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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatactaagtttgtgttttcttttggttggtttgatagtaacttagcaccctttgtcgcagGTATGATATCGATATGACAAAGTGCATCTACTGCGGATTCTGCCAAGAGGCTTGCCCAGTCGATGCTATCGTTGAGGGACCAAATTTTGAGTTTGCAACC

Basic information

species Selaginella moellendorffii
transcript EFJ08392
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ08392 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os03g56300.1 (Oryza sativa), 3'ss of exon 6
-----------------------------------------gtatactaagtttgtgttttcttttggttggtttgatagtaacttagc--accctttgtcgcagGTATGATATCGATATGACAAAGTGCATCTACTGCGGATTCTGCCAAGAGGCTTGCCCAGTCGATGCTATCGTTGAGGGACCAAATTTTGAGTTTGCAACC
                                         | | | | | ||  ||  |  |  |     |||      |    |     || | || | |||| |||||||| |||||||| || |||||||| || || ||||||||||| ||||| || || ||||| ||||||||||| || || ||||||||||| || 
gtaatcccgtggctggctttctttgatccgtgtgaattattgaaaaatgatttactgcctcttcatctgctgttaagctctgttgtgatgaactcctttttgcagATATGATATTGATATGACCAAATGCATCTATTGTGGCTTCTGCCAAGAAGCTTGTCCTGTTGATGCCATCGTTGAGGGTCCTAACTTTGAGTTTGCTACT

upper sequence: EFJ08392 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G072806_T01 (Zea mays), 3'ss of exon 6
-----------------------------------------------gtatactaagtttgtgttttcttttgg--ttggtttgatagtaacttagcaccctttg-tcgcagGTATGATATCGATATGACAAAGTGCATCTACTGCGGATTCTGCCAAGAGGCTTGCCCAGTCGATGCTATCGTTGAGGGACCAAATTTTGAGTTTGCAACC
                                                | |||  | | |||  |    ||     ||  | |||   |   ||       | |  || |||||||||||| || ||||| || ||||| ||||| || |||||||||||||||||||||||||||||||| |||||||| || || ||||||||||| || 
gtaatcaaaatgaaggtttttctctcttttttgtcaatagaactatgatttacccactgtgttctgcaattaaactttaatctgaatttctgttgcttttatctcctcacagGTATGATATTGACATGACCAAATGCATTTACTGTGGGTTCTGCCAAGAGGCTTGCCCAGTCGATGCTATTGTTGAGGGGCCTAACTTTGAGTTTGCTACT

upper sequence: EFJ08392 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: AC195340.3_FGT002 (Zea mays), 3'ss of exon 6
-----------------------------------------------------------------------------------------gtatactaagtttgtgttttcttttggttgg--tttgatagtaacttagcacccttt------gtcgcagGTATGATATCGATATGACAAAGTGCATCTACTGCGGATTCTGCCAAGAGGCTTGCCCAGTCGATGCTATCGTTGAGGGACCAAATTTTGAGTTTGCAACC
                                                                                           |  ||  |||  |||| |  |    ||    ||   |   |||||      ||||       || ||| |||||||| || ||||| || ||||| ||||| || ||||| |||||||||||||||||||||||||| |||||||| || || ||||||||||| || 
gtaatcaaaatgaagtttttcctctttcttttttggacttgtggctgatatcgggtttcaactcgagtctacctcaacttgattgggacaaagtctttgttgttgttcttatgcaattaaacttcattctgaacttgtgttgcttttttctcatcacagATATGATATTGACATGACCAAATGCATTTACTGTGGGTTCTGTCAAGAGGCTTGCCCAGTCGATGCTATTGTTGAGGGGCCTAACTTTGAGTTTGCCACT

upper sequence: EFJ08392 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA05G34890.1 (Glycine max), 3'ss of exon 6
---gtatactaagtttgtgt---tttcttttggttggtttgatagtaa-cttagcaccctttgtcg-------cagGTATGATATCGATATGACAAAGTGCATCTACTGCGGATTCTGCCAAGAGGCTTGCCCAGTCGATGCTATCGTTGAGGGACCAAATTTTGAGTTTGCAACC
      |||     ||||||   |  | ||    ||     ||   |  ||||      |||||         |||||||||||| || ||||| ||||||||||| || ||||| || |||||||| ||||| || ||||| || ||||| || ||||| ||||| ||||| || 
gtgaattaccttccttgtgtacctccccttctcctgcccctatcccattcttactgttatttgttaaatctttcagGTATGATATTGACATGACCAAGTGCATCTATTGTGGATTTTGTCAAGAGGCATGCCCTGTTGATGCCATTGTTGAAGGGCCAAACTTTGAATTTGCTACA

upper sequence: EFJ08392 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA13G31520.1 (Glycine max), 3'ss of exon 7
------------gtatactaagtttgtgttttcttttggttggtttgatagtaacttagcaccctttg--tcgcagGTATGATATCGATATGACAAAGTGCATCTACTGCGGATTCTGCCAAGAGGCTTGCCCAGTCGATGCTATCGTTGAGGGACCAAATTTTGAGTTTGCAACC
               ||     |   | |||| |||   |   |    |  |    |   |    ||   || |||||||||||| || ||||| ||||||||||| || ||||| || |||||||| ||||| || ||||| || || || |||||||| ||||| ||||| || 
gtgaattaccagccttatctgctccctcttttttttccctcactgcattcttgctctcttatttgttaaatctcagGTATGATATTGACATGACCAAGTGCATCTATTGTGGATTTTGTCAAGAGGCATGCCCTGTTGATGCCATTGTCGAAGGACCAAACTTTGAATTTGCTACT

upper sequence: EFJ08392 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA15G07790.2 (Glycine max), 3'ss of exon 6
------------gtatactaagtttgtgttttcttttggttggtttgatagtaacttagcaccctttg----tcgcagGTATGATATCGATATGACAAAGTGCATCTACTGCGGATTCTGCCAAGAGGCTTGCCCAGTCGATGCTATCGTTGAGGGACCAAATTTTGAGTTTGCAACC
               |||      | ||||||| ||   |   |    |       |   |    ||     |  |||||||||||| || ||||| |||||||| || || ||||| || |||||||| ||||| || ||||| || ||||| || ||||| ||||| ||||| || 
gtgaattacctgtcttacctgccctctgttttccttccctcactccattctagctctcttatttgttaaatctttcagGTATGATATTGACATGACCAAGTGCATTTATTGTGGATTTTGTCAAGAGGCATGCCCTGTTGATGCGATTGTTGAAGGGCCAAACTTTGAATTTGCTACA

upper sequence: EFJ08392 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: AT1G16700.1 (Arabidopsis thaliana), 3'ss of exon 7
---------------------------------------------gta-tactaagtttgtgttttcttttggttggtttgatagta-acttagcaccctttgtcg--cagGTATGATATCGATATGACAAAGTGCATCTACTGCGGATTCTGCCAAGAGGCTTGCCCAGTCGATGCTATCGTTGAGGGACCAAATTTTGAGTTTGCAACC
                                              || |     || | | |  |  ||   |   |||  ||||  | | |     |   |  |  ||||||||||||||| ||||| || |||||||| || || ||||||||||| |||||||| || ||||| ||||| || |||||||| |||||||||||||||
gtcaccctctaagttcccgtttattaaccatatatatattatttaatactgtcttgtctctatggttcttctatatatttcgtagtgtagtgattgttcggagctgtacagGTATGATATCGACATGACGAAATGCATCTATTGTGGTTTCTGCCAAGAAGCTTGCCCTGTTGATGCAATCGTGGAAGGACCAAACTTTGAGTTTGCAACC

upper sequence: EFJ08392 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: AT1G79010.1 (Arabidopsis thaliana), 3'ss of exon 6
---------------------gtatactaagtttgtgttttcttttggttggtttgatagtaacttagcaccctttgtcgcagGTATGATATCGATATGACAAAGTGCATCTACTGCGGATTCTGCCAAGAGGCTTGCCCAGTCGATGCTATCGTTGAGGGACCAAATTTTGAGTTTGCAACC
                      | ||  ||   | || |||||||       ||| ||  | | ||        | ||  |||||| |||||||| |||||||| ||||||||||| || ||||||||||| |||||||| || ||||| |||||||| ||||| || ||||| || ||||||
gtcatcatccctttagttctcatttatcaaccatctgctttctttattaccctttcatgatgatttgagctgtatcgt-acagGTACGATATCGACATGACAAAATGCATCTACTGTGGTTTCTGCCAAGAAGCTTGCCCCGTTGATGCAATCGTTGAAGGACCTAACTTTGAATTCGCAACC

