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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggttgtcttcgtttgacaagttacatacatgacttttgtcttgctttagGTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAG

Basic information

species Selaginella moellendorffii
transcript EFJ16882
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ16882 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: LOC_Os05g06460.1 (Oryza sativa), 3'ss of exon 9
----------------------------------------gttggttgtcttcgtttgacaagttacatacatgacttttgtcttgctt--tagGTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAG
                                          |  |  || | | |||    |   |  ||||| | |   | ||  ||  ||||| ||  | || || ||||| || ||||| ||||| ||||| ||||||||||| ||||||||||| ||||| || || |
gtatgttgaaacaaatgaattaccatgctttgttcagaataatcctcttcctggcttgtatgggatctaacatgccatgcatttttatttgtagGTTCCGAACTTATATTGCATTGGAGATGCCAATGGTAAACTCATGCTTGCTCATGCTGCCAGTGCACAGGGAATCTCTG

upper sequence: EFJ16882 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: LOC_Os01g23610.1 (Oryza sativa), 3'ss of exon 9
-----------------------------------------gttg-gttgtcttcg---tttgacaagttacat--acatga-cttttgtcttgctttagGTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAG
                                         |||  | | |||| |     | |  | || | |  | |||| | | | |     |  |||| ||  ||||||| || || || ||||| ||||||||||| ||||| ||||| ||||||||||| || || || ||||
gtggcacattctagttgcatgttgggtttcacttttcattagttaagatatctttggatcatcatcacttcctttgatatgaacatatattactatgcagGTTCCAAATTTGTATTGTATTGGAGATGCCAATGGCAAACTCATGCTGGCTCATGCTGCCAGTGCACAAGGAATCTCAG

upper sequence: EFJ16882 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GRMZM2G073774_T01 (Zea mays), 3'ss of exon 9
---------------------gttggttgtcttcgtttgacaagt-tacatacatgacttttgtcttgctt------------------tagGTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAG
                        | || | | | |   |||||| |||   || || || ||  |   |                    |||||||  |||| || ||||| || ||||| |||||||| || |||||||| || ||||||||||| || || |||||||
gtatgttgcaacttttattgcacggattctttccttagaacaagtgtaccctcaagatttctgcataattcacatatagcattattatacagGTACCCAATTTATATTGCATTGGAGATGCCAATGGCAAGCTCATGCTTGCCCATGCTGCCAGTGCACAAGGAATTTCAG

upper sequence: EFJ16882 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA09G04270.1 (Glycine max), 3'ss of exon 4
--------------------gttggttgtcttcgtttgacaagttacatacatgacttttgtcttgctt--tagGTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAG
                     ||  || |||| || |||||  ||   |||     |   || | |  |  ||||| ||||||||||| ||||| || ||| ||||||||||  ||||||||||||| ||||||||||| || || |||||||
gtttgtttcatgaatacataattttttttcttggtctgacacattgt-tactgatttagagtatggaatgatagGTTCCTCATTTGTATTGCATTGGTGATACAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG

upper sequence: EFJ16882 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA07G37050.2 (Glycine max), 3'ss of exon 9
---------------------gttggttgtcttcgtttgacaa---gttacatacatgacttttgtcttgctttagGTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAG
                       |  || ||      ||||     |||||  ||||    | ||   || |  |||| |||||||| ||||| || || ||||||||||||||  ||||||||||||| ||||||||||| || || |||||||
gtttgtctcaacttctcaagtaataattatccctccctgacttattgttactgacataggatgtggaatgat--agGTGCCTCATTTATACTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG

upper sequence: EFJ16882 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA17G03560.1 (Glycine max), 3'ss of exon 9
---------------------gttggttgtcttcgtttgacaa---gttacatacatgacttttgtcttgctttagGTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAG
                       |  || ||      ||||     |||||  ||||    | ||   || |  |||| |||||||| || || || || ||||||||||||||  ||||||||||||| ||||||||||| || || |||||||
gtttgtctcaatttctcatgcaataattatccctccctgacttattgttactgacataggatgtggaatgat--agGTGCCTCATTTATATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGTGCACAAGGAATTTCAG

upper sequence: EFJ16882 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA15G15310.1 (Glycine max), 3'ss of exon 9
----------------------------gttggttgtcttcgtttgacaagttacatacatgacttttgtcttgctt--tagGTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAG
                              |  || |||  || |||||  ||   | |     |   || | |  |  ||||| ||||||||||| || || || ||||||||||||||  ||||||||||||| |||||||| || || || |||||||
gtttgtttcaaatgtttcatgaacacattatttttttctctgtctgacacattgt-tgctgatttagagtatggaatgatagGTTCCTCATTTGTATTGTATTGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCTGCCAGCGCACAAGGAATTTCAG

upper sequence: EFJ16882 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: AT4G16155.1 (Arabidopsis thaliana), 3'ss of exon 9
--------------------gttggttgtcttcgtttgacaagttacatacat---gacttttg------tcttgctt--tagGTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAG
                      | | |   ||| |   | |||||| |||  |     ||  ||      ||||| ||  ||||| || || |||||||||||||| ||||| ||||| ||||||||||||||||| || || |||||||| || ||||| |
gttagtggagttttctttcatatagcttatttcttaccaaaagttatatatttttaagctactgagtcactcttggttgatagGTTCCCCACTTGTACTGCATCGGTGATGCCAATGGTAAACTGATGCTTGCTCATGCAGCTAGTGCTCAAGGAATTTCTG

upper sequence: EFJ16882 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: Vv14s0060g01330.t01 (Vitis vinifera), 3'ss of exon 9
----------------------------gttggttgtcttcgtttgacaagttacatacatgacttttgtcttgctttagGTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAG
                            ||| ||||| ||  ||   |   | |    ||||  | ||   |   |  |||| ||||| ||||| ||||| || ||||||||||| ||| ||||||||||||| ||||| ||||| || || || || |
gttggtcattaatttccttaatgtctttgtttgttgtatttattcatcttttcattggcatgtatctttgatgaat--agGTTCCTCACTTGTATTGCATTGGTGATGCAAATGGAAAAATGATGCTTGCTCATGCTGCAAGTGCCCAAGGAATCTCTG

upper sequence: EFJ16882 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: Vv05s0077g01210.t01 (Vitis vinifera), 3'ss of exon 9
--------------------------gttggttgtcttcgtttgacaa--gttacatacatgacttttgtcttgctttagGTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAG
                            |  |||| |   || | | |  |||||  |||||    || | ||   |||||| ||||| ||||| ||||| || ||||||||||| ||| ||||||||||||| || || ||||| || || |||||||
gtctgttataattctcttacaagcacactttttgtgtggcttagccgattgttactgacatggaacttttttta--ttagGTTCCTCACTTGTATTGCATAGGTGATGCAAATGGTAAAATGATGCTTGCTCATGCAGCAAGTGCACAAGGAATTTCAG

upper sequence: EFJ16882 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: PP1S112_186V6.1 (Physcomitrella patens), 3'ss of exon 9
---------------------------------------------------------------------------------------------------gttggttgtcttcgtttgacaagttacatacatgacttttgtc----ttgctttagGTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAG
                                                                                                    ||||    | |  || ||  | | ||  | ||| || |||       || | |||||||| ||||||||||||||||| ||||||||||||||  ||||||||||||| || || || || || |||||||| |
gtaagcgatcttcgtctctttatgattcaccacttatgtaaccttagttatatggtatttttcgtgacaatctggtttgcgtgagagtaaacgacgtaatttgggcaccgtgtttagaatattaactcaaatggctcttggtgacggtgttctagGTACCGCATTTGTACTGCATCGGTGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCCCAAGGCATTTCTG

upper sequence: EFJ16882 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: PP1S35_94V6.1 (Physcomitrella patens), 3'ss of exon 9
----------------------------------------------------------------------------------------gttggttgtc--ttcgtttgacaagttaca-----tacatgactt-ttgtcttgctttagGTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAG
                                                                                        ||   | | |  || || | | |||||  |        || | || | |   || |  ||||||| || ||||| |||||||||||||||||||||||  ||||||||||||| || || || ||||| |||||||| |
gtgagtagcctcctacttgtggtcctctactgagtctatcttggatgctacttttgatgttgatctgaattgcgtgagagtgaacgatgtcaatgggcgttttgtctcagaagttgtaattatcttatcatttgtagcggtggtgcagGTACCACACTTGTATTGCATCGGCGATGCAAATGGCAAGATGATGCTTGCTCATGCAGCAAGCGCTCAAGGCATTTCGG

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), 29 (downstream exon)
Score: 9

GTTAATGTTGTAACTCAACGAGGATTTGTTCCCGTCGACGAGCGAATGCAAGTGCTAGATGGGAGAGGCGAACTGgttggttgtc ... cttgctttagGTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttggttgtcttcgtttgacaagttacatacatgacttttgtcttgctttagGTACCTCATTTGTACTGCATCGGCGATGCAAATGGCAAACTGATGCTTGCTCACGCTGCCAGTGCTCAGGGCATTTCAG
                gtttgac  putative branch site (score: 9)
                                      cttttgtcttgcttt  putative PPT
                          ttacata  TA-rich tract