Skip to another splice site:
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 5'  3'   		2  
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGCGTTTGCAGGTAGAGAGCCGCCACAATGTCTGCGCGCAAGAAGATCCAGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAGgtttgggagagatctagtgaggcattgcatgaagtaagtcccttttgtttttgctcag

Basic information

species Selaginella moellendorffii
transcript EFJ26379
intron # 1
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|169066322|gb|FE472998.1|FE472998
EST:     AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAG                         GCGCTATCAGAGCTTGAGGGCGCTAATCAGGAGCTCCGAGGCGACTTGCGC
genomic: AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAGgtttgggaga ... ttttgctcagGCGCTATCAGAGCTTGAGGGCGCTAATCAGGAGCTCCGAGGCGACTTGCGC
EST: gi|169096025|gb|FE497338.1|FE497338
EST:     AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAG                         GCGCTATCAGAGCTTGAGGGCGCCAATCAGGAGCTCCGAGGCGACTTGCGC
genomic: AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAGgtttgggaga ... ttttgctcagGCGCTATCAGAGCTTGAGGGCGCTAATCAGGAGCTCCGAGGCGACTTGCGC
EST: gi|169066952|gb|FE475955.1|FE475955
EST:     AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAG                         GCGCTATCAGAGCTTGAGGGCGCTAATCAGGAGCTCCGAGGCGACTTGCGC
genomic: AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAGgtttgggaga ... ttttgctcagGCGCTATCAGAGCTTGAGGGCGCTAATCAGGAGCTCCGAGGCGACTTGCGC
EST: gi|169034273|gb|FE445113.1|FE445113
EST:     AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAG                         GCGCTATCAGAGCTTGAGGGCGCCAATCAGGAGCTCCGAGGCGACTTGCGC
genomic: AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAGgtttgggaga ... ttttgctcagGCGCTATCAGAGCTTGAGGGCGCTAATCAGGAGCTCCGAGGCGACTTGCGC
EST: gi|169034272|gb|FE445112.1|FE445112
EST:     AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAG                         GCGCTATCAGAGCTTGAGGGCGCCAATCAGGAGCTCCGAGGCGACTTGCGC
genomic: AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAGgtttgggaga ... ttttgctcagGCGCTATCAGAGCTTGAGGGCGCTAATCAGGAGCTCCGAGGCGACTTGCGC
EST: gi|169078408|gb|FE488283.1|FE488283
EST:     AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAG                         GCGCTATCAGAGCTTGAGGGCGCCAATCAGGAGCTCCGAGGCGACTTGCGC
genomic: AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAGgtttgggaga ... ttttgctcagGCGCTATCAGAGCTTGAGGGCGCTAATCAGGAGCTCCGAGGCGACTTGCGC
EST: gi|169062870|gb|FE472373.1|FE472373
EST:     AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAG                         GCGCTATCAGAGCTTGAGGGCGCCAATCAGGAGCTCCGAGGCGACTTGCGC
genomic: AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAGgtttgggaga ... ttttgctcagGCGCTATCAGAGCTTGAGGGCGCTAATCAGGAGCTCCGAGGCGACTTGCGC
EST: gi|169037033|gb|FE442680.1|FE442680
EST:     AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAG                         GCGCTATCAGAGCTTGAGGGCGCCAATCAGGAGCTCCGAGGCGACTTGCGC
genomic: AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAGgtttgggaga ... ttttgctcagGCGCTATCAGAGCTTGAGGGCGCTAATCAGGAGCTCCGAGGCGACTTGCGC
EST: gi|169093160|gb|FE494193.1|FE494193
EST:     AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAG                         GCGCTATCAGAGCTTGAGGGCGCCAATCAGGAGCTCCGAGGCGACTTGCGC
genomic: AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAGgtttgggaga ... ttttgctcagGCGCTATCAGAGCTTGAGGGCGCTAATCAGGAGCTCCGAGGCGACTTGCGC
EST: gi|169109375|gb|FE514099.1|FE514099
EST:     AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAG                         GCGCTATCAGAGCTTGAGGGCGCTAATCAGGAGCTCCGAGGCGACTTGCGC
genomic: AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAGgtttgggaga ... ttttgctcagGCGCTATCAGAGCTTGAGGGCGCTAATCAGGAGCTCCGAGGCGACTTGCGC
EST: gi|70670008|gb|DN838585.1|DN838585
EST:     AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAG                         GCGCTATCAGAGCTTGAGGGCGCCAATCAGGAGCTCCGAGGCGACTTGCGC
genomic: AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAGgtttgggaga ... ttttgctcagGCGCTATCAGAGCTTGAGGGCGCTAATCAGGAGCTCCGAGGCGACTTGCGC
EST: gi|169096024|gb|FE497337.1|FE497337
EST:     AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAG                         GCGCTATCAGAGCTTGAGGGCGCCAATCAGGAGCTCCGAGGCGACTTGCGC
genomic: AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAGgtttgggaga ... ttttgctcagGCGCTATCAGAGCTTGAGGGCGCTAATCAGGAGCTCCGAGGCGACTTGCGC
EST: gi|169031995|gb|FE440175.1|FE440175
EST:     AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAG                         GCGCTATCAGAGCTTGAGGGCGCTAATCAGGAGCTCCGAGGCGACTTGCGC
genomic: AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAGgtttgggaga ... ttttgctcagGCGCTATCAGAGCTTGAGGGCGCTAATCAGGAGCTCCGAGGCGACTTGCGC
EST: gi|169106336|gb|FE506256.1|FE506256
EST:     AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAG                         GCGCTATCAGAGCTTGAGGGCGCTAATCAGGAGCTCCGAGGCGACTTGCGC
genomic: AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAGgtttgggaga ... ttttgctcagGCGCTATCAGAGCTTGAGGGCGCTAATCAGGAGCTCCGAGGCGACTTGCGC
EST: gi|169069286|gb|FE480045.1|FE480045
EST:     GGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAG                         GCGCTATCAGAGCTTGAGGGCGCCAATCAGGAGCTCCGAGGCGACTTGCGC
genomic: GGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAGgtttgggaga ... ttttgctcagGCGCTATCAGAGCTTGAGGGCGCTAATCAGGAGCTCCGAGGCGACTTGCGC
EST: gi|169045824|gb|FE451719.1|FE451719
EST:     AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAG                         GCGCTATCAGAGCTTGAGGGCGCCAATCAGGAGCTCCGAGGCGACTTGCGC
genomic: AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAGgtttgggaga ... ttttgctcagGCGCTATCAGAGCTTGAGGGCGCTAATCAGGAGCTCCGAGGCGACTTGCGC
EST: gi|169046522|gb|FE457461.1|FE457461
EST:     AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAG                         GCGCTATCAGAGCTTGAGGGCGCTAATCAGGAGCTCCGAGGCGACTTGCGC
genomic: AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAGgtttgggaga ... ttttgctcagGCGCTATCAGAGCTTGAGGGCGCTAATCAGGAGCTCCGAGGCGACTTGCGC
EST: gi|169073723|gb|FE483983.1|FE483983
EST:     AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAG                         GCGCTATCAGAGCTTGAGGGCGCCAATCAGGAGCTCCGAGGCGACTTGCGC
genomic: AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAGgtttgggaga ... ttttgctcagGCGCTATCAGAGCTTGAGGGCGCTAATCAGGAGCTCCGAGGCGACTTGCGC
EST: gi|169064575|gb|FE471306.1|FE471306
EST:     AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAG                         GCGCTATCAGAGCTTGAGGGCGCTAATCAGGAGCTCCGAGGCGACTTGCGC
genomic: AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAGgtttgggaga ... ttttgctcagGCGCTATCAGAGCTTGAGGGCGCTAATCAGGAGCTCCGAGGCGACTTGCGC
EST: gi|169036394|gb|FE443484.1|FE443484
EST:     AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAG                         GCGCTATCAGAGCTTGAGGGCGCTAATCAGGAGCTCCGAGGCGACTTGCGC
genomic: AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAGgtttgggaga ... ttttgctcagGCGCTATCAGAGCTTGAGGGCGCTAATCAGGAGCTCCGAGGCGACTTGCGC
EST: gi|169066953|gb|FE475956.1|FE475956
EST:     AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAG                         GCGCTATCAGAGCTTGAGGGCGCTAATCAGGAGCTCCGAGGCGACTTGCGC
genomic: AGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAGgtttgggaga ... ttttgctcagGCGCTATCAGAGCTTGAGGGCGCTAATCAGGAGCTCCGAGGCGACTTGCGC

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: 80

TCGCGTTTGCAGGTAGAGAGCCGCCACAATGTCTGCGCGCAAGAAGATCCAGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAGgtttgggaga ... ttttgctcagGCGCTATCAGAGCTTGAGGGCGCTAATCAGGAGCTCCGAGGCGACTTGCGCGACCTCTCTATCAATTCAGCAAA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGCGTTTGCAGGTAGAGAGCCGCCACAATGTCTGCGCGCAAGAAGATCCAGAAGGAGGAGGGCCAGGAGCCGGATGCTTTCGAGCTCACGGTTGCGCAGgtttgggagagatctagtgaggcattgcatgaagtaagtcccttttgtttttgctcag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA