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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacacaaaagctacatattgtattaatgtaattgatgacttaattgatgactttttgtgatcagGCCATGATATACCAGCAAAAAGCTTTGGACATAAATGAGAGGGAGCTTGGACTTGACCATCCGGATACAATGAAAAGCTATGGTGACTTGGCTGTCTTTT

Basic information

species Selaginella moellendorffii
transcript EFJ08067
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ24726 (Selaginella moellendorffii), 3'ss of exon 17
lower sequence: GRMZM2G318635_T01 (Zea mays), 3'ss of exon 17
----------------------------gtacacaaaagctacatattgtatta--atgtaattgat-gacttaattgatgac----tttttgtgatcagGCCATGATATACCAGCAAAAAGCTTTGGACATAAATGAGAGGGAGCTTGGACTTGACCATCCGGATACAATGAAAAGCTATGGTGACTTGGCTGTCTTTT
                             | ||||| |||    |  | |  ||   ||| |  | |  |||| ||  |||       | ||   | ||||| |  || || || || || ||||| || || ||||||||||| |||||||||||||| || |||||||||||||||||||| ||  | ||||| || |
atatgcacttgtcaggtgtttaatttttttccacaacagcgtagttctatcctatgctgtgaaggcttaactttataaatgttgctgctctttcaaacagGCAACCATCTATCAACAGAAGGCTTTAGATATTAATGAGAGGGAACTTGGACTTGACCACCCAGATACAATGAAAAGCTATGGAGATCTTGCTGTTTTCT

upper sequence: EFJ24726 (Selaginella moellendorffii), 3'ss of exon 17
lower sequence: GLYMA08G22850.1 (Glycine max), 3'ss of exon 16
-------------------------------gtacacaaaagctacatat---tgtattaatgtaattgatgacttaattgatga-ctttttgtgatcagGCCATGATATACCAGCAAAAAGCTTTGGACATAAATGAGAGGGAGCTTGGACTTGACCATCCGGATACAATGAAAAGCTATGGTGACTTGGCTGTCTTTT
                                | |   |  |||   |     ||| | || | || |  | | ||| ||  |   |||| | |  | ||||||  || || |||||||| || ||||| ||||||||||| |||||||| |||||||| || || || |||||||||||||| ||  |  |||||||||
tatgcatgcgcttgacttgaggaagtgctgcatcctgcatggctgtgtgcacctgtttgaaggaaaatattaatttatttattattctttctttatttagGCCACCATCTATCAGCAAAAGGCCTTGGATATAAATGAGAGAGAGCTTGGGCTTGACCACCCTGACACTATGAAAAGCTATGGGGATCTTTCTGTCTTTT

upper sequence: EFJ24726 (Selaginella moellendorffii), 3'ss of exon 17
lower sequence: GLYMA07G03250.1 (Glycine max), 3'ss of exon 18
-------------------------------------gtacacaaaagctacatattgtattaatgtaattgatgacttaattgatgactttttgtgatcagGCCATGATATACCAGCAAAAAGCTTTGGACATAAATGAGAGGGAGCTTGGACTTGACCATCCGGATACAATGAAAAGCTATGGTGACTTGGCTGTCTTTT
                                     |    ||   | | ||   | |  ||||   ||| ||   ||  ||  |  |||| | |  | ||||||  || || |||||||| || ||||| ||||||||||||||||| || |||||||| || || || |||||||||||||| ||  |  | |||||||
tatacatgctcttgacttgaggaagttctgcatggctgcgtgcacctgtttcaaggtctgctaattatattaatttattttttatt--ctttatttatttagGCCACCATCTATCAGCAAAAGGCCTTGGATATAAATGAGAGGGAGCTAGGGCTTGACCACCCTGACACTATGAAAAGCTATGGGGATCTTTCCGTCTTTT

upper sequence: EFJ24726 (Selaginella moellendorffii), 3'ss of exon 17
lower sequence: GLYMA04G24430.1 (Glycine max), 3'ss of exon 14
----------------------------gtacacaaaagctacatattgtattaatgtaattgatgacttaattgatgacttt--ttgtgatc-----agGCCATGATATACCAGCAAAAAGCTTTGGACATAAATGAGAGGGAGCTTGGACTTGACCATCCGGATACAATGAAAAGCTATGGTGACTTGGCTGTCTTTT
                              |      |   |  ||     |||||   ||  |  ||     | || |||||   |||| |      |||| |  || || |||||||| ||  | ||||| ||||| || ||||||||||| |||||||| ||||| |||||||| ||||| ||  | ||||| || |
ctcgatatagagacctaccttttaagtaacatttttgaataaggtacccagttaattccatccagtaccattgtaataactttagctgtggttttgctagGCAACTATCTATCAGCAAAAGGCACTAGACATTAATGAAAGAGAGCTTGGACTGGACCATCCTGATACGATGAAAAGTTATGGGGATCTTGCTGTTTTCT

upper sequence: EFJ24726 (Selaginella moellendorffii), 3'ss of exon 17
lower sequence: GLYMA06G30000.1 (Glycine max), 3'ss of exon 15
----------------------------gtacacaaaagctacatattgtattaatgtaattgatgacttaattgatgacttt--ttgtgatc-----agGCCATGATATACCAGCAAAAAGCTTTGGACATAAATGAGAGGGAGCTTGGACTTGACCATCCGGATACAATGAAAAGCTATGGTGACTTGGCTGTCTTTT
                             |       |   |         |||||   |||||  |      | || | |||   |||| |      |||| |  || || |||||||| ||  | || || ||||| || ||||||||||| |||||||| ||||| |||||||| ||||| ||  | ||||| || |
gacttgattgacacctaatatttaaggaattttttttaataaggggccaagttaattccattgagtatcattataataaatttagctgtggttttgctagGCAACTATCTATCAGCAAAAGGCACTAGATATTAATGAAAGAGAGCTTGGACTGGACCATCCTGATACGATGAAAAGTTATGGAGATCTTGCTGTTTTCT

upper sequence: EFJ24726 (Selaginella moellendorffii), 3'ss of exon 17
lower sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 18
---------------gtacacaaaa-gctacatattgtattaatgtaattgatgacttaattgatgactttttgtgatcagGCCATGATATACCAGCAAAAAGCTTTGGACATAAATGAGAGGGAGCTTGGACTTGACCATCCGGATACAATGAAAAGCTATGGTGACTTGGCTGTCTTTT
                |    | |  |  | || ||   || || | |    ||    | |  | || ||| |   | ||||| |  ||||| |||||||| ||||| ||||| ||||||||||| ||||||||||| ||||| ||||||||||| || ||||||||  | |||||||| |
gtctgtatatattatatggttagattgtgatatctttcctttatatgacaattgtgaaactaaaagattttgttaaaacagGCTACAATATATCAGCAAAAGGCTTTAGACATCAATGAGAGGGAACTTGGACTTGATCATCCAGATACAATGAAGAGTTATGGTGATCTTGCTGTCTTCT

upper sequence: EFJ24726 (Selaginella moellendorffii), 3'ss of exon 17
lower sequence: AT4G28080.1 (Arabidopsis thaliana), 3'ss of exon 17
--------------------------------------gtacacaaaagctacatattgtattaatgtaattgatgacttaattgatgactttttgtgatcagGCCATGATATACCAGCAAAAAGCTTTGGACATAAATGAGAGGGAGCTTGGACTTGACCATCCGGATACAATGAAAAGCTATGGTGACTTGGCTGTCTTTT
                                       |     ||    || || |   ||  |  |   ||   |   |   |  | | ||| |  |||||| |  || || ||||| |||||  | ||||||||||| ||||| ||||||||||| || || || |||||||||||||| || ||| |||||||||| |
gtattctctttgaaagaaatttggaccgtctccaagacattgttcaatttcacctactccgtt--tccagcagacagcactaaccagtattgttttt--tcagGCTACCATTTATCAGCAGAAAGCACTCGACATAAATGAAAGGGAACTTGGACTTGATCACCCAGACACAATGAAAAGCTACGGCGACCTGGCTGTCTTCT

upper sequence: EFJ24726 (Selaginella moellendorffii), 3'ss of exon 17
lower sequence: AT1G15290.1 (Arabidopsis thaliana), 3'ss of exon 15
------------------------------------------------------------------gtacacaaaagctacatattgtat-taatgtaattgatga-------cttaattgatgactttttgt--------gatcagGCCATGATATACCAGCAAAAAGCTTTGGACATAAATGAGAGGGAGCTTGGACTTGACCATCCGGATACAATGAAAAGCTATGGTGACTTGGCTGTCTTTT
                                                                   |   |     |||   | ||||| |||   |||||||||       | | ||   ||| ||||| |        |||||||| |  ||||| ||||| || ||| | || ||||||||||| || ||||| || |||||||| || || |||||||||||||| ||  |  |||| ||||
gtatcatcatcttttatcttcttcccaaatggaaactttgatttcaagtaacaaatagagagtttgatgttctcgttctaggcactgtatataaataaattgatgagaggtaccgtcatctctgattttttatcctctcttgatcagGCAACAATATATCAGCAGAAGGCTCTAGATATAAATGAGAGAGAACTTGGTCTCGACCATCCCGACACTATGAAAAGCTATGGGGATCTTTCTGTATTTT

upper sequence: EFJ24726 (Selaginella moellendorffii), 3'ss of exon 17
lower sequence: Vv11s0037g00840.t01 (Vitis vinifera), 3'ss of exon 17
------------------------------------gtacacaaaagctacatattgtattaatgtaattgatgacttaattgatgactttttgtgatcagGCCATGATATACCAGCAAAAAGCTTTGGACATAAATGAGAGGGAGCTTGGACTTGACCATCCGGATACAATGAAAAGCTATGGTGACTTGGCTGTCTTTT
                                     ||    |||  ||    |   |||||  |  || ||    |      |   | ||| |  | |||| |  || || ||||||||||||||||| || |||||||| |||||||||||||| ||||| |||||||||||||| ||||| ||  | ||||| || |
cacttcatttgaagaaagacattgtcctgggattttctatttgaaaaataatattcacattaaattgtttcatattattggccctatttatttttcgt-agGCAACCATCTATCAGCAAAAAGCTTTGGATATCAATGAGAGAGAGCTTGGACTTGATCATCCTGATACAATGAAAAGTTATGGGGATCTTGCTGTTTTCT

upper sequence: EFJ24726 (Selaginella moellendorffii), 3'ss of exon 17
lower sequence: Vv09s0002g07530.t01 (Vitis vinifera), 3'ss of exon 17
-------------------------------------gtacacaaaagctacatattgtattaatgtaattgatgacttaattgatgactttttgtgatcagGCCATGATATACCAGCAAAAAGCTTTGGACATAAATGAGAGGGAGCTTGGACTTGACCATCCGGATACAATGAAAAGCTATGGTGACTTGGCTGTCTTTT
                                      |      |||  ||   |    ||  | || |   | |  | |   ||    ||   ||   |||| |  ||||| || || || |||||||| || ||||||||||| ||||| ||||||||||| |||||||||||||||||||| ||  |  | || ||||
tttccagctgcttggtctcgttggttttctgtgttgtatgtctgcaagtgactggtccagttgctttattctctaaactta--aattttcttccttgtctagGCAACTATATATCAACAGAAGGCTTTGGATATCAATGAGAGGGAACTTGGGCTTGACCATCCTGATACAATGAAAAGCTATGGAGATCTTTCAGTTTTTT

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), 30 (downstream exon)
Score: 12

GACAAAATTGATAGCTGTTTGCGGGCCTTACCATCGAATGACTGCTGGAGCATATAGTTTGCTTGCAGTGGTTCTTTACCACACAGGAGACTTCAATCAGgtacacaaaa ... ttgtgatcagGCCATGATATACCAGCAAAAAGCTTTGGACATAAATGAGAGGGAGCTTGGACTTGACCATCCGGATACAATGAAAAGCTATGGTGACTTGGCTGTCTTTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctacatattgtattaatgtaattgatgacttaattgatgactttttgtgatcagGCCATGATATACCAGCAAAAAGCTTTGGACATAAATGAGAGGGAGCTTGGACTTGACCATCCGGATACAATGAAAAGCTATGGTGACTTGGCTGTCTTTT
                                         ctttttgt  CT-rich tract
     atattgtattaatgta  TA-rich tract