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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGCGTACAGCGACTCGAGAGGTTTGCCAGGAGTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAGgtacttaagtagcttttgatctggcaaaaagcttgtcagaaactgcttcattttgtag

Basic information

species Selaginella moellendorffii
transcript EFJ30498
intron # 4
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|169066246|gb|FE475200.1|FE475200
EST:     GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAG                         TGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
genomic: GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAGgtacttaagt ... cattttgtagTGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
EST: gi|169046058|gb|FE453955.1|FE453955
EST:     GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAG                         TGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
genomic: GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAGgtacttaagt ... cattttgtagTGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
EST: gi|169054115|gb|FE462350.1|FE462350
EST:     GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAG                         TGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
genomic: GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAGgtacttaagt ... cattttgtagTGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
EST: gi|169059961|gb|FE467323.1|FE467323
EST:     GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAG                         TGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
genomic: GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAGgtacttaagt ... cattttgtagTGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
EST: gi|169056997|gb|FE466224.1|FE466224
EST:     GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAG                         TGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
genomic: GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAGgtacttaagt ... cattttgtagTGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
EST: gi|169100333|gb|FE501130.1|FE501130
EST:     GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAG                         TGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
genomic: GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAGgtacttaagt ... cattttgtagTGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
EST: gi|169035665|gb|FE445435.1|FE445435
EST:     GAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAG                         TGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
genomic: GAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAGgtacttaagt ... cattttgtagTGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
EST: gi|169098675|gb|FE497249.1|FE497249
EST:     GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAG                         TGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
genomic: GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAGgtacttaagt ... cattttgtagTGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
EST: gi|169078708|gb|FE486516.1|FE486516
EST:     GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAG                         TGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
genomic: GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAGgtacttaagt ... cattttgtagTGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
EST: gi|169111758|gb|FE511957.1|FE511957
EST:     GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAG                         TGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
genomic: GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAGgtacttaagt ... cattttgtagTGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
EST: gi|169067097|gb|FE474475.1|FE474475
EST:     GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAG                         TGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
genomic: GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAGgtacttaagt ... cattttgtagTGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
EST: gi|169045644|gb|FE452605.1|FE452605
EST:     GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAG                         TGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
genomic: GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAGgtacttaagt ... cattttgtagTGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
EST: gi|169042323|gb|FE452871.1|FE452871
EST:     GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAG                         TGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
genomic: GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAGgtacttaagt ... cattttgtagTGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
EST: gi|169057473|gb|FE465777.1|FE465777
EST:     GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAG                         TGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
genomic: GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAGgtacttaagt ... cattttgtagTGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
EST: gi|169036858|gb|FE444975.1|FE444975
EST:     GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAG                         TGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
genomic: GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAGgtacttaagt ... cattttgtagTGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
EST: gi|169097504|gb|FE497946.1|FE497946
EST:     GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAG                         TGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
genomic: GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAGgtacttaagt ... cattttgtagTGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
EST: gi|169106601|gb|FE504636.1|FE504636
EST:     GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAG                         TGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
genomic: GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAGgtacttaagt ... cattttgtagTGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
EST: gi|169065718|gb|FE476206.1|FE476206
EST:     GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAG                         TGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT
genomic: GTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAGgtacttaagt ... cattttgtagTGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGAT

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: 56

GTGCGTACAGCGACTCGAGAGGTTTGCCAGGAGTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAGgtacttaagt ... cattttgtagTGATCCGGAGCACATTTTTCTCACCGATGGTGCAAGCAAGGGAGTCATGATGATGCTAAACGCACTAATTCGAAACGAGAAAGACGGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTGCGTACAGCGACTCGAGAGGTTTGCCAGGAGTGAGGCAAGAGGTAGCAGAATTTATCCAAAAACGAGATGGATATCCAAGgtacttaagtagcttttgatctggcaaaaagcttgtcagaaactgcttcattttgtag

- - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA