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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggcaacctttggctttagaagctaagcggcattcttctttattttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCATATAGGCTGGATGAATCTACAGGTTTTATTGACTACGATCAG

Basic information

species Selaginella moellendorffii
transcript EFJ32604
intron # 6
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|169023493|gb|FE431404.1|FE431404
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
EST: gi|169036059|gb|FE446765.1|FE446765
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
EST: gi|169094385|gb|FE495585.1|FE495585
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
EST: gi|169087333|gb|FE491746.1|FE491746
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
EST: gi|169053831|gb|FE460922.1|FE460922
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
EST: gi|169051134|gb|FE458681.1|FE458681
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
EST: gi|169048578|gb|FE454447.1|FE454447
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
EST: gi|169019270|gb|FE428183.1|FE428183
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
EST: gi|169096116|gb|FE500276.1|FE500276
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
EST: gi|169082303|gb|FE488046.1|FE488046
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
EST: gi|169087154|gb|FE493101.1|FE493101
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
EST: gi|169098871|gb|FE502268.1|FE502268
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
EST: gi|169025097|gb|FE434697.1|FE434697
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
EST: gi|169077299|gb|FE485601.1|FE485601
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
EST: gi|169080654|gb|FE487175.1|FE487175
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
EST: gi|169075645|gb|FE482031.1|FE482031
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
EST: gi|169062067|gb|FE469152.1|FE469152
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
EST: gi|70670986|gb|DN839563.1|DN839563
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
EST: gi|169074936|gb|FE483818.1|FE483818
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGC
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGC
EST: gi|169088141|gb|FE493380.1|FE493380
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
EST: gi|169053051|gb|FE462014.1|FE462014
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
EST: gi|169061498|gb|FE469597.1|FE469597
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
EST: gi|169032798|gb|FE438306.1|FE438306
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
EST: gi|169019625|gb|FE427974.1|FE427974
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
EST: gi|169097028|gb|FE498419.1|FE498419
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
EST: gi|169047243|gb|FE456492.1|FE456492
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
EST: gi|169088635|gb|FE491521.1|FE491521
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
EST: gi|169087281|gb|FE491694.1|FE491694
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
EST: gi|169030300|gb|FE440025.1|FE440025
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
EST: gi|169102882|gb|FE505247.1|FE505247
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
EST: gi|169035576|gb|FE445346.1|FE445346
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
EST: gi|169094800|gb|FE492951.1|FE492951
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTNCA-TCTTTTTTGAAACGATGCC
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTT-CAATCTTTTTTGAAACGATGCC
EST: gi|169088706|gb|FE491540.1|FE491540
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGANAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
EST: gi|169087447|gb|FE492224.1|FE492224
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
EST: gi|169105943|gb|FE504303.1|FE504303
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
EST: gi|169075799|gb|FE482796.1|FE482796
EST:     TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAG                         ACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA
genomic: TTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCA

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: 158

TCCAGCAAACTTTCAAGTGTATACAGCTTTGCTTAAACCACACGAAAGAATTATGGCTCTTGATTTACCTCACGGAGGCCATTTATCTCATGGTTATCAGgtaggcaacc ... ttttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCATATAGGCTGGATGAATCTACAGGTTTTATTGACTACGATCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaggcaacctttggctttagaagctaagcggcattcttctttattttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCATATAGGCTGGATGAATCTACAGGTTTTATTGACTACGATCAG
                                 cattcttctttatttt  CT-rich tract
                                  attcttctttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggcaacctttggctttagaagctaagcggcattcttctttattttgcacagACAGATACTAAGAAAATCTCGGCTGTTTCAATCTTTTTTGAAACGATGCCATATAGGCTGGATGAATCTACAGGTTTTATTGACTACGATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA