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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttataggctctcttgagagtttgcatccataaatctcgtactttcacagGAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAAAGGAGTGGCGAAGTTTGATCTCCACAAGGATCCCGAGCTCTCCAAGGAT

Basic information

species Selaginella moellendorffii
transcript EFJ09546
intron # 11
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|169045510|gb|FE450703.1|FE450703
EST:     AAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAG                         GAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
genomic: AAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAGgttataggct ... actttcacagGAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
EST: gi|70669704|gb|DN838281.1|DN838281
EST:     AAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAG                         GAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
genomic: AAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAGgttataggct ... actttcacagGAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
EST: gi|169041728|gb|FE449299.1|FE449299
EST:     AAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAG                         GAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
genomic: AAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAGgttataggct ... actttcacagGAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
EST: gi|169115409|gb|FE516150.1|FE516150
EST:     AAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAG                         GAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
genomic: AAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAGgttataggct ... actttcacagGAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
EST: gi|169060191|gb|FE467553.1|FE467553
EST:     AAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAG                         GAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
genomic: AAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAGgttataggct ... actttcacagGAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
EST: gi|169054032|gb|FE461331.1|FE461331
EST:     AAGGGACCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAG                         GAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
genomic: AAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAGgttataggct ... actttcacagGAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
EST: gi|169106154|gb|FE507946.1|FE507946
EST:     CATCAACGAAAACTACATAGGAAG                         GAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
genomic: CATCAACGAAAACTACATAGGAAGgttataggct ... actttcacagGAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
EST: gi|169060192|gb|FE467554.1|FE467554
EST:     AAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAG                         GAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAN
genomic: AAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAGgttataggct ... actttcacagGAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
EST: gi|169052819|gb|FE461197.1|FE461197
EST:     AAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAG                         GAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATNCA-GTGAGGATC
genomic: AAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAGgttataggct ... actttcacagGAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGAT-CAAGTGAGGATC
EST: gi|169081597|gb|FE491251.1|FE491251
EST:     AAGGGACCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAG                         GAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
genomic: AAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAGgttataggct ... actttcacagGAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
EST: gi|169052818|gb|FE461196.1|FE461196
EST:     AAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAG                         GAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
genomic: AAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAGgttataggct ... actttcacagGAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
EST: gi|169099587|gb|FE502620.1|FE502620
EST:     AAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAG                         GAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
genomic: AAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAGgttataggct ... actttcacagGAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
EST: gi|169029568|gb|FE438929.1|FE438929
EST:     AAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAG                         GAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
genomic: AAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAGgttataggct ... actttcacagGAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
EST: gi|169096935|gb|FE497065.1|FE497065
EST:     AAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAG                         GAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
genomic: AAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAGgttataggct ... actttcacagGAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
EST: gi|169078720|gb|FE487555.1|FE487555
EST:     AAGGGACCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAG                         GAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
genomic: AAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAGgttataggct ... actttcacagGAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
EST: gi|169054031|gb|FE461330.1|FE461330
EST:     AAGGGACCAGCGGTGGAGTTTCCTCGCATCAACGAANACTACATAGGAAG                         GAAGCAACGTTACGTGTATGCTGCCGTTTTC-ACGATCAAGTGA
genomic: AAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAGgttataggct ... actttcacagGAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGA
EST: gi|169078771|gb|FE489621.1|FE489621
EST:     AAGGGACCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAG                         GAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
genomic: AAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAGgttataggct ... actttcacagGAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
EST: gi|169088168|gb|FE493394.1|FE493394
EST:     AAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAG                         GAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
genomic: AAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAGgttataggct ... actttcacagGAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
EST: gi|169075080|gb|FE481453.1|FE481453
EST:     AAGGGACCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAG                         GAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
genomic: AAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAGgttataggct ... actttcacagGAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
EST: gi|169088396|gb|FE495442.1|FE495442
EST:     AAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAG                         GAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA
genomic: AAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAGgttataggct ... actttcacagGAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAA

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), 15 (downstream exon)
Score: 140

AATTTCGGTTCAACATGAAGAGCGGTGCTGCTTTGCAGCGTCCACTCTCAAAGGGGCCAGCGGTGGAGTTTCCTCGCATCAACGAAAACTACATAGGAAGgttataggct ... actttcacagGAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAAAGGAGTGGCGAAGTTTGATCTCCACAAGGATCCCGAGCTCTCCAAGGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttataggctctcttgagagtttgcatccataaatctcgtactttcacagGAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAAAGGAGTGGCGAAGTTTGATCTCCACAAGGATCCCGAGCTCTCCAAGGAT
                                                tactttc  CT-rich tract
                                  ataaatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttataggctctcttgagagtttgcatccataaatctcgtactttcacagGAAGCAACGTTACGTGTATGCTGCCGTTTTCCACGATCAAGTGAGGATCAAAGGAGTGGCGAAGTTTGATCTCCACAAGGATCCCGAGCTCTCCAAGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG