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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagctagtcagcttttttctctgctacttgatactgattttcttcgtctgtacagGTCAGTCACCATCCAATGGTGGTAGCCTGTCACTGTGAGGGACGTGGATGGAAACTCTGGGGCGACAGCAATCTAAAGAGTAAATTTTGGGGGCGTTCAA

Basic information

species Selaginella moellendorffii
transcript EFJ08416
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ08416 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: LOC_Os10g40590.1 (Oryza sativa), 3'ss of exon 5
--------------------------------------gttagctagtcagcttttttctc----tgctacttgatac-tgattttcttcgtctgtacagGTCAGTCACCATCCAATGGTGGTAGCCTGTCACTGTGAGGGACGTGGATGGAAACTCTGGGGCGACAGCAATCTAAAGAGTAAATTTTGGGGGCGTTCAA
                                       |   ||  ||  | |||  | |    |   | || ||   | | ||| ||| | |   ||||| ||||| ||||| |||||  | || || || ||||| ||    || |||||| | ||||| ||||||||||||||||| |||||||||||||  || |
taaaagtggcagacactgttctgatgccaggcacattaatattcttctctacatttcacacaacatatgagttaatttgttagtttattcttgtcaccagGTTAGTCATCATCCGATGGTCATGGCATGCCATTGTGAAGGGAAAGGTTGGAAATTTTGGGGTGACAGCAATCTAAAGAGCAAATTTTGGGGGCAGTCCA

upper sequence: EFJ08416 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GRMZM2G409265_T01 (Zea mays), 3'ss of exon 5
-------------------------------------------------------------------------------------------------------------------------------gttagctagtcagcttttttctctgc-------tacttgat--actgattttcttcgtctgta----cagGTCAGTCACCATCCAATGGTGGTAGCCTGTCACTGTGAGGGACGTGGATGGAAACTCTGGGGCGACAGCAATCTAAAGAGTAAATTTTGGGGGCGTTCAA
                                                                                                                                |||       || | | || | |          || |||   | ||   || ||  |   |     ||||||||||| ||||| |||||  | || ||||||||||||||    || |||||| | ||||| ||||||||||||||||| ||||| ||||| |  || |
gtcagtttggtatccaccacataaattaatgctcaattattgtttagtcacttaacagactatactgaatataggcctgaaagaggaatcactaagagcatcacgtacatgaatacagcaatggagtattattactaaagttctattatatatgagaacacacctgactaaatgtgcttatttattcttggcaccagGTCAGTCATCATCCTATGGTCATGGCATGTCACTGTGAGGGGAAAGGTTGGAAATTTTGGGGAGACAGCAATCTAAAGAGCAAATTCTGGGGACAATCCA

upper sequence: EFJ08416 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GRMZM2G061099_T01 (Zea mays), 3'ss of exon 5
----------------------------------------------------------------------------------------------------------------------------------gttagctagtcagctttt-ttctctgc-------tacttgat--actgattttcttcgtctgtaca---gGTCAGTCACCATCCAATGGTGGTAGCCTGTCACTGTGAGGGACGTGGATGGAAACTCTGGGGCGACAGCAATCTAAAGAGTAAATTTTGGGGGCGTTCAA
                                                                                                                                  |     || | |  |||| || | |          ||||||   | || |||| ||  |   | ||   ||||||||| ||||| |||||  | || ||||||||||||||    || |||||| | ||||| ||||||||||| ||||| ||||| ||||| |  || |
gtcagtttggcacccaacacatataagtttagctaattatcaattattgtttggtcacttaacaaatcattctgaatataggcctgaaagaggaatcactaaaaacatcacgtacaaggatccaccactggagtattactaaaattttattatatatgagaacacacttgactaaatgtttttgtttattcttgcaccagGTCAGTCATCATCCTATGGTCATGGCATGTCACTGTGAGGGGAAAGGTTGGAAATTTTGGGGAGACAGCAATCTGAAGAGCAAATTCTGGGGACAATCCA

upper sequence: EFJ08416 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA13G02610.1 (Glycine max), 3'ss of exon 7
------------------------------------------gttagctagtcagcttttttctctgctacttgat-actgattttcttcgtctgtacagGTCAGTCACCATCCAATGGTGGTAGCCTGTCACTGTGAGGGACGTGGATGGAAACTCTGGGGCGACAGCAATCTAAAGAGTAAATTTTGGGGGCGTTCAA
                                          |     |||      | | | |||| |     || | |   | ||| | |     ||||||||||| ||||||||| | ||||| ||||||||||||||    || |||||| | ||||| || |||||  ||||||||||||||||||| || ||||
gaaaggaaatataatttgaatttcaacattggatatgattatgccttttagaatatgtctgtttctgttttgaaattattatatatctgctttctctcagGTCAGTCATCATCCAATGATAGTAGCATGTCACTGTGAGGGTACAGGTTGGAAATTTTGGGGAGATAGCAACTTAAAGAGTAAATTTTGGGGTCGGTCAA

upper sequence: EFJ08416 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA06G16720.1 (Glycine max), 3'ss of exon 6
-----------------------------------------gttagctagtcagcttttttctctgctacttgatactgattttcttcgtc--tgtacagGTCAGTCACCATCCAATGGTGGTAGCCTGTCACTGTGAGGGACGTGGATGGAAACTCTGGGGCGACAGCAATCTAAAGAGTAAATTTTGGGGGCGTTCAA
                                          ||   ||    | | ||   |    ||    ||||| |   | ||| ||     | |||||||||| || || ||| | || || || || ||||||||| |||| |||||| | ||||| ||||||||| |||| |||||||||||||| |||||||
agccataaacatatcaataatttaatttggcattattttttcttgtgtaaagtgatattgatttgaataaaaaatacttacgctattcatcatgagatagGTCAGTCATCACCCCATGATTGTTGCATGCCATTGTGAGGGAAGTGGCTGGAAATTTTGGGGTGACAGCAATTTAAAAAGTAAATTTTGGGGTCGTTCAA

upper sequence: EFJ08416 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA14G33410.1 (Glycine max), 3'ss of exon 5
--------------------------------------gttagctagtcagcttttttct-ctgctactt----gatactgattttcttcgtctgtacagGTCAGTCACCATCCAATGGTGGTAGCCTGTCACTGTGAGGGACGTGGATGGAAACTCTGGGGCGACAGCAATCTAAAGAGTAAATTTTGGGGGCGTTCAA
                                       |||     | ||  | | |||  | | | ||      || |   |||||   |    |||||||||||| ||||||||| | || || ||||||||||||||    || |||||| | ||||| || |||||  ||||||||||||||||||| || ||||
tgaaaggcaatagaatttgaatttcaacaatggatatgattatgcctttagaatatgtctgtttccattttgaaattattatatttctgttttctcacagGTCAGTCATCATCCAATGATAGTTGCATGTCACTGTGAGGGTACAGGTTGGAAATTTTGGGGAGATAGCAACTTAAAGAGTAAATTTTGGGGTCGGTCAA

upper sequence: EFJ08416 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA04G43220.1 (Glycine max), 3'ss of exon 5
----------------------------------------gttagctagtcagcttttttct--ctgctacttgatactgat-tttcttcgtctgtacagGTCAGTCACCATCCAATGGTGGTAGCCTGTCACTGTGAGGGACGTGGATGGAAACTCTGGGGCGACAGCAATCTAAAGAGTAAATTTTGGGGGCGTTCAA
                                         || |||  |    ||| | |   ||  ||     || | || ||| | | ||    ||||||||||| || |||||| | || || ||||||||||||||    || |||||| | ||||| || ||||| |||||||| |||||||||||||| ||||
gaacacaatttggattttggtgtgaacaaaagggatatgatttggcttttttaatttatgccgcctattagaaattattaatgtttttgcttcccctcagGTCAGTCATCACCCAATGATTGTCGCATGTCACTGTGAGGGTACAGGTTGGAAATTTTGGGGTGATAGCAACCTAAAGAGCAAATTTTGGGGGCGATCAA

upper sequence: EFJ08416 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA04G38330.1 (Glycine max), 3'ss of exon 6
---------------------------------------gttagcta--gtcagcttttttctctgctacttgatactgattttcttcgtct--gtacagGTCAGTCACCATCCAATGGTGGTAGCCTGTCACTGTGAGGGACGTGGATGGAAACTCTGGGGCGACAGCAATCTAAAGAGTAAATTTTGGGGGCGTTCAA
                                       || || |    |   || ||   |    ||    ||||| |   | ||| |||    | |||||||||| || |||||| | || || || || |||||||||   || |||||| | ||||| ||||||||| |||| |||||||||||||| |||||||
gacatatcaataatttaatttggcattattttttcttgtgtaaggtgctattgcctattcgtttgaataaaaaatacttacgctattcatcttgagatagGTCAGTCATCACCCAATGATTGTTGCATGCCATTGTGAGGGAAAAGGCTGGAAATTTTGGGGTGACAGCAATTTAAAAAGTAAATTTTGGGGTCGTTCAA

upper sequence: EFJ08416 (Selaginella moellendorffii), 3'ss of exon 6
lower sequence: GLYMA06G11470.1 (Glycine max), 3'ss of exon 6
----------------------------------------gttagctagtcagcttttttctctgctacttga---tactgat-tttcttcgtctgtacagGTCAGTCACCATCCAATGGTGGTAGCCTGTCACTGTGAGGGACGTGGATGGAAACTCTGGGGCGACAGCAATCTAAAGAGTAAATTTTGGGGGCGTTCAA
                                         || |||  |    |||| | ||  ||| | ||   || | || ||| | | ||    ||||||||||| || |||||| | || || ||||||||||||||    || |||||| | ||||| || ||||| |||||||| ||||| |||||||| ||||
caagacaatttggattttggtgtgaacaaaaaggatatgatttggctttttta-ttttatgtcgcctattagaaattattaatgtttttgcttcccctcagGTCAGTCATCACCCAATGATTGTCGCATGTCACTGTGAGGGTACAGGTTGGAAATTTTGGGGTGATAGCAACCTAAAGAGCAAATTCTGGGGGCGATCAA

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: 28 (upstream exon), 8 (downstream exon)
Score: 1

ATCCACAGATGGTCGAATATGTAAGCCGTTCAATCCTTTGCTAGGAGAAACGTATGAAGCAGACTATCCTGATAAGGGAGTCAAATTTTTCTCCGAGAAGgttagctagt ... gtctgtacagGTCAGTCACCATCCAATGGTGGTAGCCTGTCACTGTGAGGGACGTGGATGGAAACTCTGGGGCGACAGCAATCTAAAGAGTAAATTTTGGGGGCGTTCAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagctagtcagcttttttctctgctacttgatactgattttcttcgtctgtacagGTCAGTCACCATCCAATGGTGGTAGCCTGTCACTGTGAGGGACGTGGATGGAAACTCTGGGGCGACAGCAATCTAAAGAGTAAATTTTGGGGGCGTTCAA
                               tactgat  putative branch site (score: 1)
                                     ttttcttcgtctgt  CT-rich tract
            ttttttct  TA-rich tract