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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtccactgtcaccgcttttccttgtctgtaagatcatgtgtgtgtgttgtgtgaaaagGTTTCATCATGATGTGCCCCCAGCTCTTCATCAACTACAAGCTCAAGTCCGTGGCGCACCTCCCCTGGCGCCAAATGACTTACAAGTTCCTCAACACAAT

Basic information

species Selaginella moellendorffii
transcript EFJ29253
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ29253 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: LOC_Os04g36050.1 (Oryza sativa), 3'ss of exon 10
---------------------------gtgagtccactgtcaccgcttttccttgtctgtaagatcatgtgtgtgtgttgtgtgaaaagGTTTCATCATGATGTGCCCCCAGCTCTTCATCAACTACAAGCTCAAGTCCGTGGCGCACCTCCCCTGGCGCCAAATGACTTACAAGTTCCTCAACACAAT
                           |||| || |||   ||   ||  |  ||  | | |   ||||| | ||   | |      ||||||||||||||||||||| || || ||||||||||||||||| ||||| || || ||  | || ||| | |||||||| ||||||||||||||||| ||
gtaagtaattactttctagttctctctgtga-tctactag-acaaattagcaatggattttaatgcatgtctttgcactcttc----agGTTTCATCATGATGTGCCCACAACTATTCATCAACTACAAGCTGAAGTCTGTTGCTCATATGCCATGGAGGCAAATGACCTACAAGTTCCTCAACACCAT

upper sequence: EFJ29253 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: GRMZM2G437119_T02 (Zea mays), 3'ss of exon 10
---------------------------gtgagtccactgtcaccgcttttccttgtctgtaagatcatgtg--tgtgtgttgtgtgaaaagGTTTCATCATGATGTGCCCCCAGCTCTTCATCAACTACAAGCTCAAGTCCGTGGCGCACCTCCCCTGGCGCCAAATGACTTACAAGTTCCTCAACACAAT
                           ||   |    ||| |     |      |  |  ||| |  | |   |   | |    |    ||||||||||||||||||||||||  | || |||||||||||||| ||||| || || ||  | || ||| | |||||||| ||||||||||||||||| ||
gtaagcaactattccactgtccctccagtttatttgatgtgataatctacataagcttagaagcttgtataattaactttccattcttcagGTTTCATCATGATGTGCCCCCAATTATTTATCAACTACAAGCTGAAGTCTGTTGCTCATATGCCATGGAGACAAATGACCTACAAGTTCCTCAACACTAT

upper sequence: EFJ29253 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: GRMZM2G016894_T01 (Zea mays), 3'ss of exon 9
---------------------------gtgagtccactgtcaccgcttttccttgtctgtaagatcatgtgtgtgtgttgtgtgaaa---agGTTTCATCATGATGTGCCCCCAGCTCTTCATCAACTACAAGCTCAAGTCCGTGGCGCACCTCCCCTGGCGCCAAATGACTTACAAGTTCCTCAACACAAT
                           ||  ||    | | |   | |    | |      || | || | |||   || |         ||||||||| ||||||||||||||  | || |||||||||||||| ||||| || || ||  | || ||| | |||||||| ||||||||||||||||| ||
gtaagcaactattccactccctcaccagtttgtttgatatgataacctgcattagctgtggagcttatatatgtaacttttccattcttcagGTTTCATTATGATGTGCCCCCAATTGTTTATCAACTACAAGCTGAAGTCTGTTGCTCATATGCCATGGAGACAAATGACCTACAAGTTCCTCAACACTAT

upper sequence: EFJ29253 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: GLYMA04G38120.1 (Glycine max), 3'ss of exon 10
--------------------------------gtgagtccactgtcaccgcttttccttgtct-gtaagatcat--gtgtgtgtgttgtgtgaa---aagGTTTCATCATGATGTGCCCCCAGCTCTTCATCAACTACAAGCTCAAGTCCGTGGCGCACCTCCCCTGGCGCCAAATGACTTACAAGTTCCTCAACACAAT
                                 ||       | | |     |||    || | ||||  |  |   ||| |||  | | || |    |||||| || ||||||||||| ||  | |||||||||||||||||||| || || || || || || ||| | ||||||||||||||||| |||||||| ||
aacacagatagtcacacacttaaccaatttcaatgcagattatattattaagtttataagttttgtaaactttttaatgtttgtactctttgtactgtagGTTTTATTATGATGTGCCCTCAATTGTTCATCAACTACAAGCTCAAATCTGTTGCTCATCTACCTTGGAGGCAAATGACTTACAAGTTTCTCAACACCAT

upper sequence: EFJ29253 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: GLYMA06G16940.1 (Glycine max), 3'ss of exon 10
----------------------------------------gtgagtccactgtcaccgcttttccttgtctgtaagatcatgtgtgtgtgttgtgtgaaaagGTTTCATCATGATGTGCCCCCAGCTCTTCATCAACTACAAGCTCAAGTCCGTGGCGCACCTCCCCTGGCGCCAAATGACTTACAAGTTCCTCAACACAAT
                                        ||   |    | |    |||||    ||| |||    |  |||   ||     |||   | || || || ||||||||||| ||  | |||||||||||||||||||| || || || || || || ||| | |||||||| |||||||| |||||||| ||
tctcacacttatccaatttcaatgcagattatatcattaagtttataagttttttaagctttgtaatgtttgtgctctt-tgtacttgaaaactgttgca-gGCTTTATTATGATGTGCCCTCAATTGTTCATCAACTACAAGCTCAAATCTGTTGCTCATCTACCTTGGAGGCAAATGACATACAAGTTTCTCAACACCAT

upper sequence: EFJ29253 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: AT5G23575.1 (Arabidopsis thaliana), 3'ss of exon 10
-------------------gtgagtccactgtcaccgcttttccttgtct-gtaagatcatgtgtgtgtgttgtgt-gaaaagGTTTCATCATGATGTGCCCCCAGCTCTTCATCAACTACAAGCTCAAGTCCGTGGCGCACCTCCCCTGGCGCCAAATGACTTACAAGTTCCTCAACACAAT
                    | |    |||||      | |  |||||   |     |   || || |  |||| | |   |||||||||||||||||| || ||||| ||||||||||||||||| || || ||||| ||  | || ||| | || ||||||||||||||||||||||| ||
gtaatagccttcaccatccttaaaataactgttgagaatctctcttgtgaagctgttttgagtttggggtttgttttgtgcagGTTTCATCATGATGTGTCCTCAGCTATTCATCAACTACAAGCTTAAATCAGTGGCACATTTACCATGGAGACAGATGACTTACAAGTTCCTCAACACCAT

upper sequence: EFJ29253 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: AT5G08500.1 (Arabidopsis thaliana), 3'ss of exon 10
--------------------------gtgagtccactgtcaccgcttttccttgtctgtaagatc---atgtgtgtgtgttgtgtga--aaagGTTTCATCATGATGTGCCCCCAGCTCTTCATCAACTACAAGCTCAAGTCCGTGGCGCACCTCCCCTGGCGCCAAATGACTTACAAGTTCCTCAACACAAT
                             ||| ||       ||  |       ||  |    ||   ||   ||||| ||||||    | ||||||||| |||||||| || ||  | ||||||||||| ||||| ||||| || || ||  | || ||| | |||||||| || |||||||||||||||||
gtaaaaatccttcaaaattaccttagaccagttcaaaactctcgtgtggttgattcaattgagtcgaaatcaatgtgttttgtgtttttacagGTTTCATAATGATGTGTCCTCAATTGTTCATCAACTATAAGCTGAAGTCAGTAGCACATTTACCATGGAGGCAAATGACATATAAGTTCCTCAACACAAT

upper sequence: EFJ29253 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: Vv07s0130g00170.t01 (Vitis vinifera), 3'ss of exon 10
----------------------------------------------------------------------------------------------gtgagtccactgtcaccgcttttccttgtctgtaa------gatcatgtgtgtgtgttgtgtga--aaagGTTTCATCATGATGTGCCCCCAGCTCTTCATCAACTACAAGCTCAAGTCCGTGGCGCACCTCCCCTGGCGCCAAATGACTTACAAGTTCCTCAACACAAT
                                                                                              |    |   || ||||  ||||   ||   | |||      ||  |  ||           |      ||||||||| ||||||||||| ||| | ||||| ||||| ||||| || || ||||| || || |||||| | || ||||| |||||||||||||| || ||
gtaagcccttgaattccttttattgttttctgctgctgctgctgctgttgttcccgagttcacatcagcccagttgggccatcaattcgcctcagcatctgttctttcacatctttgttttcgttataaatatctgacaacttgaacaaaaaactttgttgcagGTTTCATTATGATGTGCCCTCAGTTGTTCATAAACTATAAGCTGAAATCTGTGGCTCATCTACCCTGGAGGCAGATGACGTACAAGTTCCTCAATACCAT

upper sequence: EFJ29253 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: EDP02622 (Chlamydomonas reinhardtii), 3'ss of exon 14
------------------------------------------gtgagtccactgtcaccgcttttccttgtctgtaagatcatgtgtgtgtgttgt------gtgaaaagGTTTCATCATGA---TGTGCCCCCAGCTCTTCATCAACTACAAGCTCAAGTCCGTGGCGCACCTCCCCTGGCGCCAAATGACTTACAAGTTCCTCAACACAAT-----------------------
                                               | |  |   || |    | |    ||| | | |||     |    ||        ||       || |  |         |  || ||||| | | | ||||||||||||||||||||||||||||| ||||||||||| ||||||||||||||||||||||| ||                       
gtgcgcgcggtttggtaatcgcgtttgggcgcgcaactatccacagctacctttggactgacaatgcactcctgcaggctcagtcccgctacttaccccctagttgcgcccttccgccgctcacccatcaccgcagCTTTACTTGAACTACAAGCTCAAGTCCGTGGCGCACCTTCCCTGGCGCCAGATGACTTACAAGTTCCTCAACACCATTATCGACGACCTGTTCGCGTTCG

upper sequence: EFJ29253 (Selaginella moellendorffii), 3'ss of exon 10
lower sequence: PP1S64_201V6.1 (Physcomitrella patens), 3'ss of exon 10
------------------------------------------------------------------------------------gtgagtccactgtcaccgcttttccttgtctgtaagatcatgtgt--gtgtgtt-gtgtgaaa-agGTTTCATCATGATGTGCCCCCAGCTCTTCATCAACTACAAGCTCAAGTCCGTGGCGCACCTCCCCTGGCGCCAAATGACTTACAAGTTCCTCAACACAAT
                                                                                    || | |  || |||||   |  |   ||   || |  ||  ||       ||||  | || |  |||||| ||||||||||| || ||||| || |||||||||||| | ||||| || || ||| | || ||||| || ||||| |||||||||||||| || ||
gtaagttcaaggccatcattggtgattattcatgtttttctgggtgcacttgttggcttctctggatatcaattcaagtaattggttattagacagtcacacgtcgttaatggtggttatgtcgagtactaacctgttcatatgtaccagGTTTTATCATGATGTGTCCACAGCTTTTTATCAACTACAAGTTGAAGTCTGTAGCTCACATGCCTTGGCGACAGATGACCTACAAGTTCCTCAATACTAT

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: 31 (upstream exon), 33 (downstream exon)
Score: 8

GTTGTGTTGGGCTTCGCGATATATTCCCTTATTTATGACCGTCACAAGAGCTGGTACTCATGGATCCTGTCATCGCTTACGAGCTGTGTCTACACTTTTGgtgagtccac ... gtgtgaaaagGTTTCATCATGATGTGCCCCCAGCTCTTCATCAACTACAAGCTCAAGTCCGTGGCGCACCTCCCCTGGCGCCAAATGACTTACAAGTTCCTCAACACAAT




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