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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtctgtttggtgattgggagaaagtggcatctaaaaaccttgtcttctcttctgcagGCGCACCGTTTCCTCCCAACTTCAAGGAGGTTGTAAAGACCATTTTCAAAAGATTATTCCGGGTATACGCCCACATATACCACTCGCATTTCCAGAAGAT

Basic information

species Selaginella moellendorffii
transcript EFJ17641
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ17641 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os03g38020.1 (Oryza sativa), 3'ss of exon 5
--------------------------------------------------------------------------gtacgtctgtttggtgattgggagaaagtggcatctaaaaaccttgtcttctcttctgcagGCGCACCGTTTCCTCCCAACTTCAAGGAGGTTGTAAAGACCATTTTCAAAAGATTATTCCGGGTATACGCCCACATATACCACTCGCATTTCCAGAAGAT
                                                                           ||  |||||    |  || |     | || ||   |      ||   |||  ||   ||||| |||| || || || ||||||||||||||||||||||| ||||||||  | || || || || || ||||||||||| ||||| ||||| ||||||||
gtaatcattgtttatcacaaatatttgatgttggaatggtcgtttgtaccttagaaatagtgcaggcactactcatatatctgtccaat--tttgacactaatgacactgatctgggtttaattcctttac-cagGCACACCATTCCCGCCAAACTTCAAGGAGGTTGTAAAGACAATTTTCAAGCGCTTGTTTCGTGTTTATGCCCACATATATCACTCCCATTTTCAGAAGAT

upper sequence: EFJ17641 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: LOC_Os08g06610.1 (Oryza sativa), 3'ss of exon 1
--------------------------------------------------------------------------gtacgtctgtttggtgattgggagaaa--gtggcatctaaaaaccttgtcttctcttctgcagGCGCACCGTTTCCTCCCAACTTCAAGGAGGTTGTAAAGACCATTTTCAAAAGATTATTCCGGGTATACGCCCACATATACCACTCGCATTTCCAGAAGAT
                                                                           ||  | |||    |  |||  | ||    || ||   | |    ||   |||  ||   ||||| |||| || || || ||||||||||||||||||||||| ||||||||  | || || || || || ||||||||||| |||||   ||| ||||||||
gtaatcattgtttgtcacaaacatttgatgttggaatggtcatgtgtaccttagaaatagtgcaggcactactcatatatttgtccaatt-ttgacacaactcatgacactgatatgggtttaattcctttac-cagGCACACCATTCCCGCCAAACTTCAAGGAGGTTGTAAAGACAATTTTCAAGCGCTTGTTTCGTGTTTATGCCCACATATATCACTCCAGTTTTCAGAAGAT

upper sequence: EFJ17641 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GRMZM2G098819_T02 (Zea mays), 3'ss of exon 4
----------------------------------------------gtacgtctgtttggtgat-tgggagaaagtggcatctaa---aaaccttgtcttctcttctgca-gGCGCACCGTTTCCTCCCAACTTCAAGGAGGTTGTAAAGACCATTTTCAAAAGATTATTCCGGGTATACGCCCACATATACCACTCGCATTTCCAGAAGAT
                                              | ||  ||| |   ||||      ||   ||  |||| |     |  |||| | | |||   || ||| |||| || || || ||||||||||| || || ||||| || |||||  | || || || || || ||||||||||||||||||||||||||||||||
gtatgttgcttttttgtggatttatggagctctctcggtttcttgagaacacctggtatctgatgcaatcgagcatgttatctgattcggattttgtttcccctttgtcaagGCACACCATTCCCACCAAACTTCAAGGAAGTAGTGAAGACGATATTCAAGCGCTTGTTTCGTGTTTATGCCCACATATACCACTCGCATTTCCAGAAGAT

upper sequence: EFJ17641 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA09G34550.1 (Glycine max), 3'ss of exon 5
--------------------------gtacgtctgtttggtgattgggagaa----agtggcatctaaaaaccttgtcttctc---ttctgcagGCGCACCGTTTCCTCCCAACTTCAAGGAGGTTGTAAAGACCATTTTCAAAAGATTATTCCGGGTATACGCCCACATATACCACTCGCATTTCCAGAAGAT
                            | |  | || | ||||   |  |     | |  ||| |    ||| |  | | |    |  || |||  |||| |||||||||||||| ||||| ||||| ||||| || |||||  | || ||||| ||||| || ||||||||||| || || || ||||| ||
gtgaagatttttaatattttctttcttaaaggttcttagatgatatagtcattatcattttcattttggtaccataacctataaaatcatgtagGTTCACCATTTCCTCCCAACTTTAAGGAAGTTGTGAAGACAATATTCAAGCGGTTGTTCCGTGTATATGCTCACATATACCATTCTCACTTTCAGAAAAT

upper sequence: EFJ17641 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: GLYMA01G35130.2 (Glycine max), 3'ss of exon 5
-------------------------gtacgtctgtttggtgattgggaga----aagtggcatctaaaaaccttgtcttct---cttctgcagGCGCACCGTTTCCTCCCAACTTCAAGGAGGTTGTAAAGACCATTTTCAAAAGATTATTCCGGGTATACGCCCACATATACCACTCGCATTTCCAGAAGAT
                           | |  | || | ||||  ||  |     | |  ||| |    ||| |  | | |    |  || |||  |||| |||||||||||||| ||||| ||||| ||||| || |||||  | || ||||| ||||| || ||||||||||| || || || ||||| ||
gtaaagattttaatattttctttcttaaagattcttagatgatatggtcatcatcattttcattttggtaccataacctataaaatcatgtagGTTCACCATTTCCTCCCAACTTTAAGGAAGTTGTGAAGACAATATTCAAGCGGTTGTTCCGTGTATATGCTCACATATACCATTCTCACTTTCAGAAAAT

upper sequence: EFJ17641 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: AT4G19045.1 (Arabidopsis thaliana), 3'ss of exon 5
-----------------gtacgtctgtttggtgattg-ggagaaagtggcatc--taaaaaccttgtcttctcttctgcagGCGCACCGTTTCCTCCCAACTTCAAGGAGGTTGTAAAGACCATTTTCAAAAGATTATTCCGGGTATACGCCCACATATACCACTCGCATTTCCAGAAGAT
                    | | | |||| |||||  ||| |||  | |||   |   || |     |    |    |||| ||| | |||||||| ||||||||||| || || ||||| || || ||| || ||||||| || ||||| |||||||||||||| ||||||||||| ||
gtaaaataaccttactctggcatatctttgatgattatggataaaaagacattggtctcaatccatggtaaattctgacagGTGCAGCTTTTCCTCCAAACTTCAAGGAAGTGGTGAAGACAATCTTTAAACGACTATTCCGAGTTTACGCACACATATACCACTCTCATTTCCAGAAAAT

upper sequence: EFJ17641 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: Vv04s0043g00130.t01 (Vitis vinifera), 3'ss of exon 5
-------------------------------gtacgtctgt-ttggtgattgggagaaagtggcatctaaaaaccttgtc-------ttctcttctgcagGCGCACCGTTTCCTCCCAACTTCAAGGAGGTTGTAAAGACCATTTTCAAAAGATTATTCCGGGTATACGCCCACATATACCACTCGCATTTCCAGAAGAT
                               | | |   || |  ||   |             || |  | || |  ||       ||   || || ||| ||||| |||||||||||||| | ||| ||||| ||||| || |||||| |  ||||||||||||| |||||||| || ||||| || || ||||| ||
gttgttattattttcaatgcctggagggtgagcaggctggtatctgtagctttcccttcactttatttctatacttcatcggctacttttaattttgtagGTGCACCTTTTCCTCCCAACTTTAGGGAAGTTGTGAAGACGATATTCAAACGTCTATTCCGGGTATATGCCCACATTTATCACTCTCACTTTCAGAAAAT

upper sequence: EFJ17641 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: PP1S99_129V6.1 (Physcomitrella patens), 3'ss of exon 5
-----------------------------------gtacgtctgtttggtgattgggagaaagtggcatctaaaaaccttgtcttctctt----ctgcagGCGCACCGTTTCCTCCCAACTTCAAGGAGGTTGTAAAGACCATTTTCAAAAGATTATTCCGGGTATACGCCCACATATACCACTCGCATTTCCAGAAGAT
                                     |    || |    |  || |    | |    | ||| |   |   |||   ||    ||||||| || |||||||||   || |||| ||| ||||||||||| |||||||| ||||| |||||||| || || || ||||||||||| || || ||||||||
taatggagctcccgagagcttgtaaatctagaatctcaaaattgatctaagcatgaggattattcttttgtaatatgttccgcttgatttggcactgcagGGGCTCCGTTTCCTGTAAATTTCAGGGAAGTTGTAAAGACTATTTTCAAGAGATTGTTCCGGGTTTATGCACATATATACCACTCTCACTTTCAGAAGAT

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: 32 (upstream exon), 32 (downstream exon)
Score: 6

AAAAAGCCCATTGAAGTCTCGGCTCCGAAGTACGTCGAGTATCTTATGGATTGGATCGAAGGCCAGCTCGACGACGAAGCGATCTTTCCCCAGAAACTTGgtacgtctgt ... tcttctgcagGCGCACCGTTTCCTCCCAACTTCAAGGAGGTTGTAAAGACCATTTTCAAAAGATTATTCCGGGTATACGCCCACATATACCACTCGCATTTCCAGAAGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgtttggtgattgggagaaagtggcatctaaaaaccttgtcttctcttctgcagGCGCACCGTTTCCTCCCAACTTCAAGGAGGTTGTAAAGACCATTTTCAAAAGATTATTCCGGGTATACGCCCACATATACCACTCGCATTTCCAGAAGAT
                          atctaaa  putative branch site (score: 6)
                                   ccttgtcttctcttct  putative PPT
                          atctaaaaa  TA-rich tract