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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtataggaaaaatcaaaaagttttctagattgaattgatggtttttgtgaccagATTTTTGCAAAGAAGGGCATCATTGTCCTGCCCGACATCCTTGCAAACTCAGGCGGTGTCACAGTGAGCTACTTCGAATGGGTACAG

Basic information

species Selaginella moellendorffii
transcript EFJ06181
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ06181 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: LOC_Os03g58040.1 (Oryza sativa), 3'ss of exon 8
---------------------------------------gtataggaaaaatcaaaaagttttctagattgaattg---atggtttttgtgaccagATTTTTGCAAAGAAGGGCATCATTGTCCTGCCCGACATCCTTGCAAACTCAGGCGGTGTCACAGTGAGCTACTTCGAATGGGTACAG
                                         |     |||||  |  | || |||  | ||  ||     ||  ||   |   |||||  |  | ||||| ||| |  |  | || || |||||||| || ||||| || ||||||||||||||||||||||| ||||| |||
gcaagcacatctgacagtatctggcagacaaataccccaacagcaacaaaatgtaccatttgtctgaaatgctttctctctgaattccttctgcagATCCTGTCCAAGAAAGGCGTTCTCATTCTTCCAGACATCCTCGCGAACTCCGGTGGTGTCACAGTGAGCTACTTCGAGTGGGTTCAG

upper sequence: EFJ06181 (Selaginella moellendorffii), 3'ss of exon 7
lower sequence: GRMZM2G178415_T05 (Zea mays), 3'ss of exon 8
-----------gtataggaaaaatcaa-----------aaagttttctagattgaattg-atggt-ttttgtgaccagATTTTTGCAAAGAAGGGCATCATTGTCCTGCCCGACATCCTTGCAAACTCAGGCGGTGTCACAGTGAGCTACTTCGAATGGGTACAG
           |   |  | ||| | |           || |||||||         || ||    ||   |  ||||||  |  ||||||| ||| || |  |||| |||||||| || || ||||| || || |||||||||||||||||||| |||||||| 
gcaagcccgtagctcaaaacaaaccgactgctttctgcaatgttttctgatcccctctgtatcccgttccatccccagATCCTGTCAAAGAAAGGCGTCCTCATCCTCCCCGACATACTGGCCAACTCTGGTGGCGTCACAGTGAGCTACTTCGAGTGGGTACAA
















