
        tatagttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatagtttgttttggtttctcttaagtgcttaacgtcgtgtttccagCCTTCATTGTCCAGATTAGAAGTTTGGATGATCATAAGCCTTTGCCTGGAGTTACTGTTGCTGATATTGGTGTAAAGTTTGGAAATGCTGGTTACAACAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG