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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgcttcaacctttggtatttccatcacatcctttgtttttccagATTGTTTTCTTGTGGAACAAGCAAGGATGGTGAGTCTTTTCTTGTGGAGTGGAATGAAAGTGAAGGTGCAATTAAAAACACCTACAATGGTTTTCGGAAA

Basic information

species Selaginella moellendorffii
transcript EFJ30926
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: EFJ30926 (Selaginella moellendorffii), 3'ss of exon 14
lower sequence: LOC_Os03g14980.1 (Oryza sativa), 3'ss of exon 15
-----------------------------------------gtttgcttcaacctttggtatttccatcacatcctttgttttt--ccagATTGTTTTCTTGTGGAACAAGCAAGGATGGTGAGTCTTTTCTTGTGGAGTGGAATGAAAGTGAAGGTGCAATTAAAAACACCTACAATGGTTTTCGGAAA
                                          |  | ||    ||||| | |  |     | |  |    || |    || || ||||||||||| || ||||||||||| || ||   ||| ||||| ||||||||||||||||| ||  | || |  || ||| | || ||||| || 
gttcataattatttctttgttagcatgattcatgtgggtaactgggtttttgtctttgttttcactgattctttttgcccttgtgagtagGTTATTTTCTTGTGGGACTAGCAAGGATGGCGAATCACATCTAGTGGAATGGAATGAAAGTGAAGGAGCTGTCAAGAGAACTTACCAGGGATTTCGCAAG

upper sequence: EFJ30926 (Selaginella moellendorffii), 3'ss of exon 14
lower sequence: GLYMA10G29090.1 (Glycine max), 3'ss of exon 15
------------------------------------------------------------------------gt-ttgcttcaacctttggtatttccatcacatcctttgtttttccagATTGTTTTCTTGTGGAACAAGCAAGGATGGTGAGTCTTTTCTTGTGGAGTGGAATGAAAGTGAAGGTGCAATTAAAAACACCTACAATGGTTTTCGGAAA
                                                                        || ||   | ||  |||  |||  |  |  |     |  ||| ||||| || ||||||||||| ||||| || ||||| |||||||||||||| || ||||||||||||||||| || ||||| |  || |||||||| ||  | |||
gtaagttggatatggatgagggtaattattcctttacagtatcatgcttggtgcttggtggacgtttaagatgtattatattaaagtttcttatgacattttccaaaatattttctccagGTTATTTTCTTGTGGGACAAGTAAAGATGGAGAGTCTTTTCTTGTTGAATGGAATGAAAGTGAAGGAGCCATTAAGAGAACATACAATGGATTCAGAAAA

upper sequence: EFJ30926 (Selaginella moellendorffii), 3'ss of exon 14
lower sequence: GLYMA20G38230.1 (Glycine max), 3'ss of exon 15
-----------------------------------------------------------------gt-ttgcttcaacctttggtatttccatcacatcctttgtttttccagATTGTTTTCTTGTGGAACAAGCAAGGATGGTGAGTCTTTTCTTGTGGAGTGGAATGAAAGTGAAGGTGCAATTAAAAACACCTACAATGGTTTTCGGAAA
                                                                 || ||   | ||  |||  |||  |  |  |     |  ||| ||||| || ||||||||||| ||||| || ||||| |||||||||||||| || ||||||||||||||||| || || || |  || |||||||| ||  | |||
gtaagatggatttggatgagggtaattattcggttacagtatcatgctcaatggataattaagatgtattatattaaagtttcttatgacactttccaaaatattttctccagGTTATTTTCTTGTGGGACAAGTAAAGATGGAGAGTCTTTTCTTGTTGAATGGAATGAAAGTGAAGGCGCCATCAAGAGAACATACAATGGATTCAGAAAA

upper sequence: EFJ30926 (Selaginella moellendorffii), 3'ss of exon 14
lower sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 15
--------------------------------------------------------------------gtttgcttcaacct--ttggtatttccatcacatcct--ttgtttttccagATTGTTTTCTTGTGGAACAAGCAAGGATGGTGAGTCTTTTCTTGTGGAGTGGAATGAAAGTGAAGGTGCAATTAAAAACACCTACAATGGTTTTCGGAAA
                                                                     ||   |  ||||   ||   || ||   |   |  |  || ||| |  ||| |||||||||| ||||| || || ||||| ||||| |||||||| || ||||||||||||||||| || ||||| |  || |||||||| ||  | || 
gtaagaaggatttgggtgcggataagtatttaagtttcatgttcaatggataattgaatttgagatgtattaaataaaaccgtattaacatgtcttcctatttatcattatttctatagACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAGTCATTTCTTGTTGAATGGAATGAAAGTGAAGGAGCCATTAAGAGAACATACAATGGGTTCAGAAAG

upper sequence: EFJ30926 (Selaginella moellendorffii), 3'ss of exon 14
lower sequence: GLYMA19G41840.2 (Glycine max), 3'ss of exon 14
-----------------------------------------------------------------------gtttgcttcaacctttggtatttccatca--catcctttgtttttccagATTGTTTTCTTGTGGAACAAGCAAGGATGGTGAGTCTTTTCTTGTGGAGTGGAATGAAAGTGAAGGTGCAATTAAAAACACCTACAATGGTTTTCGGAAA
                                                                           |  | ||| |   || || | ||    | ||| || ||| |  ||| |||||||||| ||||| || || ||||| || || |||||||| || ||||||||||||||| | || ||||| |  || |||||||| ||  | || 
gtaagaaggatttgggtgcggataagtatttaagtttcatgttcaatggataattaagatgtattaaataaaaccgtattaacat---gtcttcctatttgtcttccattatttctatagACTGTTTTCTTGCGGAACTAGTAAAGATGGAGAATCATTTCTTGTTGAATGGAATGAAAGTGAAAGAGCTATTAAGAGAACATACAATGGGTTCAGAAAG

upper sequence: EFJ30926 (Selaginella moellendorffii), 3'ss of exon 14
lower sequence: AT5G27030.2 (Arabidopsis thaliana), 3'ss of exon 13
-------------------------------------------------------------------------------------------------------------------------------------------gtttgcttcaaccttt--ggtatttccatcacatcctttgtttttccagATTGTTTTCTTGTGGAACAAGCAAGGATGGTGAGTCTTTTCTTGTGGAGTGGAATGAAAGTGAAGGTGCAATTAAAAACACCTACAATGGTTTTCGGAAA
                                                                                                                                            |||   |  ||||||   ||  || | | |  |  |||     | ||||||||| ||||||||||| || || ||||| || ||||| || || ||||||||||||||||||||  |||||||||  || || || |  |||| ||||
gtaagatcttaaactcataaacatttccctcttctataccgcttgttcttcactcctcagtttccaaaatcttcagattcttttgtttactccggaggatactgagttgtgtccttgagtttctaatcttatctttctgttttaagtttaccttttcagtgctttc-tgatgttttttcccccttcagATTGTTCTCTTGTGGAACGAGTAAAGATGGAGATTCTTTCCTAGTTGAGTGGAATGAAAGTGAAGGATCAATTAAAAGGACGTATAAAGAGTTTCAGAAA

upper sequence: EFJ30926 (Selaginella moellendorffii), 3'ss of exon 14
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 14
----------------------------------------------------------------------------------------------------------------------------------------------------------gtttgcttcaacctttggtatttccatcacatcctttgtttttccagATTGTTTTCTTGTGGAACAAGCAAGGATGGTGAGTCTTTTCTTGTGGAGTGGAATGAAAGTGAAGGTGCAATTAAAAACACCTACAATGGTTTTCGGAAA
                                                                                                                                                           ||||   | |  ||  |  |||   |  | || | | | ||| ||||||||| |||||||||||||| || ||||| || |||||| | || || ||||||||||||||||| ||||| || |  || || ||||| ||| | || 
gtaagattggtgaaattcacaattccagacctaataaaattttattttatttttctttttgctcaatttaaaatttcaacttttctgtaatgttgttatagttgtcttttcataccatactgtgctacttttgatcaaatatatctgacagaacatttgtaactaatttgtgactttttttttcctcttct-tcttttcagATTGTTCTCTTGTGGAACAAGTAAAGATGGGGACTCTTTTTTGGTTGAATGGAATGAAAGTGAAGGAGCAATAAAGAGGACGTATAATGGGTTTAGAAAG

upper sequence: EFJ30926 (Selaginella moellendorffii), 3'ss of exon 14
lower sequence: Vv09s0002g08370.t01 (Vitis vinifera), 3'ss of exon 14
---------------------------------------------------------------------------gtttgcttcaacctttggtatttccatcacat------cctttgtttttccagATTGTTTTCTTGTGGAACAAGCAAGGATGGTGAGTCTTTTCTTGTGGAGTGGAATGAAAGTGAAGGTGCAATTAAAAACACCTACAATGGTTTTCGGAAA
                                                                           |  |  ||  |  |||    ||||  ||   |        ||  | ||| |||  | ||||| ||||||||||| |||||||| || || | | | || || ||||||||||||||||| ||| ||||||  |||||| | || ||  |||||
gttggtttactcttacccatttgctagtgctacaagtcctcatcatttgttggtgtgccaatcagaattattgatgagtattttgatgtttaccttttctttcgggtggtgggttttcatatttacagGCTCTTTTCATGTGGAACAAGTAAGGATGGGGATTCATATATCGTTGAATGGAATGAAAGTGAAGGGGCAGTTAAAAGGACCTACCAAGGGTTCAGGAAA

upper sequence: EFJ30926 (Selaginella moellendorffii), 3'ss of exon 14
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 14
---------------------------------------------------gtttgcttcaacc-tttggtatttccatcacatcctttgttt-ttccagATTGTTTTCTTGTGGAACAAGCAAGGATGGTGAGTCTTTTCTTGTGGAGTGGAATGAAAGTGAAGGTGCAATTAAAAACACCTACAATGGTTTTCGGAAA
                                                    |||||  |||   |||   |||   |     | ||||||     ||||| | |||||||||||||| ||||| ||||| || |||| ||| ||||| |||||||| || ||||| ||||||||    || |||   ||||| || || 
tcgctttcgaattaagttgagtgaatttaggacgtgatgtgtccatcttgtatttgcgacaatgatttttgattatgaattttttctttgtggacgccagACTCTTTTCTTGTGGAACTAGCAAAGATGGAGAATCTTATCTGGTGGAATGGAATGAGAGCGAAGGCGCAATTAAGCGGACATACTCAGGTTTCCGCAAG

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: 9

AAATCAAAGCTTGGCTTTACGATAATCTCGGTTCTCGAGTAGATTATGATGCTCCTGGTCGCTGGTGCACAACAATGGCTTACAGTGCGGATGGAACAAGgtttgcttca ... gtttttccagATTGTTTTCTTGTGGAACAAGCAAGGATGGTGAGTCTTTTCTTGTGGAGTGGAATGAAAGTGAAGGTGCAATTAAAAACACCTACAATGGTTTTCGGAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtttgcttcaacctttggtatttccatcacatcctttgtttttccagATTGTTTTCTTGTGGAACAAGCAAGGATGGTGAGTCTTTTCTTGTGGAGTGGAATGAAAGTGAAGGTGCAATTAAAAACACCTACAATGGTTTTCGGAAA
                                            catcctttgtttttcc  CT-rich tract
                                          tttgttttt  TA-rich tract