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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagaccatagctctttcccataggctttgacaactaaagcacaaagcaatcgtccttttctttcagTACCACCTGCATACTACGCTCACCTGGCTGCGTTCCGCGCGAGATTCTACATGGAGCCGGACGCGTCCGAGGCTGGCTCCGTCCACCGGAACACTGCTCC

Basic information

species Selaginella moellendorffii
transcript EFJ19862
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ14095 (Selaginella moellendorffii), 3'ss of exon 19
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 21
--------------------------------------------------gtaaagaccatagctc-tttcccataggctttgacaactaaagc-acaaagcaatcgtccttttctttcagTACCACCTGCATACTACGCTCACCTGGCTGCGTTCCGCGCGAGATTCTACATGGAGCCGGACGCGTCCGAGG--CTGGCTCCGTCCACCGGAACACTGCTCC
                                                    |      ||   |  ||   ||     | |||     ||     ||   |  |  ||||  ||   |||| |||||||||||||| || || ||||||||||| || ||| | |||||||||||||| ||   ||| |||   | | |  |||| |   || | |  ||  
gtacgttcttctgaaatgatctgaacatttttccatcattttctttgtattcatgtgttattattagttggacacgaattctgaaggtgaatcttgcatttcttttttcctggtccaacagTTCCACCTGCATACTATGCGCATCTGGCTGCGTTTCGAGCGCGGTTCTACATGGAGCCAGAGATGTCGGAGAACCAGACGACGTCGA--AGAGCTCCACTGG

upper sequence: EFJ14095 (Selaginella moellendorffii), 3'ss of exon 19
lower sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 20
-------------------------------------------------gtaaagaccatagctctttcccataggctttga-caactaaagcacaaagcaat-cgtccttttcttt----cagTACCACCTGCATACTACGCTCACCTGGCTGCGTTCCGCGCGAGATTCTACATGGAGCCGGACGCGTCCGAGGCTGGCTCCGTCCACCGGAACACTGCTCC
                                                  |  |  |  ||||    || | |   |    | |||||    |         |   || ||| |||     |||| || |||||||||||||| |||||||| || ||||| ||| | ||||||||||| || ||   ||| |||       |     |  |   || ||   |
gtatgtcctgtgctttacagacaaacgttttcccagctccacaattgtcatcgactctttagcctgctcacctgttcaggaagcaacttcgacctgtgatgctgtatcttttgcttcttaacagTCCCTCCTGCATACTACGCACACCTGGCAGCATTCCGGGCGCGGTTCTACATGGAACCAGAGATGTCGGAGAACCAGACGTCGAAGAGCTCCAATGGCAC
















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), 34 (downstream exon)
Score: 79

GTACTTTGGGACGAGAACAAGTTCACTGCCGATGGCTTGCAGTCCCTCACCAACAGCCTGTGCTACACTTACGCTCGCTGCACACGCTCAGTCTCGATAGgtaaagacca ... tttctttcagTACCACCTGCATACTACGCTCACCTGGCTGCGTTCCGCGCGAGATTCTACATGGAGCCGGACGCGTCCGAGGCTGGCTCCGTCCACCGGAACACTGCTCC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttcccataggctttgacaactaaagcacaaagcaatcgtccttttctttcagTACCACCTGCATACTACGCTCACCTGGCTGCGTTCCGCGCGAGATTCTACATGGAGCCGGACGCGTCCGAGGCTGGCTCCGTCCACCGGAACACTGCTCC
                    aactaaa  putative branch site (score: 79)
                                      tcgtccttttctttc  putative PPT
                                            ttttcttt  TA-rich tract