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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgagatgtctgatcatcgagatcatctactgacttactcgcagATATCACTCATCCGATTCCGGATCTCACTGGTTACATTACTGAGGGACAGATTTATGTGGACCGTCAACTCTACAATCGTCAG

Basic information

species Selaginella moellendorffii
transcript EFJ11911
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GRMZM2G181151_T01 (Zea mays), 3'ss of exon 10
-------------------------------------------------------gtacgagatgtctgatcatcgagatcatctactgacttactcgcagATATCACTCATCCGATTCCGGATCTCACTGGTTACATTACTGAGGGACAGATTTATGTGGACCGTCAACTCTACAATCGTCAG
                                                          | || | |   ||     | ||  |   ||          |||||||||| || || | |||||| || ||||| |||||||||||||||||||| ||  | ||  | || ||| | ||  | |||
taataaaacacagctctcctgtgttttcgaggagaaaaaaattgttggccatttaacgcaag-tataccatggctaatattgtaatctactcctaaaacagATATCACACACCCAACTCCGGACCTTACTGGATACATTACTGAGGGACAGATATACATTGATAGGCAGCTCCATAACAGACAG

upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: AT1G20260.1 (Arabidopsis thaliana), 3'ss of exon 10
--------------------------------gtacgagatgtctgatcatcg-----agatcat-------ctactgacttactcgcagATATCACTCATCCGATTCCGGATCTCACTGGTTACATTACTGAGGGACAGATTTATGTGGACCGTCAACTCTACAATCGTCAG
                                 ||  | |||| |  | ||       || ||||       ||  | | | |  | ||||||||||||| || | ||||||||| |||||||||||||||||||| ||||| ||| | ||  | |||||  ||||  | |||
gtaattttttttatcgtttttggattccattcatatcaaatgttttttgattaaacaaagctcataatatttcttgttattaaaactcagATATCACTCACCCTACTCCGGATCTTACTGGTTACATTACTGAGGGTCAGATATATATTGATAGGCAACTTCACAACAGACAG

upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 10
----------------------------------------------gtacgagatgtctgatcatcgagatcatctactgacttactcg-cagATATCACTCATCCGATTCCGGATCTCACTGGTTACATTACTGAGGGACAGATTTATGTGGACCGTCAACTCTACAATCGTCAG
                                               |  || |  ||   || |     |  |    ||||  | |   |||||||||||||||| | ||||||||| ||||||||||||||||| || ||||| ||| | ||  | |||||  ||||  | |||
gtaaaatcatctttcttaagccaatccctagattctattttttatcttgagaaaactcaattcttactcgttgttgtttgacaaattgatcagATATCACTCATCCAACTCCGGATCTTACTGGTTACATTACTGAAGGTCAGATATATATCGATAGGCAACTTCACAACAGACAG

