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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaccaattgatatttacgtttcccttcacggactcatcctgtttgtgtaacagTACGATGAAGCTGAGAGGAGGAGGGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCA

Basic information

species Selaginella moellendorffii
transcript EFJ08409
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ08409 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 9
--------------------------gtaccaattgat-atttacgtttcccttcacgg---actcatcctgtttgt-----gtaacagTACGATGAAGCTGAGAGGAGGAGGGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCA
                           ||  | || || ||||   |||    |   ||   | |  | ||| ||       || |||||| |||||| |||| ||||| || |||||||| ||||||||| | |||||||||||||| || || || || |||||  | ||  | || 
gtacagttctaatctgagatattttcttaatactttattatttttatttaatattgtggttaatttgtgctgcttcgcactggttacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACACTATTATGAACGGTGGGCAGCCAATCAGTCG

upper sequence: EFJ08409 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GRMZM2G006428_T01 (Zea mays), 3'ss of exon 9
-------------------------------------------gtaccaattga--tatttac--gtttcccttcacggactcat--cctgtttgtgtaacagTACGATGAAGCTGAGAGGAGGAGGGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCA
                                           | |  | |||    || |||  | ||  ||  |   | | ||    ||||   |  |||||| |||||| |||| ||||| || |||||||| ||||||||| | ||||||||||||||||| || || ||||||||  | ||  | || 
gtagcaattctgagcttccaatctgatatcttttgtccggcctgcaaaatttgggtcatgtactagattttctgaatttatttatgttttgttgtggctacagTATGATGAATCTGAAAGGAGAAGAGAAATGGCAAAGAACTCGCTTGAGAGATATACACATTATTATGAACGATGGGCAGCCAATCAGTCG

upper sequence: EFJ08409 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: Vv00s0207g00090.t01 (Vitis vinifera), 3'ss of exon 9
------------------------------------------gtaccaatt--gatatttacgtt----tcccttcacggactcatcctgtttgtgtaacagTACGATGAAGCTGAGAGGAGGAGGGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCA
                                          ||| |   |  |  | | | |      | |  |    || | ||  || |  |    ||||| ||||| |||||||   | ||||| |||||||||||||| || ||||||||||| ||||| || || |||||||| || ||| |||| 
tggtcctcgcccccttagaaatgtattgacggtgctacagaagtatcttctatggcactaatgggaaggtgctgtacttgatttattttgctgctt--gcagTATGATGAGGCTGAGAAACGAAGGGATATGGCTAAGAACTCTTTGGAGAGATATACTCATTATTATGAACGATGGGCGACCAACCAATCT

upper sequence: EFJ08409 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: PP1S178_72V6.2 (Physcomitrella patens), 3'ss of exon 10
--------------------------------------------gtacca---attgatatttacgtt--tcccttcacggactcatcctgtttgtgtaacagTACGATGAAGCTGAGAGGAGGAGGGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCA
                                             || ||    ||||   |||  |   |   || |  |  | |   ||||| ||   |||||||||||||| ||| |||||||||||||||||||||||||  | ||  | || ||||||||||| || || ||||| || || || || 
tcaagcaaagagattgttgcttttggctctatcgtccccgttatatatcagaggttgacgcttatataaataagttgatagttttagtttgtttctg---cagTACGATGAAGCAGAGCGGAGGAGGGAAATGGCTAAGAACTCTCTTGAACGCTACACACATTACTATGAACGTTGGGCTACAAATGAGTCT

upper sequence: EFJ08409 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: PP1S114_2V6.1 (Physcomitrella patens), 3'ss of exon 9
--------------------------------------------gtaccaattgatatttacgtttcccttcacgg-actcatcctgtttgtgta-acagTACGATGAAGCTGAGAGGAGGAGGGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCA
                                            ||     ||  || ||||  | |       |    | |    ||||| ||   ||||| |||||||| ||| |||| ||||||||||||||||||||| | ||  | |||||||||||||| || || ||||| || |||||||| 
tagaggctggcacttgaattcaagcgacgagatttatcttttgggtctgttttcctagttacaatccagagagtgacgtttacttagtttgagtttgcagTATGATGAAGCAGAGCGGAGAAGGGAAATGGCTAAGAACTCGCTTGAACGCTATACACATTACTATGAACGTTGGGCTACAAACGAATCT

upper sequence: EFJ08409 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: PP1S156_28V6.1 (Physcomitrella patens), 3'ss of exon 9
------------------------------------------gt-accaattgatatttacgtttcccttcacggactca-tcctgtttgtg--taacagTACGATGAAGCTGAGAGGAGGAGGGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCA
                                          || |   | |  | | |  || ||     | |  || | | ||     |   |  ||||| |||||||| ||| |||||||||| ||||||||||||||  | ||  | || |||||||| || || || ||||| ||||| ||||| 
cgagctggtcacactcaacagaagatcctaggtttttgctaggtgatggagtcctgtctgagtctctgcagatgagctaactgctacagataatttgcagTATGATGAAGCAGAGCGGAGGAGGGAGATGGCTAAGAACTCCCTTGAACGTTACACACATTATTATGAACGCTGGGCAACGAATGAATCT

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: 34 (upstream exon), 31 (downstream exon)
Score: 16

GCTATGCCTCGGTCCGTGGTCAGAACACGGCGAACGAACCGGAGGGTTCTACGCTTGCAATCGATACGAAGCGGCTAAGCAGGAGGGAGTGgtaccaattg ... tgtgtaacagTACGATGAAGCTGAGAGGAGGAGGGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaccaattgatatttacgtttcccttcacggactcatcctgtttgtgtaacagTACGATGAAGCTGAGAGGAGGAGGGAAATGGCTAAGAACTCGTTAGAGAGATATACACATTACTACGAGCGATGGGCCACGAACGAATCA
      aattgat  putative branch site (score: 16)
                                      tcctgttt  putative PPT
      aattgatattta  TA-rich tract