JAR3D on RF02265

RF02265 MAT2A 3'UTR stem loop F

Input Summary

      0000000001111111111222222222233333333334444444444555555555566666666
1234567890123456789012345678901234567890123456789012345678901234567
((((....((.((((.(....(((........)))....).)))))).....)))).((()))....
>AY603043.1_620-685
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>ABRT010239600.1_5971-6036
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAAAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>AAIY01292066.1_5286-5350
CAUGGAG-AG-GCUGACUUGGCCGGUGUGCUACAGAGAAGCCAGCUUGUUGACAUGCUCCUCCAUUG
>BC001686.2_2616-2681
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>AAYZ01081944.1_5969-6034
CAUGGAGGAA-GCGGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>BC062394.1_3163-3228
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>BT030708.1_2625-2690
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>AAPN01391386.1_6556-6622
CGUGGGGAGACGCUGACUUGGCUGGUGUUGUACAGAGAAGCCAGCUUGUUUACAGGCUCAUCCCAUG
>AALT01193755.1_758-823
CAUGGAGAAA-GCGGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>AC016753.9_112052-112117
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>AC116115.11_197073-197008
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>AANN01466464.1_6628-6693
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUGCUCCAUG
>AAFR03050370.1_29132-29197
CAUGGAGGAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCCUACUCCAUG
>AC190303.9_101604-101539
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>BC001854.2_2616-2681
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>AC154002.8_25257-25192
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>BC058360.1_3179-3244
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>AK054569.1_1861-1796
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>AC207174.3_18990-19055
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>AAQQ01101557.1_1002-938
CGUGGAGAGA-GCGGACUUGGCUGGCGUGGUACAGAGAAGCCAGCUUGUUUACAUGC-UACUCCAUG
>ABBA01166058.1_319-254
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>L43509.1_2508-2573
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>AB168627.1_1740-1805
CAUGGAGAAA-GCUGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUCCAUG
>ABRP01178872.1_23996-23931
CAUGGAAAAA-GCAGACCUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUAUUUCAUG
>AAGW02007302.1_51363-51428
CAUGGAGAAA-GCGGACUUGGCUGGUGUGGUACAGAGAAGCCAGCUUGUUUACAUGCUUCAUCCAUG
>AAWZ02030028.1_3579-3514
CCUGGGAGGG-GCUGACUUGGCCGGUGUGGUACAGAGAAGCCGGCUUGUUUACUUACCCGUCCCACG

There are no chains in PDB that we map to Rfam family RF02265.

Jump to results for:

Loop 1IL Column numbers: 4-9, 47-53
Loop 2IL Column numbers: 10-12, 45-46
Loop 3IL Column numbers: 15-17, 40-42
Loop 4IL Column numbers: 17-22, 35-40
Loop 5HL Column numbers: 24-33
Loop 6HL Column numbers: 60-61

Loop 1 Internal loop

Column numbers: 4-9, 47-53

    Scored sequences and counts

    
    GGAGAA*UGUUUAC   19

    
    GGAGGA*UGUUUAC    2

    
    GGAAAA*UGUUUAC    1

    
    GGAGAG*UGUUUAC    1

    
    GGGAGG*UGUUUAC    1

    
    GGGGAG*UGUUUAC    1

    
    GGAG-A*UGUUGAC    1

Click on headings to reorder table - View All Results for this Loop

#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group IL_88269.4 View motif instance in 3D Basepair signature: cWW-tWW-cSH-tWH-tHS-cWW	92.31	16.51	4	2	6x5 Sarcin-Ricin; G-bulge
2	Motif group IL_70801.1 View motif instance in 3D Basepair signature: cWW-cWW-L-R-tWW-L-R-L-cWW	88.46	14.45	6	4
3	Motif group IL_26307.2 View motif instance in 3D Basepair signature: cWW-tSH-tHH-cSH-tWH-tHS-cWW	80.77	-5.88	5	3	7x6 Sarcin-Ricin; G-bulge
4	Motif group IL_68243.1 View motif instance in 3D Basepair signature: cWW-L-cWW-cWW-R-L-tHS-cWW	76.92	1.33	6	4
5	Motif group IL_02349.4 View motif instance in 3D Basepair signature: cWW-tSH-tWH-cSH-tWH-tHS-cWW	73.08	-8.80	7	3	8x6 Sarcin-Ricin with bulged A; G-bulge
6	Motif group IL_20047.1 View motif instance in 3D Basepair signature: cWW-tSH-tWH-cSH-cHW-cWH-cWW-cWW	3.85	-30.49	6	4

Loop 2 Internal loop

Column numbers: 10-12, 45-46

    Scored sequences and counts

    
    A-G*CU   23

    
    G-G*CU    2

    
    ACG*CU    1

Click on headings to reorder table - View All Results for this Loop

#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	100.00	23.32	2	1	Multiple bulged bases
2	Motif group IL_73452.2 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	22.10	3	1
3	Motif group IL_81831.1 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	22.00	3	1	Intercalated cWS
4	Motif group IL_07039.3 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	18.17	3	1	Major groove platform
5	Motif group IL_00225.13 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	4.61	1	1	Single bulged G
6	Motif group IL_84476.1 View motif instance in 3D Basepair signature: cWW-cWW	96.15	30.19	2	2	Multiple bulged bases
7	Motif group IL_26793.1 View motif instance in 3D Basepair signature: cWW-L-cWW	92.31	19.57	1	1	Single stack bend
8	Motif group IL_66635.5 View motif instance in 3D Basepair signature: cWW-L-cWW	92.31	16.95	2	1	Major groove intercalation
9	Motif group IL_90729.1 View motif instance in 3D Basepair signature: cWW-L-cWW	92.31	16.34	1	1	Single stack bend
10	Motif group IL_16386.4 View motif instance in 3D Basepair signature: cWW-L-cWW	92.31	12.80	3	1

Loop 3 Internal loop

Column numbers: 15-17, 40-42

    Scored sequences and counts

    
    GAC*GCC   26

Click on headings to reorder table - View All Results for this Loop

#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group IL_67095.2 View motif instance in 3D Basepair signature: cWW-tWW-cWW	100.00	96.47	2	0	Isolated tWW turn
2	Motif group IL_87907.2 View motif instance in 3D Basepair signature: cWW-cWW-cWW	100.00	94.85	0	0	Isolated non-canonical cWW pair
3	Motif group IL_42997.3 View motif instance in 3D Basepair signature: cWW-L-R-cWW	100.00	75.00	1	0	Isolated cWS basepair
4	Motif group IL_08770.1 View motif instance in 3D Basepair signature: cWW-L-R-cWW	100.00	72.28	4	1
5	Motif group IL_57744.1 View motif instance in 3D Basepair signature: cWW-cWW-cWW	100.00	70.15	2	0	Isolated non-canonical cWW pair
6	Motif group IL_07785.1 View motif instance in 3D Basepair signature: cWW-cWW-cWW	100.00	63.98	1	1	Isolated non-canonical cWW pair
7	Motif group IL_31737.3 View motif instance in 3D Basepair signature: cWW-L-cWW	100.00	58.79	2	1	Stack and bulge
8	Motif group IL_28037.2 View motif instance in 3D Basepair signature: cWW-cWW-cWW	100.00	54.49	2	1	Isolated non-canonical cWW pair
9	Motif group IL_14688.1 View motif instance in 3D Basepair signature: cWW-cWW-cWW	100.00	47.16	3	1	Isolated non-canonical cWW pair
10	Motif group IL_42771.1 View motif instance in 3D Basepair signature: cWW-cWW	100.00	40.36	4	1	Multiple bulged bases

Loop 4 Internal loop

Column numbers: 17-22, 35-40

    Scored sequences and counts

    
    CUUGGC*GAGAAG   24

    
    CCUGGC*GAGAAG    1

    
    CUUGGC*GAAAAG    1

Click on headings to reorder table - View All Results for this Loop

#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group IL_76308.6 View motif instance in 3D Basepair signature: cWW-tSH-tHW-tHS-cWW-cWW	96.15	12.91	4	3	tSH-tWH-tHS-cWW
2	Motif group IL_80926.1 View motif instance in 3D Basepair signature: cWW-cWW-tSH-tHS-L-cWW	96.15	1.77	3	3
3	Motif group IL_71294.3 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-R-L-R-cWW	3.85	-4.14	4	3	Double sheared; A in syn; two near cWW pairs
4	Motif group IL_12745.1 View motif instance in 3D Basepair signature: cWW-tWH-tWH-tHW-tHW-cWW	3.85	-19.38	6	5	tWH-tWH-tHW-tHW
5	Motif group IL_34822.1 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-R-L-R-cWW	3.85	-34.96	9	5
6	Motif group IL_22564.1 View motif instance in 3D Basepair signature: cWW-L-R-L-R-L-cWW	3.85	-42.76	7	5

Loop 5 Hairpin loop

Column numbers: 24-33

    Scored sequences and counts

    
    GGUGUGGUAC   23

    
    GGCGUGGUAC    1

    
    GGUGUGCUAC    1

    
    GGUGUUGUAC    1

Click on headings to reorder table - View All Results for this Loop

#	Matching motif group	Acceptance Rate	Mean Cutoff Score	Full Edit Distance	Interior Edit Distance	Basepair Diagram and most common annotation
1	Motif group HL_53454.2 View motif instance in 3D Basepair signature: cWW-tSH-F-F-F-F-F	100.00	59.77	3	1
2	Motif group HL_66853.7 View motif instance in 3D Basepair signature: cWW-cWS-F-cSH	96.15	20.49	4	2
3	Motif group HL_49941.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	96.15	19.39	5	3	tRNA D-loop
4	Motif group HL_58224.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	92.31	17.76	5	3
5	Motif group HL_45175.1 View motif instance in 3D Basepair signature: cWW-cWS-F-F	92.31	15.07	4	2	tRNA D-loop
6	Motif group HL_04642.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F	92.31	14.60	5	3	tRNA D-loop
7	Motif group HL_91503.7 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F-F	92.31	6.17	4	3
8	Motif group HL_23010.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F	92.31	-1.54	6	4
9	Motif group HL_85367.2 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F	88.46	-5.15	5	3
10	Motif group HL_99867.1 View motif instance in 3D Basepair signature: cWW-F-F-F-F-F-F-F-F	7.69	-4.94	4	4

Loop 6 Hairpin loop

Column numbers: 60-61

    Scored sequences and counts

    
    AU   20

    
    AC    2

    
    CA    1

    
    CU    1

    
    GC    1

    
    GU    1

No Matches Found View All Results for this Loop

Nucleotide numbers Coloring options:

JAR3D Query RF02265-CCF-3.98 completed Run on Motif Atlas Version 3.98 using the CaCoFold secondary structure. Run with the Rfam secondary structure.

RF02265 MAT2A 3'UTR stem loop F

Input Summary

Jump to results for:

Loop 1 Internal loop

Loop 2 Internal loop

Loop 3 Internal loop

Loop 4 Internal loop

Loop 5 Hairpin loop

Loop 6 Hairpin loop

JAR3D Query RF02265-CCF-3.98 completed
Run on Motif Atlas Version 3.98 using the CaCoFold secondary structure. Run with the Rfam secondary structure.