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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgctggtattttgcagtgtacatgtaacacttctctttggctgcttgtgtttcagATCTATCCACCTATCAACGTGTTGCCATCGCTTTCTCGTTTGATGAAG

Basic information

species Selaginella moellendorffii
transcript EFJ11911
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: GRMZM2G181151_T01 (Zea mays), 3'ss of exon 11
----------------------------------------------------------------------------------------------------------------------------------gtttgtgct--ggtattttg-cagtgtacatgtaacact-tctctttggctgcttgtgtttcagATCTATCCACCTATCAACGTGTTGCCATCGCTTTCTCGTTTGATGAAG
                                                                                                                                  |||| |  |    ||  |||  ||  ||  |||     | |         |  || | |||||||| |||||||||||||| ||  ||||||| || ||||| |||||||||
gtgcttttctttgtcttttattcttgagttatctaatgttataccttcacatgcggcaggtctggaattatttataactaaatttagcatttcttattttctcatatttgatatagaatatgaagtatttgtttattttttactaccttgatagcttatctgtgttgatgtgatcacattttattttatttcagATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAG

upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: GRMZM2G181151_T03 (Zea mays), 3'ss of exon 11
----------------------------------------------------------------------------------------------------------------------------------gtttgtgct--ggtattttg-cagtgtacatgtaacact-tctctttggctgcttgtgtttcagATCTATCCACCTATCAACGTGTTGCCATCGCTTTCTCGTTTGATGAAG----------------------------------------------------
                                                                                                                                  |||| |  |    ||  |||  ||  ||  |||     | |         |  || | |||||||| |||||||||||||| ||  ||||||| || ||||| |||||||||                                                    
gtgcttttctttgtcttttattcttgagttatctaatgttataccttcacatgcggcaggtctggaattatttataactaaatttagcatttcttattttctcatatttgatatagaatatgaagtatttgtttattttttactaccttgatagcttatctgtgttgatgtgatcacattttattttatttcagATTTATCCACCTATCAATGTCCTGCCATCTCTATCTCGATTGATGAAGGTAAGATAAGTTTTCTGTATGTTTTCAGCATTTATGTTGAAGGTTAGTTGTA

upper sequence: EFJ11911 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: AT1G76030.1 (Arabidopsis thaliana), 3'ss of exon 11
-------------------------------------gttt--gtgctggtattttgcag-tgtacatgtaacacttctctttggctgcttgtgtttcagATCTATCCACCTATCAACGTGTTGCCATCGCTTTCTCGTTTGATGAAG
                                     ||||  ||  |  |||  | | | | |  ||| |    |  |  ||   | | ||     ||||| |||||||| ||||||||| | ||||| ||||||||||| ||||||
gtaataaataactaccgctgaggccctgatcttactggtttcagtaatattatgatccggctctgaatgaatgtatctttgtttcttccctgaaaaacagATATATCCACCCATCAACGTGCTTCCATCCCTTTCTCGTTTAATGAAG