upper sequence: EFJ08392 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: Vv03s0063g02550.t01 (Vitis vinifera), 3'ss of exon 6
-----gtatactaagtttgtgttttct-tttggttggtttgat-agtaacttag-caccctttg--------tcgcagGTATGATATCGATATGACAAAGTGCATCTACTGCGGATTCTGCCAAGAGGCTTGCCCAGTCGATGCTATCGTTGAGGGACCAAATTTTGAGTTTGCAACC
     |  | || | || ||| | ||| | |   |   |   | | || || |  |||   |||        || |||||| || || || ||||| |||||||| ||||| ||||||||||||||||| ||||| || ||||| || || || || || || ||||| ||  | || 
gtgatgggt-cttacttggtgatctctatctcactcactcactcactagctcactcactagttggtttaacttcacagGTACGACATTGACATGACCAAGTGCATTTACTGTGGATTCTGCCAAGAGGCATGCCCTGTTGATGCCATTGTGGAAGGTCCCAACTTTGAATTCACTACA

upper sequence: EFJ08392 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: PP1S24_200V6.1 (Physcomitrella patens), 3'ss of exon 5
--------------------------------gtatactaagtttgtgttttcttttggttggtttgatagtaac------ttagcaccctttgtcgcagGTATGATATCGATATGACAAAGTGCATCTACTGCGGATTCTGCCAAGAGGCTTGCCCAGTCGATGCTATCGTTGAGGGACCAAATTTTGAGTTTGCAACC
                                 | | |||   | ||||     ||| |    ||  | | | ||      ||        || |||||| |||||||| || ||||| || ||||||||||| || ||||||||||| |||||||| || || ||||| || || || || ||||| |||||| | |||
catggttgtacctatcgtatgtttcgaatctattcttctattctggtgtaggggttttgagaattctaaaatcacgcctattttttgtgtattttcgcagATATGATATAGACATGACGAAATGCATCTACTGTGGCTTCTGCCAAGAAGCTTGCCCTGTGGACGCTATTGTAGAAGGTCCTAATTTCGAGTTTACCACC

upper sequence: EFJ08392 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: PP1S83_83V6.1 (Physcomitrella patens), 3'ss of exon 5
-------------------------------gtatactaagtttgtgttttcttttggttggtttgatag---taacttagcaccctttgt----cgcagGTATGATATCGATATGACAAAGTGCATCTACTGCGGATTCTGCCAAGAGGCTTGCCCAGTCGATGCTATCGTTGAGGGACCAAATTTTGAGTTTGCAACC
                                |||    || |   | ||  ||| |  | ||  |  ||   ||| ||    |    |||     |||| |||||||| || ||||| || |||||||||||||| || |||||||| |||||||| || || ||||| || || || || || ||||||||  | || 
acctgtcactaataccctcatttccactcggttatctacagctgtcgcttgatttagagtcgtaggcgagctctaagtttattctgcctgtattttgcagATATGATATTGACATGACTAAATGCATCTACTGCGGCTTTTGCCAAGAAGCTTGCCCTGTGGACGCTATTGTGGAAGGTCCTAACTTTGAGTTCACCACG

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: 48

GTCTGTCCGGCACAAGCCATAACTATAGAAGCCGAAGAAAGAGAGGATGGTAGTCGTCGAACTACGAGgtatactaag ... tttgtcgcagGTATGATATCGATATGACAAAGTGCATCTACTGCGGATTCTGCCAAGAGGCTTGCCCAGTCGATGCTATCGTTGAGGGACCAAATTTTGAGTTTGCAACC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagtttgtgttttcttttggttggtttgatagtaacttagcaccctttgtcgcagGTATGATATCGATATGACAAAGTGCATCTACTGCGGATTCTGCCAAGAGGCTTGCCCAGTCGATGCTATCGTTGAGGGACCAAATTTTGAGTTTGCAACC
                             tagtaac  putative branch site (score: 48)
                                          ccctttgtc  putative PPT
         ttttctttt  TA-rich tract