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|169073033|gb|FE483683.1|FE483683
EST:     GATTCATCGTAGAAGCAGCAAACCATCCCACTGAGCCCGAGGCGGATGAG                         ATTTTTGCAAAGAAGGGCATCATTGTGCTGCCCGACATCCTTGCAAACTCA
genomic: GATTCATCGTAGAAGCAGCAAACCATCCCACTGAGCCCGAGGCGGATGAGgtataggaaa ... ttgtgaccagATTTTTGCAAAGAAGGGCATCATTGTCCTGCCCGACATCCTTGCAAACTCA
EST: gi|169029682|gb|FE437353.1|FE437353
EST:     GATTCATCGTAGAAGCAGCAAACCATCCCACTGAGCCCGAGGCGGATGAG                         ATTTTTGCAAAGAAGGGCATCATTGTGCTGCCCGACATCCTTGCAAACTCA
genomic: GATTCATCGTAGAAGCAGCAAACCATCCCACTGAGCCCGAGGCGGATGAGgtataggaaa ... ttgtgaccagATTTTTGCAAAGAAGGGCATCATTGTCCTGCCCGACATCCTTGCAAACTCA
EST: gi|169020858|gb|FE431962.1|FE431962
EST:     GCAACCCATCCCACTGAGCCCGAGGCGGATGAG                         ATTTTTGCAAAGAAGGGCATCATTGTGCTGCCCGACATCCTTGCAAACTCA
genomic: GCAAACCATCCCACTGAGCCCGAGGCGGATGAGgtataggaaa ... ttgtgaccagATTTTTGCAAAGAAGGGCATCATTGTCCTGCCCGACATCCTTGCAAACTCA
EST: gi|169114202|gb|FE515737.1|FE515737
EST:     GATTCATCGTAGAAGCAGCAAACCATCCCACTGAGCCCGAGGCGGATGAG                         ATTTTTGCAAAGAAGGGCATCATTGTCCTGCCCGACATCCTTGCAAACTCA
genomic: GATTCATCGTAGAAGCAGCAAACCATCCCACTGAGCCCGAGGCGGATGAGgtataggaaa ... ttgtgaccagATTTTTGCAAAGAAGGGCATCATTGTCCTGCCCGACATCCTTGCAAACTCA
EST: gi|169034524|gb|FE444571.1|FE444571
EST:     GATTCATCGTAGAAGCAGCAAACCATCCCACTGAGCCCGAGGCGGATGAG                         ATTTTTGCAAAGAAGGGCATCATTGTGCTGCCCGACATCCTTGCAAACTCA
genomic: GATTCATCGTAGAAGCAGCAAACCATCCCACTGAGCCCGAGGCGGATGAGgtataggaaa ... ttgtgaccagATTTTTGCAAAGAAGGGCATCATTGTCCTGCCCGACATCCTTGCAAACTCA
EST: gi|169114203|gb|FE515738.1|FE515738
EST:     GATTCATCGTAGAAGCAGCAAACCATCCCACTGAGCCCGAGGCGGATGAG                         ATTTTTGCAAAGAAGGGCATCATTGTCCTGCCCGACATCCTTGCAAACTCA
genomic: GATTCATCGTAGAAGCAGCAAACCATCCCACTGAGCCCGAGGCGGATGAGgtataggaaa ... ttgtgaccagATTTTTGCAAAGAAGGGCATCATTGTCCTGCCCGACATCCTTGCAAACTCA
EST: gi|169046220|gb|FE456379.1|FE456379
EST:     GATTCATCGTAGAAGCAGCAAACCATCCCACTGAGCCCGAGGCGGATGAG                         ATTTTTGCAAAGAAGGGCATCATTGTGCTGCCCGACATCCTTGCAAACTCA
genomic: GATTCATCGTAGAAGCAGCAAACCATCCCACTGAGCCCGAGGCGGATGAGgtataggaaa ... ttgtgaccagATTTTTGCAAAGAAGGGCATCATTGTCCTGCCCGACATCCTTGCAAACTCA
EST: gi|169067884|gb|FE474755.1|FE474755
EST:     GATTCATCGTAGAAGCAGCAAACCATCCCACTGAGCCCGAGGCGGATGAG                         ATTTTTGCAAAGAAGGGCATCATTGTCCTGCCCGACATCCTTGCAAACTCA
genomic: GATTCATCGTAGAAGCAGCAAACCATCCCACTGAGCCCGAGGCGGATGAGgtataggaaa ... ttgtgaccagATTTTTGCAAAGAAGGGCATCATTGTCCTGCCCGACATCCTTGCAAACTCA
EST: gi|169022697|gb|FE429724.1|FE429724
EST:     GATTCATCGTAGAAGCAGCAAACCATCCCACTGAGCCCGAGGCGGATGAG                         ATTTTTGCAAAGAAGGGCATCATTGTCCTGCCCGACATCCTTGCAAACTCA
genomic: GATTCATCGTAGAAGCAGCAAACCATCCCACTGAGCCCGAGGCGGATGAGgtataggaaa ... ttgtgaccagATTTTTGCAAAGAAGGGCATCATTGTCCTGCCCGACATCCTTGCAAACTCA
EST: gi|169030555|gb|FE437888.1|FE437888
EST:     GATTCATCGTAGAAGCAGCAAACCATCCCACTGAGCCCGAGGCGGATGAG                         ATTTTTGCAAAGAAGGGCATCATTGTCCTGCCCGACATCCTTGCAAACTCA
genomic: GATTCATCGTAGAAGCAGCAAACCATCCCACTGAGCCCGAGGCGGATGAGgtataggaaa ... ttgtgaccagATTTTTGCAAAGAAGGGCATCATTGTCCTGCCCGACATCCTTGCAAACTCA
EST: gi|169054883|gb|FE463487.1|FE463487
EST:     GATTCATCGTAGAAGCAGCAAACCATCCCACTGAGCCCGAGGCGGATGAG                         ATTTTTGCAAAGAAGGGCATCATTGTGCTGCCCGACATCCTTGCAAACTCA
genomic: GATTCATCGTAGAAGCAGCAAACCATCCCACTGAGCCCGAGGCGGATGAGgtataggaaa ... ttgtgaccagATTTTTGCAAAGAAGGGCATCATTGTCCTGCCCGACATCCTTGCAAACTCA

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: 59

GGAGAATGCAAAGGATGTCAAGGCACGATTCATCGTAGAAGCAGCAAACCATCCCACTGAGCCCGAGGCGGATGAGgtataggaaa ... ttgtgaccagATTTTTGCAAAGAAGGGCATCATTGTCCTGCCCGACATCCTTGCAAACTCAGGCGGTGTCACAGTGAGCTACTTCGAATGGGTACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtataggaaaaatcaaaaagttttctagattgaattgatggtttttgtgaccagATTTTTGCAAAGAAGGGCATCATTGTCCTGCCCGACATCCTTGCAAACTCAGGCGGTGTCACAGTGAGCTACTTCGAATGGGTACAG
                                 aattgat  putative branch site (score: 59)
                                          tttttgt  putative PPT
        aaaaatcaaaaagttt  TA-rich tract