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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTGCCAAGGCAATAGCTCGAGTGTCAGGCGGGATCTACGTCGTGACTGCCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAGgtaataaaacaaaactttgccttgagattctacaactgactgggtgattatccgagcag

Basic information

species Selaginella moellendorffii
transcript EFJ07706
intron # 7
splice site 5'
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|169065499|gb|FE475857.1|FE475857
EST:     CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAG                         GCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
genomic: CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAGgtaataaaac ... atccgagcagGCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
EST: gi|169070025|gb|FE476494.1|FE476494
EST:     CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAG                         GCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
genomic: CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAGgtaataaaac ... atccgagcagGCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
EST: gi|169057396|gb|FE465700.1|FE465700
EST:     CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAG                         GCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
genomic: CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAGgtaataaaac ... atccgagcagGCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
EST: gi|169019341|gb|FE427651.1|FE427651
EST:     CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGNGTGTCCCAG                         GCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
genomic: CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAGgtaataaaac ... atccgagcagGCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
EST: gi|169059367|gb|FE467509.1|FE467509
EST:     CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAG                         GCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
genomic: CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAGgtaataaaac ... atccgagcagGCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
EST: gi|169029314|gb|FE439442.1|FE439442
EST:     CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGNGTGTCCCAG                         GCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
genomic: CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAGgtaataaaac ... atccgagcagGCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
EST: gi|169070026|gb|FE476495.1|FE476495
EST:     CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAG                         GCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
genomic: CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAGgtaataaaac ... atccgagcagGCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
EST: gi|169019340|gb|FE427650.1|FE427650
EST:     CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAG                         GCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
genomic: CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAGgtaataaaac ... atccgagcagGCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
EST: gi|169050567|gb|FE459635.1|FE459635
EST:     CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAG                         GCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
genomic: CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAGgtaataaaac ... atccgagcagGCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
EST: gi|169067246|gb|FE473051.1|FE473051
EST:     CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAG                         GCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
genomic: CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAGgtaataaaac ... atccgagcagGCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
EST: gi|169038570|gb|FE446895.1|FE446895
EST:     CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAG                         GCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
genomic: CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAGgtaataaaac ... atccgagcagGCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
EST: gi|169114973|gb|FE516338.1|FE516338
EST:     CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAG                         GCTAGCTTCAAACCTCTAGGCATTACCATA
genomic: CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAGgtaataaaac ... atccgagcagGCTAGCTTCAAACCTCTAGGCATTACCATA
EST: gi|169044934|gb|FE450856.1|FE450856
EST:     CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAG                         GCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
genomic: CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAGgtaataaaac ... atccgagcagGCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
EST: gi|169029313|gb|FE439441.1|FE439441
EST:     CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAG                         GCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
genomic: CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAGgtaataaaac ... atccgagcagGCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
EST: gi|169102150|gb|FE505776.1|FE505776
EST:     CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAG                         GCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
genomic: CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAGgtaataaaac ... atccgagcagGCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
EST: gi|169036582|gb|FE444140.1|FE444140
EST:     AGGAGCTATGATCGCATCTTGGGTGTCCCAG                         GCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
genomic: AGGAGCTATGATCGCATCTTGGGTGTCCCAGgtaataaaac ... atccgagcagGCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
EST: gi|169111537|gb|FE510397.1|FE510397
EST:     CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAG                         GCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
genomic: CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAGgtaataaaac ... atccgagcagGCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
EST: gi|169035367|gb|FE444305.1|FE444305
EST:     CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAG                         GCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
genomic: CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAGgtaataaaac ... atccgagcagGCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
EST: gi|169114972|gb|FE516337.1|FE516337
EST:     CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAG                         GCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
genomic: CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAGgtaataaaac ... atccgagcagGCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
EST: gi|169113900|gb|FE515955.1|FE515955
EST:     CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAG                         GCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
genomic: CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAGgtaataaaac ... atccgagcagGCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
EST: gi|169099896|gb|FE503384.1|FE503384
EST:     CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAG                         GCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
genomic: CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAGgtaataaaac ... atccgagcagGCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
EST: gi|169030941|gb|FE436844.1|FE436844
EST:     CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAG                         GCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
genomic: CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAGgtaataaaac ... atccgagcagGCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
EST: gi|169061129|gb|FE470135.1|FE470135
EST:     CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAG                         GCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT
genomic: CCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAGgtaataaaac ... atccgagcagGCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCT

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: 33 (upstream exon), 33 (downstream exon)
Score: 9

TGTTGCCAAGGCAATAGCTCGAGTGTCAGGCGGGATCTACGTCGTGACTGCCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAGgtaataaaac ... atccgagcagGCTAGCTTCAAACCTCTAGGCATTACCATAGCAGTCGCCAAAGACAGAGCTATCGAGTCTCTCATGCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTGCCAAGGCAATAGCTCGAGTGTCAGGCGGGATCTACGTCGTGACTGCCTTTAAAGGCTCAACAAAAGGAGCTATGATCGCATCTTGGGTGTCCCAGgtaataaaacaaaactttgccttgagattctacaactgactgggtgattatccgagcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT