JAR3D on RF03125

RF03125 Sarbecovirus 3'UTR

Input Summary

      000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000000111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111111122222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222222223333333333333333333333333333333333333333333333333333333333333
000000000111111111122222222223333333333444444444455555555556666666666777777777788888888889999999999000000000011111111112222222222333333333344444444445555555555666666666677777777778888888888999999999900000000001111111111222222222233333333334444444444555555555566666666667777777777888888888899999999990000000000111111111122222222223333333333444444444455555555556
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.............(...........................................................................................................................................................................................................(((((....(((...((.....))......)))...))))).)....(((((.......((.....)).....)))))........................((((((((((.....))))))))))................
>DQ071615.1_29386-29716
-----------------------------GAUGACCACACAAGGCAGAUGGGCUAUGUAAACGUUUUCGCAAUUCCGUUUACGAUACAUAGUCUACUCUUGCGUAGAAUGAGUUCUCGUAGCUAAACAGCACAAGUAGGUUUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCAAUGUGUAACAUUAGGGAGGACUUGAAAGAGCCACCACAUUUUCACCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUAAUGCUAGGGAGAGCUGCCUAUAUGGAAGAGCCCUAAUGUGUAAAAUUAAUUUUAGUAGUGCUAUCCCCAUGUGAUUUUAAUAGCUUCUUAGGAGAAUGAC
>DQ022305.2_29378-29704
---------------------------------ACCACACAAGGCAGAUGGGCUAUGUAAACGUUUUCGCAAUUCCGUUUACGAUACAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAGCUAAACAGCACAAGUAGGUUUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCAAUGUGUAACAUUAGGGAGGACUUGAAAGAGCCACCACAUUUUCACCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUAAUGCUAGGGAGAGCUGCCUAUAUGGAAGAGCCCUAAUGUGUAAAAUUAAUUUUAGUAGUGCUAUCCCCAUGUGAUUUUAAUAGCUUCUUAGGAGAAUGAC
>KJ473812.1_29093-29436
----------------CAUAAACACUCAUGAUGACCACACAAGGCAGAUGGGCUAUGUAAACGUUUUCGCAAUUCCGUUUACGAUACAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAACUAAACAGCACAAGUAGGUUUAGUUAACUUUAAUUUCACAUAGCAAUCUUUAAUAAAUGUGUAAUGUUAGGGAGGACUUGAAAGAGCCACCACAUUUUCACCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUAAUGCUAGGGAGAGCUGCCUAUAUGGAAGAGCCCUAAUGUGUAAAAUUAAUUUUAGUAGUGCUAUCCCCAUGUGAUUUUAAUAGCUUCUUAGGAGAAUGAC
>AY772062.1_29111-29460
----------CUCAGGCAUAAACACUCAUGAUGACCACACAAGGCAGAUGGGCUAUGUAAACGUUUUCGCAAUUCCGUUUACGAUACAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAACUAAACAGCACAAGUAGGUUUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCAAUGUGUAACAUUAGGGAGGACUUGAAAGAGCCACCACAUUUUCAUCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUAAUGCUAGGGAGAGCUGCCUAUAUGGAAGAGCCCUAAUGUGUAAAAUUAAUUUUAGUAGUGCUAUCCCCAUGUGAUUUUAAUAGCUUCUUAGGAGAAUGAC
>KF367457.1_29959-30293
-------------------------UCAUGAUGACCACACAAGGCAGAUGGGCUAUGUAAACGUCUUCGCAAUUCCGUUUACGAUACAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAGCUAAACAGCACAAGUAGGUUUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCAAUGUGUAACAUUAGGGAGGACUUGAAAGAGCCACCACAUUUUCACCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUAAUGCUAGGGAGAGCUGCCUAUAUGGAAGAGCCCUAAUGUGUAAAAUUAAUUUUAGUAGUGCUAUCCCCAUGUGAUUUUAAUAGCUUCUCAGGAGAAUGAC
>DQ412043.1_29399-29733
-------------------------UCAUGAUGACCACACAAGGCAGAUGGGCUAUGUAAACGUUUUCGCAAUUCCGUUUACGAUACAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAACUAAACAGCACAAGUAGGUUUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCAAUGUGUAACAUUAGGGAGGACUUGAGAGAGCCACCACAUUUUCACCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUAAUGCUAGGGAGUGCUGCCUAUAUGGAAGAGCCCUAAUGUGUAAAAUUAAUUUUAGUAGUGCUAUCCCCAUGUGAUUUUAAUAGCUUCUUAGGAGAAUGAC
>KP886809.1_29373-29707
-------------------------UCAUGAUGACCACACAAGGCAGAUGGGCUAUGUAAACGUUUUCGCAAUUCCGUUUACGAUACAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAACUAAACAGCACAAGUAGGUUUAGUUAACUUUAAUUUCACAUAGCAAUCUUCAAUCAAUGUGUAACAUUAGGGAGGACUUAAAAGAGCCACCACACUUUCACCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGAAUAAUGCUAGGGAGAGCUGCCUAUAUGGAAGAGCCCUAAUGUGUAAAAUUAAUUUUAGUAGUGCUAUCCCCAUGUGAUUUUAAUAGCUUCUUAGGAGAAUGAC
>NC_014470.1_28926-29254
----------U--------------------UGACCACACAAGGCAGAUGGGCUAUGUAAACGUUUUCGCUAUUCCGUUUACGAUACAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAGCUAAACAGCACAAGUAGGUUUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCAAUGUGUAACAUUAGGGAGGACUGGAAAGAGCCACCACAUAGUCACCGAGGCCACGCGGAGUACGAUCGAGGGUACAGUGACUAAUGCUAGGGAGAGCUGCCUAUAUGGAAGAGCCCUAAUGUGUAAAAUU-AUUUUAGUAGUGCUAUCCCCAUGUGAUUUUAAUAGCUUCUUAGGAGAAUGAC
>MT276597.1_29501-29850
----------AACUCAGGCCUAAACUCAUGCAGACCACACAAGGCAGAUGGGCUAUAUAAACGUUUUCGCUUUUCCGUUUACGAUAUAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAACUACAUAGCACAAGUAGAUGUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCAGUGUGUAACAUUAGGGAGGACUUGAAAGAGCCACCACAUUUUCACCGAGGCCACGCGGAGUACGAUCGAGUGUACAGUGAACAAUGCUAGGGAGAGCUGCCUAUAUGGAAGAGCCCUAAUGUGUAAAAUUAAUUUUAGUAGUGCUAUCCCCAUGUGAUUUUAAUAGCUUCUUAGGAGAAUGAC
>MT007544.1_29543-29860
--------------------------------GACCACACAAGGCAGAUGGGCUAUAUAAACGUUUUCGCUUUUCCGUUUACGAUAUAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAACUACAUAGCACAAGUAGAUGUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCAGUGUGUAACAUUAGGGAGGACUUGAAAGAGCCACCACAUUUUCACCGAGGCCACGCGGAGUA----------UACAGUGAACAAUGCUAGGGAGAGCUGCCUAUAUGGAAGAGCCCUAAUGUGUAAAAUUAAUUUUAGUAGUGCUAUCCCCAUGUGAUUUUAAUAGCUUCUUAGGAGAAUGAC
>MT344952.1_29511-29849
GUGCUGACUCAACUCAGGCCUAAACUCAUGCAGACCACACAAGGCAGAUGGGCUAUAUAAACGUUUUCGCUUUUCCGUUUACGAUAUAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAACUACAUAGCACAAGUAGAUGUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCAGUGUGUAACAUUAGGGAGGACUUGAAAGAGCCACCACAUUUUCACCGAG---------------------UGUACAGUGAACAAUGCUAGGGAGAGCUGCCUAUAUGGAAGAGCCCUAAUGUGUAAAAUUAAUUUUAGUAGUGCUAUCCCCAUGUGAUUUUAAUAGCUUCUUAGGAGAAUGAC

There are no chains in PDB that we map to Rfam family RF03125.

Rfam family RF03125 is part of clan CL00117, which includes Rfam families RF03121, RF03123, RF03125, RF03122, RF00164, RF03124, RF00165 .
There is 1 chain in PDB that we map to these Rfam families: 1XJR|1|A . See it at RNA 3D Hub by filtering on Rfam family, clan, or chain.

Jump to results for:

Loop 1IL Column numbers: 14-218, 258-260
Loop 2IL Column numbers: 222-227, 250-254
Loop 3IL Column numbers: 229-233, 241-248
Loop 4HL Column numbers: 234-240
Loop 5IL Column numbers: 269-277, 285-291
Loop 6HL Column numbers: 278-284
Loop 7HL Column numbers: 329-335

Loop 1 Internal loop

Column numbers: 14-218, 258-260

    Scored sequences and counts

    
    UCAGGCCUAAACUCAUGCAGACCACACAAGGCAGAUGGGCUAUAUAAACGUUUUCGCUUUUCCGUUUACGAUAUAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAACUACAUAGCACAAGUAGAUGUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCAGUGUGUAACAUUAGGGAGGACUUGAAAGAGCCACCACAUUU*ACA    2

    
    AGGCAUAAACACUCAUGAUGACCACACAAGGCAGAUGGGCUAUGUAAACGUUUUCGCAAUUCCGUUUACGAUACAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAACUAAACAGCACAAGUAGGUUUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCAAUGUGUAACAUUAGGGAGGACUUGAAAGAGCCACCACAUUU*AUA    1

    
    ---CAUAAACACUCAUGAUGACCACACAAGGCAGAUGGGCUAUGUAAACGUUUUCGCAAUUCCGUUUACGAUACAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAACUAAACAGCACAAGUAGGUUUAGUUAACUUUAAUUUCACAUAGCAAUCUUUAAUAAAUGUGUAAUGUUAGGGAGGACUUGAAAGAGCCACCACAUUU*AUA    1

    
    ------------UCAUGAUGACCACACAAGGCAGAUGGGCUAUGUAAACGUCUUCGCAAUUCCGUUUACGAUACAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAGCUAAACAGCACAAGUAGGUUUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCAAUGUGUAACAUUAGGGAGGACUUGAAAGAGCCACCACAUUU*AUA    1

    
    ------------UCAUGAUGACCACACAAGGCAGAUGGGCUAUGUAAACGUUUUCGCAAUUCCGUUUACGAUACAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAACUAAACAGCACAAGUAGGUUUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCAAUGUGUAACAUUAGGGAGGACUUGAGAGAGCCACCACAUUU*AUA    1

    
    ------------UCAUGAUGACCACACAAGGCAGAUGGGCUAUGUAAACGUUUUCGCAAUUCCGUUUACGAUACAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAACUAAACAGCACAAGUAGGUUUAGUUAACUUUAAUUUCACAUAGCAAUCUUCAAUCAAUGUGUAACAUUAGGGAGGACUUAAAAGAGCCACCACACUU*AUA    1

    
    ----------------GAUGACCACACAAGGCAGAUGGGCUAUGUAAACGUUUUCGCAAUUCCGUUUACGAUACAUAGUCUACUCUUGCGUAGAAUGAGUUCUCGUAGCUAAACAGCACAAGUAGGUUUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCAAUGUGUAACAUUAGGGAGGACUUGAAAGAGCCACCACAUUU*AUA    1

    
    ------------------UGACCACACAAGGCAGAUGGGCUAUGUAAACGUUUUCGCUAUUCCGUUUACGAUACAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAGCUAAACAGCACAAGUAGGUUUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCAAUGUGUAACAUUAGGGAGGACUGGAAAGAGCCACCACAUAG*CUA    1

    
    -------------------GACCACACAAGGCAGAUGGGCUAUAUAAACGUUUUCGCUUUUCCGUUUACGAUAUAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAACUACAUAGCACAAGUAGAUGUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCAGUGUGUAACAUUAGGGAGGACUUGAAAGAGCCACCACAUUU*ACA    1

    
    --------------------ACCACACAAGGCAGAUGGGCUAUGUAAACGUUUUCGCAAUUCCGUUUACGAUACAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAGCUAAACAGCACAAGUAGGUUUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCAAUGUGUAACAUUAGGGAGGACUUGAAAGAGCCACCACAUUU*AUA    1

No Matches Found View All Results for this Loop

Loop 2 Internal loop

Column numbers: 222-227, 250-254

    Scored sequences and counts

    
    CCGAGG*UACAG    9

    
    UCGAGG*UACAG    1

    
    CCGAG-*UACAG    1

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#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group IL_75294.1 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-cWW	90.91	8.90	4	1
2	Motif group IL_45444.1 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-cWW	81.82	3.38	4	2

Loop 3 Internal loop

Column numbers: 229-233, 241-248

    Scored sequences and counts

    
    CACGC*GAUCGAGG    8

    
    CACGC*GAUCGAGU    1

    
    Omitted sequenced and counts

    
    CACGC*--------    1

    
    -----*-------U    1

No Matches Found View All Results for this Loop

Loop 4 Hairpin loop

Column numbers: 234-240

    Scored sequences and counts

    
    GGAGUAC    9

    
    GGAGUA-    1

    
    Omitted sequenced and counts

    
    -------    1

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#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group HL_59843.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F	100.00	57.79	3	1
2	Motif group HL_97917.2 View motif instance in 3D Basepair signature: cWW-F-F-F-F	100.00	40.93	1	1
3	Motif group HL_37824.7 View motif instance in 3D Basepair signature: cWW-F-F-F-F	100.00	32.52	0	0	GNRA
4	Motif group HL_75660.5 View motif instance in 3D Basepair signature: cWW-F	100.00	8.87	2	1
5	Motif group HL_65794.5 View motif instance in 3D Basepair signature: cWW-F-F-F-F	100.00	0.63	2	1	Pseudoknot geometry
6	Motif group HL_80922.2 View motif instance in 3D Basepair signature: cWW-tSH-F	90.00	57.64	2	1
7	Motif group HL_49922.4 View motif instance in 3D Basepair signature: cWW-F-F-F	90.00	29.96	3	1
8	Motif group HL_50537.6 View motif instance in 3D Basepair signature: cWW-F-F-F	90.00	24.68	4	2	tRNA anticodon loop with synthetase
9	Motif group HL_86769.4 View motif instance in 3D Basepair signature: cWW-cWW-cSH-F	90.00	22.85	4	2
10	Motif group HL_31585.4 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	90.00	21.82	3	1	Purine riboswitch

Loop 5 Internal loop

Column numbers: 269-277, 285-291

    Scored sequences and counts

    
    GAGAGCUGC*GAAGAGC   10

    
    GAGUGCUGC*GAAGAGC    1

No Matches Found View All Results for this Loop

Loop 6 Hairpin loop

Column numbers: 278-284

    Scored sequences and counts

    
    CUAUAUG   11

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#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance
1	Motif group HL_25967.2 View motif instance in 3D Basepair signature: cWW-cWW-F-F-F	100.00	48.02	3	1
2	Motif group HL_43517.1 View motif instance in 3D Basepair signature: cWW-F-F-F	100.00	36.89	3	1
3	Motif group HL_69752.2 View motif instance in 3D Basepair signature: cWW-F	100.00	30.13	2	2
4	Motif group HL_39243.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F	100.00	24.03	4	2
5	Motif group HL_59735.5 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	100.00	21.80	2	2
6	Motif group HL_08100.1 View motif instance in 3D Basepair signature: cWW-F-F-F	100.00	13.89	2	2
7	Motif group HL_57875.1 View motif instance in 3D Basepair signature: cWW-F-F	100.00	9.37	3	2
8	Motif group HL_70782.2 View motif instance in 3D Basepair signature: cWW-F	100.00	9.02	4	2
9	Motif group HL_49922.4 View motif instance in 3D Basepair signature: cWW-F-F-F	100.00	8.02	2	2
10	Motif group HL_53890.2 View motif instance in 3D Basepair signature: cWW-F-F-F	100.00	5.93	3	2

Loop 7 Hairpin loop

Column numbers: 329-335

    Scored sequences and counts

    
    AUGUGAU   11

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#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group HL_37344.1 View motif instance in 3D Basepair signature: cWW-F-F	100.00	27.11	4	2
2	Motif group HL_69752.2 View motif instance in 3D Basepair signature: cWW-F	100.00	18.62	4	2
3	Motif group HL_13963.3 View motif instance in 3D Basepair signature: cWW-F-F	100.00	10.21	4	2
4	Motif group HL_67667.2 View motif instance in 3D Basepair signature: cWW-F-F	100.00	5.68	4	2
5	Motif group HL_50537.6 View motif instance in 3D Basepair signature: cWW-F-F-F	100.00	3.98	3	3	tRNA anticodon loop with synthetase
6	Motif group HL_28075.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	100.00	3.12	3	3
7	Motif group HL_30680.3 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	100.00	0.36	4	2	Pseudoknot geometry

Nucleotide numbers Coloring options:

JAR3D Query RF03125-CCF-3.98 completed Run on Motif Atlas Version 3.98 using the CaCoFold secondary structure. Run with the Rfam secondary structure.

RF03125 Sarbecovirus 3'UTR

Input Summary

Jump to results for:

Loop 1 Internal loop

Loop 2 Internal loop

Loop 3 Internal loop

Loop 4 Hairpin loop

Loop 5 Internal loop

Loop 6 Hairpin loop

Loop 7 Hairpin loop

JAR3D Query RF03125-CCF-3.98 completed
Run on Motif Atlas Version 3.98 using the CaCoFold secondary structure. Run with the Rfam secondary structure.