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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagattgtcgtcattcttaactcttatctttgaatcgggttctacagGTGGGCTTACCAGCAAGGGGGAAAACTTTCACTGCTGTCAAGCTAACAAGATATCTTCGTTGGCTTGGTCATGACACTAAACACTTCAACGTTGGAAAA

Basic information

species Selaginella moellendorffii
transcript EFJ07288
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ07288 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GRMZM5G824405_T01 (Zea mays), 3'ss of exon 6
-----------------------------------------------------gtagat-tgtcgtcattcttaactcttatctttgaatcgggttctacagGTGGGCTTACCAGCAAGGGGGAAAACTTTCACTGCTGTCAAGCTAACAAGATATCTTCGTTGGCTTGGTCATGACACTAAACACTTCAACGTTGGAAAA
                                                      ||  | ||    || |  |   | | ||| |    |    |||||  ||| ||  |||||||  | || || || || || || |  || || ||||||||||| || ||| | |||||||| || ||||||||||| |||||||| 
agctggaactattccagttaatccattgagatgtctttctttctttctttcagataagtatgcatgcagttctttttttaatcatctgctgatattcta--gGTTGGGCTACCAGCTCGAGGTAAGACCTTTACAGCAGCTAAACTTACAAGATATCTCCGATGGTTAGGTCATGAAACAAAACACTTCAATGTTGGAAAG

upper sequence: EFJ07288 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 7
-------------------------------------------------------gtagattgtcgtcattcttaactcttatctttgaatcgggttctacagGTGGGCTTACCAGCAAGGGGGAAAACTTTCACTGCTGTCAAGCTAACAAGATATCTTCGTTGGCTTGGTCATGACACTAAACACTTCAACGTTGGAAAA
                                                        || |      | ||| |||| | ||  ||   |||    || |  |||||||  | ||||| || || |||||||||||||| |  || || |||||||||||||||||| | |||||| | || ||||||||||| ||||| || 
ctggcaaaaatgtcatttccatttgtagttcatcaaagttagtaaatttggttttttaaaagtaaattatttttaattttttact---aatttttttatgtagGTGGGTCTGCCAGCCAGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCGTTGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG

upper sequence: EFJ07288 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 12
-------------------------------------------------------gtagattgtcgtcattcttaactcttatctttgaatcgggttctacagGTGGGCTTACCAGCAAGGGGGAAAACTTTCACTGCTGTCAAGCTAACAAGATATCTTCGTTGGCTTGGTCATGACACTAAACACTTCAACGTTGGAAAA
                                                        || |      | ||| |||| | ||  ||   |||    || |  |||||||  | ||||| || || |||||||||||||| |  || || ||||||||||||| |||| | |||||| | || ||||||||||| ||||| || 
ctggcaaaaatgtcatttccatttgtagttcatcaaagttagtaaatttgtttttttaaaagtaaattatttttaattttttact---aatttttttatgtagGTGGGTCTGCCAGCCAGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCATTGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG

upper sequence: EFJ07288 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 8
----------------------------------------------gtagat--tgtcgtcattcttaactcttatctttgaatcgggttct----acagGTGGGCTTACCAGCAAGGGGGAAAACTTTCACTGCTGTCAAGCTAACAAGATATCTTCGTTGGCTTGGTCATGACACTAAACACTTCAACGTTGGAAAA
                                              ||| ||  | |  | |    ||| | | || ||| | |    |  |      |||||||  | |||||  | || |||||||||||||| |  || || |||||||||||||| ||| | |||||| | || ||||||||||| ||||| || 
ggtatggaaaaaatgtcatatttccatctgtagttcatcaaagttagtaaataattttttaaaaaataaatttaatttttaactaatttcttttatgtagGTGGGTCTGCCAGCCCGAGGTAAAACTTTCACTGCAGCTAAACTTACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGGAAG

