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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaatttcgctatacatagaaggaaactttggatctgttttaccag

Basic information

species Selaginella moellendorffii
transcript EFJ32604
intron # 3
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|169023493|gb|FE431404.1|FE431404
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169041587|gb|FE449548.1|FE449548
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169036059|gb|FE446765.1|FE446765
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169094385|gb|FE495585.1|FE495585
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169087333|gb|FE491746.1|FE491746
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169053831|gb|FE460922.1|FE460922
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169051134|gb|FE458681.1|FE458681
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169019270|gb|FE428183.1|FE428183
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169096116|gb|FE500276.1|FE500276
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169082303|gb|FE488046.1|FE488046
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169087154|gb|FE493101.1|FE493101
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169025097|gb|FE434697.1|FE434697
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169077299|gb|FE485601.1|FE485601
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169036890|gb|FE443850.1|FE443850
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169080654|gb|FE487175.1|FE487175
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169075645|gb|FE482031.1|FE482031
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169062067|gb|FE469152.1|FE469152
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|70670986|gb|DN839563.1|DN839563
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169074936|gb|FE483818.1|FE483818
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169088141|gb|FE493380.1|FE493380
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169053051|gb|FE462014.1|FE462014
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169061498|gb|FE469597.1|FE469597
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169032798|gb|FE438306.1|FE438306
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169019625|gb|FE427974.1|FE427974
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169097028|gb|FE498419.1|FE498419
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169047243|gb|FE456492.1|FE456492
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169088635|gb|FE491521.1|FE491521
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169087281|gb|FE491694.1|FE491694
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169030300|gb|FE440025.1|FE440025
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169102882|gb|FE505247.1|FE505247
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169035576|gb|FE445346.1|FE445346
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169094800|gb|FE492951.1|FE492951
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169088706|gb|FE491540.1|FE491540
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169087447|gb|FE492224.1|FE492224
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169105943|gb|FE504303.1|FE504303
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
EST: gi|169075799|gb|FE482796.1|FE482796
EST:     ATCCGGAAATCGCTGATATAATTGAGCTGGNNNNNNNTCGTCAATGGAAG                         GGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA
genomic: ATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAA

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: 119

TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaat ... gttttaccagGGACTGGAGCTAATTCCCTCGGAGAATTTTACTTCAACTTCAGTCATGCAAGCAGTGGGATCCATCATGACCAACAAGTATAGCGAGGGCTATCCAGGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGCCAAAGCAGCTCAACGCTCCACTTGGCGACGTTGATCCGGAAATCGCTGATATAATTGAGCTGGAAAAAAATCGTCAATGGAAGgttggtaaatttcgctatacatagaaggaaactttggatctgttttaccag

- - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG