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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcgctctctgttttttggactccattgaaattttccttttgtttctcagATTTATAGAATATCAGATTTGAAACTAGTGCGAGTTCTCCCAAGTGCTGAAGATGAAGTTAATGTAGCGTGCTTTCATCCTCGAGTTGGCGGAGGGCTTG

Basic information

species Selaginella moellendorffii
transcript EFJ26270
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ26270 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: LOC_Os09g12550.1 (Oryza sativa), 3'ss of exon 12
---------------------------------------gtttgcgctctctgttttttggact-----ccattgaaattttccttttg---tttctcagATTTATAGAATATCAGATTTGAAACTAGTGCGAGTTCTCCCAAGTGCTGAAGATGAAGTTAATGTAGCGTGCTTTCATCCTCGAGTTGGCGGAGGGCTTG
                                         |    || || |  | |  | ||     | | |   ||||   | |||   || |  || | |||||| | |||||  || | || ||  ||||| |||| ||||||||||||||||| ||||| || || |||||||||     ||| | ||| ||||
actgtggggttacgatttatgtgcagtaatgactaatgacctcatactttcaggatataaggctatgggctaatactatttctttattgcacttccatagGTGTATAGAGTTTCAGACATGGAGCTTGTAAGAGTTATCCCTAGTGCTGAAGATGAAGTCAATGTCGCATGTTTTCATCCTTCCCCTGGTGCAGGTCTTG

upper sequence: EFJ26270 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: LOC_Os02g18820.2 (Oryza sativa), 3'ss of exon 13
----------------------------------gtttgcgctctctgttttt-----tgga------ctccattgaaattttcct-tttgtttc-tcagATTTATAGAATATCAGATTTGAAACTAGTGCGAGTTCTCCCAAGTGCTGAAGATGAAGTTAATGTAGCGTGCTTTCATCCTCGAGTTGGCGGAGGGCTTG
                                    || |   ||| ||| ||     || |      ||  ||   | | ||||| ||  |  | | || | |||||| |||| ||  || | || ||  ||||||| || ||||||||||||||||| || || || ||||||||||||     ||| || || ||||
tcatgtgttaattgcttgctccggtttctgtgccacttacaagctcagttcttacttatgaatgaagccttaatctcattattcctattcatcacgttagGTCTATAGAGTATCGGACATGGAGCTGGTAAGAGTTCTTCCTAGTGCTGAAGATGAAGTAAACGTTGCATGCTTTCATCCTTCCCCTGGAGGTGGTCTTG

upper sequence: EFJ26270 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: GRMZM2G007229_T01 (Zea mays), 3'ss of exon 12
-----------------------------------------gtttgcgctctctgttt--tttggactccattgaaattttcct--tttgtt--tctcagATTTATAGAATATCAGATTTGAAACTAGTGCGAGTTCTCCCAAGTGCTGAAGATGAAGTTAATGTAGCGTGCTTTCATCCTCGAGTTGGCGGAGGGCTTG
                                         | |    || | |||    | |       |||   |||||| |  ||| ||  | | || | |||||| | |||||| || | || ||| |||| || || || |||||||||||||||||||| || ||||||||||||  |   || || || ||||
tcaaaataatttacttattatcctcctcaactactaatattgctcatactttgtgtacaatgtaagtcaaattatcattttcttcatttattacttttagGTATATAGAGTTTCAGATATGGAGCTTGTGAGAGTGCTTCCTAGCGCTGAAGATGAAGTTAATGTTGCATGCTTTCATCCTTCACCAGGAGGTGGCCTTG

upper sequence: EFJ26270 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: AT1G04140.1 (Arabidopsis thaliana), 3'ss of exon 11
--------------------------------------------------------------------------------gtttgcgctctctgtttttt-----ggactccattgaaattttccttttgt---ttctcagATTTATAGAATATCAGATTTGAAACTAGTGCGAGTTCTCCCAAGTGCTGAAGATGAAGTTAATGTAGCGTGCTTTCATCCTCGAGTTGGCGGAGGGCTTG
                                                                                 | | | ||     | |  |      |  |  | ||   |||||| ||| |      ||||||||| ||| | |||||| || |||| ||| |||| || |||||  | || |||||||||||||| || ||||||||||||     ||| ||||| ||||
gtaacgtctatgctccagtagttatgaatttctagaccagcagaacaatgtttagcagatgccattttatatcattaactatatacacttggaatatcatacaagagtttagactgtgtttttccctttctattccttcagATTTACAGAGTTTCAGATATGGAACTGGTGAGAGTACTTCCAAGCTCAGAGGATGAAGTTAATGTTGCTTGCTTTCATCCTTCTCCTGGGGGAGGTCTTG

upper sequence: EFJ26270 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: Vv07s0005g04630.t01 (Vitis vinifera), 3'ss of exon 11
-----------------------------------------------------------------------------------------------gtttgcgctctctgttttttggactccattgaaattttccttttgtttctcagATTTATAGAATATCAGATTTGAAACTAGTGCGAGTTCTCCCAAGTGCTGAAGATGAAGTTAATGTAGCGTGCTTTCATCCTCGAGTTGGCGGAGGGCTTG
                                                                                                 || |  |     | |||  |    ||  |      || ||||||  ||||| ||||  || | |||||| || |||| ||  |||| || || |||||||||||||| || |||||||| ||||||||||||  |  ||| ||||| ||||
gtaacacttcaaaattttaatagcattaggcagtaaatatggtactgaagatctccaattgaagtgctggtcaagtactttattatctgttcaaatcttactgttctgatctttcaggtctcacagg----ctctttttgtcactcagGTTTACCGAGTCTCAGATATGGAACTTGTTAGAGTGCTTCCCAGTGCTGAAGATGAGGTCAATGTAGCTTGCTTTCATCCTTTACCTGGAGGAGGTCTTG

upper sequence: EFJ26270 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: Vv05s0077g00140.t01 (Vitis vinifera), 3'ss of exon 11
-----------------------------------------gtttgcgctctctgttttttggactccattgaaattttc------cttttgtttctcagATTTATAGAATATCAGATTTGAAACTAGTGCGAGTTCTCCCAAGTGCTGAAGATGAAGTTAATGTAGCGTGCTTTCATCCTCGAGTTGGCGGAGGGCTTG
                                          |||      | | || |||  | |  |||  || ||||       |||| |    ||| | || ||| | || ||| || |||| ||| ||||||| || ||||| || ||||| ||||||||||| ||||||||||||   ||||| || || ||||
tgctacttatgttgtgattataggaataaaactcttggattttttatttatttttttatttctattttatttcaactttcaaaatatttttatcatgcagGTCTACAGAGTTTCTGATATGGAACTTGTGAGAGTTCTTCCTAGTGCAGAGGATGAGGTTAATGTAGCTTGCTTTCATCCTTCTGTTGGAGGTGGCCTTG

upper sequence: EFJ26270 (Selaginella moellendorffii), 3'ss of exon 12
lower sequence: PP1S150_95V6.1 (Physcomitrella patens), 3'ss of exon 11
-------------------------------------------------------------------------------------------------------gtttgcgctctctgttttt---tggact--ccattgaaattttccttttgtttctcagATTTATAGAATATCAGATTTGAAACTAGTGCGAGTTCTCCCAAGTGCTGAAGATGAAGTTAATGTAGCGTGCTTTCATCCTCGAGTTGGCGGAGGGCTTG
                                                                                                       | ||  | |   |  ||||   ||| |   ||| ||    | || | |  |||  ||| |||| ||| | |||||| || | || ||| | ||  | || |||||||||||||| || ||||| |||||||||||||| | |||||| || || ||||
gtttgggattcttttcattcaacccaatagtcttagtggcaagtaactacttgtgtaacttttaaaaaatttgacagtgaacgtcagttctatattcctgcttgattcagttaagtaattttacttgggccaaccactgtctctctcttgtgttttaacagGTTTACAGAGTTTCAGATATGGAGCTTGTGAGGGTATTACCTAGTGCTGAAGATGAGGTGAATGTGGCGTGCTTTCATCCCCAAGTTGGTGGTGGTCTTG

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), 23 (downstream exon)
Score: 6

TGGTCATATACTTTTGGCCTATGGTCGACGTCACGGCTCACTCTTGAGGAGCATCGTGTTGGATGGAACAACTACGATTCCTGTATATACAATACTCGAGgtttgcgctc ... tgtttctcagATTTATAGAATATCAGATTTGAAACTAGTGCGAGTTCTCCCAAGTGCTGAAGATGAAGTTAATGTAGCGTGCTTTCATCCTCGAGTTGGCGGAGGGCTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgcgctctctgttttttggactccattgaaattttccttttgtttctcagATTTATAGAATATCAGATTTGAAACTAGTGCGAGTTCTCCCAAGTGCTGAAGATGAAGTTAATGTAGCGTGCTTTCATCCTCGAGTTGGCGGAGGGCTTG
                                     ttttccttttgtttct  CT-rich tract
                             attgaaatttt  TA-rich tract