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:     ACATTACTGAGGGACAGATTTATGTGGACCGTCAACTCTACAATCGTCAG                         ATCTATCCACCTATCAACGTGTTGCCATCGCTTTCTCGTTTGATGAAG
genomic: ACATTACTGAGGGACAGATTTATGTGGACCGTCAACTCTACAATCGTCAGgtttgtgctg ... tgtgtttcagATCTATCCACCTATCAACGTGTTGCCATCGCTTTCTCGTTTGATGAAG
EST: gi|169057425|gb|FE465729.1|FE465729
EST:     ACATTACTGAGGGACAGATTTATGTGGACCGTCAACTCTACAATCGTCAG                         ATCTATCCACCTATCAACGTGTTGCCATCGCTTTCTCGTTTGATGAAG
genomic: ACATTACTGAGGGACAGATTTATGTGGACCGTCAACTCTACAATCGTCAGgtttgtgctg ... tgtgtttcagATCTATCCACCTATCAACGTGTTGCCATCGCTTTCTCGTTTGATGAAG
EST: gi|169049332|gb|FE458243.1|FE458243
EST:     ACATTACTGAGGGACAGATTTATGTGGACCGTCAACTCTACAATCGTCAG                         ATCTATCCACCTATCAACGTGTTGCCATCGCTTTCTCGTTTGATGAAG
genomic: ACATTACTGAGGGACAGATTTATGTGGACCGTCAACTCTACAATCGTCAGgtttgtgctg ... tgtgtttcagATCTATCCACCTATCAACGTGTTGCCATCGCTTTCTCGTTTGATGAAG
EST: gi|169031673|gb|FE437474.1|FE437474
EST:     ACATTACTGAGGGACAGATTTATGTGGACCGTCAACTCTACAATCGTCAG                         ATCTATCCACCTATCAACGTGTTGCCATCGCTTTCTCGTTTGATGAAG
genomic: ACATTACTGAGGGACAGATTTATGTGGACCGTCAACTCTACAATCGTCAGgtttgtgctg ... tgtgtttcagATCTATCCACCTATCAACGTGTTGCCATCGCTTTCTCGTTTGATGAAG
EST: gi|169035380|gb|FE444318.1|FE444318
EST:     ACATTACTGAGGGACAGATTTATGTGGACCGTCAACTCTACAATCGTCAG                         ATCTATCCACCTATCAACGTGTTGCCATCGCTTTCTCGTTTGATGAAG
genomic: ACATTACTGAGGGACAGATTTATGTGGACCGTCAACTCTACAATCGTCAGgtttgtgctg ... tgtgtttcagATCTATCCACCTATCAACGTGTTGCCATCGCTTTCTCGTTTGATGAAG
EST: gi|169092668|gb|FE496262.1|FE496262
EST:     ACATTACTGAGGGACAGATTTATGTGGACCGTCAACTCTACAATCGTCAG                         ATCTATCCACCTATCAACGTGTTGCCATCGCTTTCTCGTTTGATGAAG
genomic: ACATTACTGAGGGACAGATTTATGTGGACCGTCAACTCTACAATCGTCAGgtttgtgctg ... tgtgtttcagATCTATCCACCTATCAACGTGTTGCCATCGCTTTCTCGTTTGATGAAG
EST: gi|169088664|gb|FE491524.1|FE491524
EST:     ACATTACTGAGGGACAGATTTATGTGGACCGTCAACTCTACAATCGTCAG                         ATCTATCCACCTATCAACGTGTTGCCATCGCTTTCTCGTTTGATGAAG
genomic: ACATTACTGAGGGACAGATTTATGTGGACCGTCAACTCTACAATCGTCAGgtttgtgctg ... tgtgtttcagATCTATCCACCTATCAACGTGTTGCCATCGCTTTCTCGTTTGATGAAG
EST: gi|169114882|gb|FE515831.1|FE515831
EST:     ACATTACTGAGGGACAGATTTATGTGGACCGTCAACTCTACAATCGTCAG                         ATCTATCCACCTATCAACGTGTTGCCATCGCTTTCTCGTTTGATGAAG
genomic: ACATTACTGAGGGACAGATTTATGTGGACCGTCAACTCTACAATCGTCAGgtttgtgctg ... tgtgtttcagATCTATCCACCTATCAACGTGTTGCCATCGCTTTCTCGTTTGATGAAG
EST: gi|169028054|gb|FE435932.1|FE435932
EST:     ACATTACTGAGGGACAGATTTATGTGGACCGTCAACTCTACAATCGTCAG                         ATCTATCCACCTATCAACGTGTTGCCATCGCTTTCTCGTTTGATGAAG
genomic: ACATTACTGAGGGACAGATTTATGTGGACCGTCAACTCTACAATCGTCAGgtttgtgctg ... tgtgtttcagATCTATCCACCTATCAACGTGTTGCCATCGCTTTCTCGTTTGATGAAG
EST: gi|169059084|gb|FE468229.1|FE468229
EST:     ACATTACTGAGGGACAGATTTATGTGGACCGTCAACTCTACAATCGTCAG                         ATCTATCCCCCTATCAACGTGTTGCCATCGCTTTCTCGTTTGATGAAG
genomic: ACATTACTGAGGGACAGATTTATGTGGACCGTCAACTCTACAATCGTCAGgtttgtgctg ... tgtgtttcagATCTATCCACCTATCAACGTGTTGCCATCGCTTTCTCGTTTGATGAAG

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: 41

ATATCACTCATCCGATTCCGGATCTCACTGGTTACATTACTGAGGGACAGATTTATGTGGACCGTCAACTCTACAATCGTCAGgtttgtgctg ... tgtgtttcagATCTATCCACCTATCAACGTGTTGCCATCGCTTTCTCGTTTGATGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctggtattttgcagtgtacatgtaacacttctctttggctgcttgtgtttcagATCTATCCACCTATCAACGTGTTGCCATCGCTTTCTCGTTTGATGAAG
                     atgtaac  putative branch site (score: 41)
      tatttt  TA-rich tract