upper sequence: EFJ07288 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 14
-------------------------------------------------gtagattgtcgtcattct---taactcttatctttgaatcgggttctacagGTGGGCTTACCAGCAAGGGGGAAAACTTTCACTGCTGTCAAGCTAACAAGATATCTTCGTTGGCTTGGTCATGACACTAAACACTTCAACGTTGGAAAA
                                                 ||| | |    |  ||     | | |  | || ||   |    |||   ||||| | || |||||  | || || |||| |||||| |  || ||||||||||||||||| ||| | |||||| | || ||||||||||| ||||| || 
tacctggaaaaaaaaatgccacattcccatctgtagttcatctaatttagtaaaataaaatatttgaaaatgaataatttcattagtttcttttccttagGTGAGTTTGCCAGCTCGAGGCAAGACTTACACTGCAGCTAAACTAACAAGATATCTTCGATGGTTAGGTCATAATACCAAACACTTCAATGTTGGTAAG

upper sequence: EFJ07288 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 6
-----------------------------------------------gtagattgtcgtcattcttaactctta-tctttgaatcgggttc----tacagGTGGGCTTACCAGCAAGGGGGAAAACTTTCACTGCTGTCAAGCTAACAAGATATCTTCGTTGGCTTGGTCATGACACTAAACACTTCAACGTTGGAAAA
                                                |   ||  |    || ||||   | | |  ||| | |   ||     | ||||| ||||| |||||  | || |||||||| ||||| |  || || |||||||||||||| ||| | |||||||| || ||||||||||| |||||||| 
gcaacttccagtaacagcaggttaattccatttgttgcacctaaaaattcatttaccaattttgttaaaaatgaatggttgtaacaaatttatatttcagGTTGGCTTGCCAGCTCGAGGTAAAACTTTTACTGCAGCTAAACTTACAAGATATCTTCGCTGGTTGGGTCATGAGACCAAACACTTCAATGTTGGAAAG

upper sequence: EFJ07288 (Selaginella moellendorffii), 3'ss of exon 2
lower sequence: PP1S414_24V6.1 (Physcomitrella patens), 3'ss of exon 6
-----------------------------------------------gtagattgtcgtcattcttaact--cttatctttgaatcgggttc---tacagGTGGGCTTACCAGCAAGGGGGAAAACTTTCACTGCTGTCAAGCTAACAAGATATCTTCGTTGGCTTGGTCATGACACTAAACACTTCAACGTTGGAAAA
                                                 | ||||   |   | | || |  || ||| |       | ||    | ||||| || ||||| ||| | || || || || || || |  ||  | || ||||||||| | ||||| || ||||| |||||||||||||| |||||||||
cagcgcgattaaacgaattgaagcagaagcgtcgatttttcatgtgaaaatattggaatttctttcaaataactcatcctactggttgctttgggttcagGTTGGGTTACCTGCACGAGGCAAGACGTTTACGGCAGCAAAATTGACGAGATATCTTAGGTGGCTAGGCCATGATACTAAACACTTCAATGTTGGAAAA

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), 33 (downstream exon)
Score: 27

GATATGCCGGAGGCCACTGGAGCTGTGGCAGCTGCAGCGGTCTCTGAAAGAATGCTGCTTCCAAAAGAACGGCGCCAACTCGCTATTGTGCTGgtagattgtc ... ggttctacagGTGGGCTTACCAGCAAGGGGGAAAACTTTCACTGCTGTCAAGCTAACAAGATATCTTCGTTGGCTTGGTCATGACACTAAACACTTCAACGTTGGAAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtagattgtcgtcattcttaactcttatctttgaatcgggttctacagGTGGGCTTACCAGCAAGGGGGAAAACTTTCACTGCTGTCAAGCTAACAAGATATCTTCGTTGGCTTGGTCATGACACTAAACACTTCAACGTTGGAAAA
                      tcttaac  putative branch site (score: 27)
                           attcttaa  TA-rich tract