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|169093628|gb|FE492360.1|FE492360
EST:     GCGAATGGGATCAATCACTCAAATTCCCATTCTCAGTATGCCAAACGATG                         ATATCACTCATCCGATTCCGGATCTCACTGGTTACATTACTGAGGGACAGA
genomic: GCGAATGGGATCAATCACTCAAATTCCCATTCTCAGTATGCCAAACGATGgtacgagatg ... ttactcgcagATATCACTCATCCGATTCCGGATCTCACTGGTTACATTACTGAGGGACAGA
EST: gi|169057425|gb|FE465729.1|FE465729
EST:     ACGAATGGGATCAATCACTCAAATTCCCATTCTCAGTATGCCAAACGATG                         ATATCACTCATCCGATTCCTGATCTCACTGGTTACATTACTGAGGGACAGA
genomic: GCGAATGGGATCAATCACTCAAATTCCCATTCTCAGTATGCCAAACGATGgtacgagatg ... ttactcgcagATATCACTCATCCGATTCCGGATCTCACTGGTTACATTACTGAGGGACAGA
EST: gi|169049332|gb|FE458243.1|FE458243
EST:     ACGAATGGGATCAATCACTCAAATTCCCATTCTCAGTATGCCAAACGATG                         ATATCACTCATCCGATTCCTGATCTCACTGGTTACATTACTGAGGGACAGA
genomic: GCGAATGGGATCAATCACTCAAATTCCCATTCTCAGTATGCCAAACGATGgtacgagatg ... ttactcgcagATATCACTCATCCGATTCCGGATCTCACTGGTTACATTACTGAGGGACAGA
EST: gi|169035380|gb|FE444318.1|FE444318
EST:     GCGAATGGGATCAATCACTCAAATTCCCATTCTCAGTATGCCAAACGATG                         ATATCACTCATCCGATTCCGGATCTCACTGGTTACATTACTGAGGGACAGA
genomic: GCGAATGGGATCAATCACTCAAATTCCCATTCTCAGTATGCCAAACGATGgtacgagatg ... ttactcgcagATATCACTCATCCGATTCCGGATCTCACTGGTTACATTACTGAGGGACAGA
EST: gi|169092668|gb|FE496262.1|FE496262
EST:     GCGAATGGGATCAATCACTCAAATTCCCATTCTCAGTATGCCAAACGATG                         ATATCACTCATCCGATTCCGGATCTCACTGGTTACATTACTGAGGGACAGA
genomic: GCGAATGGGATCAATCACTCAAATTCCCATTCTCAGTATGCCAAACGATGgtacgagatg ... ttactcgcagATATCACTCATCCGATTCCGGATCTCACTGGTTACATTACTGAGGGACAGA
EST: gi|169049517|gb|FE458740.1|FE458740
EST:     GCGAATGGGATCAATCACTCAAATTCCCATTCTCAGTATGCCAAACGATG                         ATATCACTCATCCGATTCCGGATCTCACTGGTTACATTACTGAGGGA
genomic: GCGAATGGGATCAATCACTCAAATTCCCATTCTCAGTATGCCAAACGATGgtacgagatg ... ttactcgcagATATCACTCATCCGATTCCGGATCTCACTGGTTACATTACTGAGGGA
EST: gi|169088664|gb|FE491524.1|FE491524
EST:     ACGAATGGGATCAATCACTCAAATTCCCATTCTCAGTATGCCAAACGATG                         ATATCACTCATCCGATTCCTGATCTCACTGGTTACATTACTGAGGGACAGA
genomic: GCGAATGGGATCAATCACTCAAATTCCCATTCTCAGTATGCCAAACGATGgtacgagatg ... ttactcgcagATATCACTCATCCGATTCCGGATCTCACTGGTTACATTACTGAGGGACAGA
EST: gi|169114882|gb|FE515831.1|FE515831
EST:     GCGAATGGGATCAATCACTCAAATTCCCATTCTCAGTATGCCAAACGATG                         ATATCACTCATCCGATTCCGGATCTCACTGGTTACATTACTGAGGGACAGA
genomic: GCGAATGGGATCAATCACTCAAATTCCCATTCTCAGTATGCCAAACGATGgtacgagatg ... ttactcgcagATATCACTCATCCGATTCCGGATCTCACTGGTTACATTACTGAGGGACAGA
EST: gi|169028054|gb|FE435932.1|FE435932
EST:     ACGAATGGGATCAATCACTCAAATTCCCATTCTCAGTATGCCAAACGATG                         ATATCACTCATCCGATTCCTGATCTCACTGGTTACATTACTGAGGGACAGA
genomic: GCGAATGGGATCAATCACTCAAATTCCCATTCTCAGTATGCCAAACGATGgtacgagatg ... ttactcgcagATATCACTCATCCGATTCCGGATCTCACTGGTTACATTACTGAGGGACAGA
EST: gi|169059084|gb|FE468229.1|FE468229
EST:     CAGTATGCCAAACGATG                         ATATCACTCATCCGATTCCGGATCTCACTGGTTACATTACTGAGGGACAGA
genomic: CAGTATGCCAAACGATGgtacgagatg ... ttactcgcagATATCACTCATCCGATTCCGGATCTCACTGGTTACATTACTGAGGGACAGA

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: 17

ATGTATACAGATTTGGCAACAATTTACGAGCGTGCTGGACGAATTGAAGGGCGAATGGGATCAATCACTCAAATTCCCATTCTCAGTATGCCAAACGATGgtacgagatg ... ttactcgcagATATCACTCATCCGATTCCGGATCTCACTGGTTACATTACTGAGGGACAGATTTATGTGGACCGTCAACTCTACAATCGTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtacgagatgtctgatcatcgagatcatctactgacttactcgcagATATCACTCATCCGATTCCGGATCTCACTGGTTACATTACTGAGGGACAGATTTATGTGGACCGTCAACTCTACAATCGTCAG
                                                    cttactc  CT-rich tract