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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttactcttttcccttttagattctaaagagctccatatttatttattgaactctttgttatcatcttttctttgtgttgatgaatttcttatatgtatatttattgaactacaaggatcatacaattcctgttgatgcattacattatgaatttagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATGGACAAAGAATTCAA

Basic information

species Glycine max
transcript GLYMA08G22140.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os06g05180.1 (Oryza sativa), 3'ss of exon 15
gtatttactcttttcccttttagattctaaagagctccatatttatttattgaactctttgttatcatcttttctttgtgttgatgaatttcttatatgtatatttattgaactacaaggatcatacaattcctgttgatgcattacattatgaatttagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATGGACAAAGAATTCAA
                                         | ||| |  ||  |||  ||  |  || |||  |||||  | ||| ||||  |||     |||||  || |||||||     ||  |  ||| ||||      ||||||     |  |||| || || |||| ||| ||||| || ||||||||||||||||||||||| || |  |||||    || ||| | || ||||| ||||||||
----------------------------------------gtatatattgtgtgctccatgcaagaatttttattttgt--taatgtattttctattgtagtattttgtgcactacaa-----attta--tcccgttg------tacatt-----tacagGTCACCACGATGTATCACTTGGATCGCCCTATGTACTTGTTGGGATATCTAGCGAATCAAAGCCGAGTTTATCTTATTGACAAGGAATTCAA

upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G000645_T01 (Zea mays), 3'ss of exon 15
gtatttactcttttcccttttagattctaaagagctccatatttatttattgaactctttgttatcatcttttctttgtgttgatgaatttcttatatgtatatttattgaactacaaggatcatacaattcctgttgatgcattacattatgaatttagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATGGACAAAGAATTCAA
                                           ||  ||| |  ||  | |  | ||| | ||||    |||  | ||||   ||||||   | ||  ||     || |  |   |    |    | | |  |   | ||||   |  |||| |||||||||| ||||||||| || ||||||||||||||||||||| |||| | |||||||   || ||| | || ||||| || || ||
------------------------------------------gtaaatatagt-ctgctcgaaaacatttcttct----gtt--taaattctctatatgggcacttcatgt----catgacttcaattgcttacatagttataa-gctttatacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACTTGTTGGGATATATTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTGAA

upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G095348_T03 (Zea mays), 3'ss of exon 15
gtatttactcttttcccttttagattctaaagagctccatatttatttattgaactctttgttatcatcttttctttgtgttgatgaatttcttatatgtatatttattgaactacaaggatcatacaattcctgttgatgcattacattatgaatttagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATGGACAAAGAATTCAA
                                         |  |  || |  |||| |||  | | | || |  |   |||  | | ||   ||||||   | ||  |||   || |   |   |   ||      | |  |   | || |   |  |||| |||||||||| ||||||||| || ||||||||| | |||||||||||||| | |||||||   || ||| | || ||||| || || ||
----------------------------------------gtaaaaatagtctactccttgaaaacgttttcttct---gtt--taagttctctatatggccactttgtgagtcacgac--ttcaattgtttacacagttataa-gctttgtacttacagGTCACTACAATGTATCATTTGGATCGCCCTATGTACCTATTGGGATATCTTGCGAACCAAAGTCGAGTTTATCTTATTGACAAGGAGTTTAA

upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G443953_T03 (Zea mays), 3'ss of exon 16
gtatttactcttttcccttttagattctaaagagctccatatttatttattgaactctttgttatcatct--tttctttgtgttgatgaatttcttatatgtatatttattgaactacaaggatcatacaattc------ctgttgatgcattacattatgaatt-tagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATGGACAAAGAATTCAA
                                                            |||| ||  |  ||||    |  |    |   ||||  ||| |||| | ||  | | |   ||   |    ||       || |  ||  |  |  | |||  ||  ||||||||||||||||||| ||||| || |||||||| || || ||||||||||| | |||||||   || ||| | || ||||| ||||| ||
------------------------------------------------------------gttaacacttaatttcaccataatctgtagaatcttgaatgcatatctgtttgattcctgagagtgtttggttttatgtgctatctatttaccatctcatgtgttacagGTTACTACAATGTTTCACTTGGATCGGCCTATGTATTTATTAGGATATCTTGCTAACCAAAGTCGTGTATATCTTATTGACAAGGAATTTAA

upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 15
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 19
gtatttactcttttcccttttagattctaaagagctccatatttatttattgaactctttgttatcatcttttctttgtgtt--gatgaatttcttatatgtatatttattgaactacaaggatcatacaattcctgttgatgcattacattatgaatttagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATGGACAAAGAATTCAA
                                                            || |   || |||||  || ||  ||   |    || ||||| | ||||||    |  ||     || || | |   |       ||| ||||       |||| |||||||||| |||| ||||||||||||||||||||||||| ||||| || |  ||||| | ||| |||||||| |||||||| |||||
------------------------------------------------------------gtaaggctcatttctaggtttttggaaagaaacgttttatgttt-tttattttgttgtaattgagattcagtactcctc------ttatatta------cagGTAACTACAATGTATCATCTGGACCGTCCTATGTACTTGTTGGGTTATCTCGCTAATCAAAGCAGGGTTTATTTGATTGACAAAGAGTTCAA

upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 15
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 3'ss of exon 15
gtatttactcttttcccttttagattctaaagagctccatatttatttattgaactctttgttatcatcttttctttgtgttgatgaattt-cttatatgtatatttat-tgaactacaaggatcatacaattcctgttgatgcattacattatgaatttagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATGGACAAAGAATTCAA
                                                                             ||  | | || | |  || ||| | || | || |  |  |     || ||| |||  ||| | ||  |      | ||     |||| || ||||||| |||||||||||| || ||||| ||||| || ||| |||||| ||||||   ||| || ||| | ||||||||||||||
-----------------------------------------------------------------------------gtactcaagagtctatttttatttctaatcatctttatgagctacattatataatagctgctaatatacc----tgtgg---cagGTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTAGGCTATATTGCCAACCAAAGCCGGGTTTACTTGGTAGACAAAGAATTCAA

upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 15
lower sequence: AT1G52360.2 (Arabidopsis thaliana), 3'ss of exon 15
gtatttactcttttcccttttagattctaaagagctccatatttatttattgaactctttgttatcatcttttctttgtgttgatgaatttcttatatgtatatttattgaactacaaggatcatacaattcctgttgatgcattacattatgaatttagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATGGACAAAGAATTCAA
                                                                  ||  |   | | ||||| | | | |  | |     |  |||| |||||    ||||  ||       || || |   | ||||  | |   ||||| || ||||||| |||||||||||| || ||||| ||||||||||||||||| || ||||||  ||| |  ||| | ||||||||||||||
----------------------------------------------------------------gtattgtgcatatatgttggttactctgatttggaagttgttat-gaact----ggattctaa------tgatggttgctaacatcgtaatactagGTAACCACAATGTATCATTTGGACCGCCCAATGTATTTGTTGGGATATCTTGCAAGTCAAAGTCGGGTTTTCTTGGTAGACAAAGAATTCAA

upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 15
gtatttactcttttcccttttagattctaaagagctccatatttatttattgaactctttgttatcatcttttctttgtgttgatgaatttcttatatgtatatttattgaactacaaggatcataca-attcctgttgatgcattacattatgaatttagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATGGACAAAGAATTCAA
                                                   | | | | | || ||  |  || | | ||    | | || | ||| || | ||    |  | | || ||||       |    | ||| |  || ||  ||||  |  |||| || |||||||||||||||||||| |||||||| |||||||||||||| || |  |||||   ||| ||| | || |||||||| |||||
---------------------------------------------------gtattgtgtattgtccacccttgtct-tgaaagt-atttccatatgtgcagatgatatccatttcatggatttcttggagcttttttgttaaataaccatatgt-tccagGTAACCACAATGTTTCATTTGGACCGGCCTATGTATTTGTTGGGATATCTAGCTAATCAAAGCCGGGTGTATCTCATAGACAAAGAGTTCAA

upper sequence: GLYMA08G22140.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 15
gtatttactcttttcccttttagattctaaagagctccatatttatttattgaactctttgttatcatcttttctttgtgttgatgaatttcttatatgtatatttattgaactacaaggatcatacaattcctgttgatgcattacattatgaatttagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATGGACAAAGAATTCAA
                                                           | | |     ||   |    ||||    |||||| |||| |||  |  |   | |  ||||    | || | | | |  ||   | |  | |||| || |||| || || |||||||| |||||||| |||||||| ||||| |||||||||||||| ||||||   || ||| | || |||||||| || ||
----------------------------------------------------------gtataagagagttgattccaggttg---tatttct-atatatatgatcttc--attctaagg----tgcagt-catataaattgttaatgtgatgatttcagGTAACCACCATGTTTCACTTGGACCGGCCTATGTATTTGTTAGGATATCTTGCCAGTCAAAGTCGCGTTTATCTTATAGACAAAGAGTTTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgaactacaaggatcatacaattcctgttgatgcattacattatgaatttagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATGGACAAAGAATTCAA
                            tgttgat  putative branch site (score: 4)
                                     attacattatgaattt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttactcttttcccttttagattctaaagagctccatatttatttattgaactctttgttatcatcttttctttgtgttgatgaatttcttatatgtatatttattgaactacaaggatcatacaattcctgttgatgcattacattatgaatttagGTTACTACAATGTTTCATTTGGACCGTCCTATGTACTTGTTGGGATATCTTGCCAGCCAAAGTAAGGTCTATTTGATGGACAAAGAATTCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA