RetrogeneDB ID: retro_mmus_14

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:119260977..119262855(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000021908
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Ncoa4
• Ensembl ID: ENSMUSG00000056234
• Aliases: Ncoa4, ARA70, Rfg
• Description: nuclear receptor coactivator 4 [Source:MGI Symbol;Acc:MGI:1350932]

Sequence

>retro_mmus_14
ATGAACACATCCCTGGAACAGAGTGGCTGCTACAGTAATAGAGAAACTCTTCTGAGGTGCAGTGATGCAAGGAGGGAGCT
GGAGCTTGCTATTGGTGGAGTACTTCGGGCTGAACAGCAAATTAAAGATAATTTACGAGAGGTAAAAGCTCAGATTCACA
GCTGCATAAGTCGCCACCTGGAATGCCTTCGGAGCCGAGAGGTGTGGCTCAATGAACAGGTCGATCTCATCTATCAGCTT
AAAGAGGAGACACTGCAGCAGCAGGCTCAGCAGCTCTATTGGCTAATGGGCCAATTCAATTGTCTTATTCATCAACTGGA
GTATACTCAGAACAAAGATCTTGCCAATCAAGTCTCTGTGTGCTTGGAGAGACTGGGCAGTTTGGCCCTGAAGCCTGAAG
ATTCAACTGTCCTACTCTTTGAAGCAGATACATCTGCTCTGCGCCAGACCATCACCACATTTGGATCCCTTAAGACCATT
CAAATCCCTGAGCATCTGATGGCTCACGCGAGCTCCTCAAGTATTGGGCCTTTCCTAGAGAAAAGAGGCTATATCCAGGT
GCCAGAGCAGAAGTCAGCATCCAGTGGCACAGCTGTATCTCTGAGTGAGTGGCTTCTTGTAAGCAAACCTGCCATTGGTC
TTCAGGCTCCTTATGTACCCAGTACCAACCCACAGGACTGGCTTATCCCAAAACAGACTTCAGAGAATAGTCAGACTTCT
GCCAGAGCCTGCAGTTTCTTCAGCGATGCCTGGGGCAATCTGAAGGGCTTAGAAAATTGGCTCCTTAACAGTCATCAACA
AGAAATTGCTGGAAAACCAAGTTCCTCAAAATGTAACAGCCATTGTAGCACCAGTTCTTTCTCTCCTGAAGCTGAAAAGG
CTGAAGATGTAGAGCTCCTTGATCAAGACGAGCTGGACCTGTCTGATTGGTTGGTGACTCCTCAGGAACCCTGTGAGCTG
GAGAAGCCTGTGGATGGCAGCTGGGAAACCAGCGAGAAGTTTAAACTCTTGTTCCAGGTGTTCAGAGAGCCCTACAATGT
GAGTGATTGGCTTGTCAAGCCTGACTCCTGTACCAACTGTCAGGGCAACCAGCCTAGAGGTGTGGAGATTGAGAACCTGG
GCAATCTGAAATGCCTAAATGACCACTTGGAGGCCAAAAAATCAGTGTCGGTCCCCGGCGCAACAATCAGCGACGGCTGG
CTTGCCCAGAACCATCAGGACACATGGAAAGTAGAGGAAGTGTGTAAAGCCAACGAGCCCTGCACCAGTTTTGCAGAGTG
TGTGTGTGATGACAACTGTGAGAAGGAAGCCGTGTATAAATGGCTTCTGAAGAAGGGAGGAAAGGACAAGAATGGAATGC
CTATGGAACCTAAATCTGAGCCTGAGAAACACAGAGAGTCCCTGACACTGTGGCTCTGCCCTTCCAGAAATGAGCTAACA
GAACAAGCTAAGGCACCCAAGGCTATGGCTCCTGCTAGAATTGCTGATTCCTTCCACGTCATAAAGAATAGTTCCTTGTC
AGAGTGGCTTATAGGGCCTACGTGCAAAGGAGGCCCTAAGGACGTGCCTAATACAGAGGAGAGAGCTGGCAAAGAGATGC
TTCAAAGCTCCATGGCCACTTCCTGGTGTCCCTTTAACACTGCCGACTGGGTTTTACCAGGAAAGAAAGTGGGAAGCCTC
AGCCAGTTCCCCTCTGGAGAAGATAAGTGGCTACTTCGAAAGAAGGCACAGGAAGCATTTCTTAATTCACCCCTACAAGA
AGAACGTAACTTTCGCCCCGACTGTTACGGCCTCCCAGCAGTTTGTGATCTCTTTGCCTGTATGCAGCTTAAGGTTGATA
AAGAAAAATGGCTGTACAGAACTCCTCTACAGATGTGA

Alignment

ORF - retro_mmus_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.68 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNTSLEQSGCYSNRETLLRCSDARRELELAIGGVLRAEQQIKDNLREVKAQIHSCISRHLECLRSREVWL
          MNTSLEQSGCYSNRETLLRCSDARRELELAIGGVLRAEQQIKDNLREVKAQIHSCISRHLECLRSREVWL
Retrocopy MNTSLEQSGCYSNRETLLRCSDARRELELAIGGVLRAEQQIKDNLREVKAQIHSCISRHLECLRSREVWL

Parental  NEQVDLIYQLKEETLQQQAQQLYWLMGQFNCLIHQLEYTQNKDLANQVSVCLERLGSLALKPEDSTVLLF
          NEQVDLIYQLKEETLQQQAQQLYWLMGQFNCLIHQLEYTQNKDLANQVSVCLERLGSLALKPEDSTVLLF
Retrocopy NEQVDLIYQLKEETLQQQAQQLYWLMGQFNCLIHQLEYTQNKDLANQVSVCLERLGSLALKPEDSTVLLF

Parental  EADTSALRQTITTFGSLKTIQIPEHLMAHASSSSIGPFLEKRGYIQVPEQKSASSGTAVSLSEWLLVSKP
          EADTSALRQTITTFGSLKTIQIPEHLMAHASSSSIGPFLEKRGYIQVPEQKSASSGTAVSLSEWLLVSKP
Retrocopy EADTSALRQTITTFGSLKTIQIPEHLMAHASSSSIGPFLEKRGYIQVPEQKSASSGTAVSLSEWLLVSKP

Parental  AIGLQAPYVPSTNPQDWLIPKQTSENSQTSARACSFFSDAWGNLKGLENWLLNSHQQEIAGKPSSSKCNS
          AIGLQAPYVPSTNPQDWLIPKQTSENSQTSARACSFFSDAWGNLKGLENWLLNSHQQEIAGKPSSSKCNS
Retrocopy AIGLQAPYVPSTNPQDWLIPKQTSENSQTSARACSFFSDAWGNLKGLENWLLNSHQQEIAGKPSSSKCNS

Parental  HCSTSSFSPEAEKAEDVELLDQDELDLSDWLVTPQEPCELEKPVDGSWETSEKFKLLFQVFREPYNVSDW
          HCSTSSFSPEAEKAEDVELLDQDELDLSDWLVTPQEPCELEKPVDGSWETSEKFKLLFQVFREPYNVSDW
Retrocopy HCSTSSFSPEAEKAEDVELLDQDELDLSDWLVTPQEPCELEKPVDGSWETSEKFKLLFQVFREPYNVSDW

Parental  LVKPDSCTNCQGNQPRGVEIENLGNLKCLNDHLEAKKSVSVPGATISDGWLAQNHQDTWKVEEVCKANEP
          LVKPDSCTNCQGNQPRGVEIENLGNLKCLNDHLEAKKSVSVPGATISDGWLAQNHQDTWKVEEVCKANEP
Retrocopy LVKPDSCTNCQGNQPRGVEIENLGNLKCLNDHLEAKKSVSVPGATISDGWLAQNHQDTWKVEEVCKANEP

Parental  CTSFAECVCDDNCEKEAMYKWLLKKGGKDKNGMPMEPKSEPEKHRESLTLWLCPSRNELTEQAKAPKAMA
          CTSFAECVCDDNCEKEA.YKWLLKKGGKDKNGMPMEPKSEPEKHRESLTLWLCPSRNELTEQAKAPKAMA
Retrocopy CTSFAECVCDDNCEKEAVYKWLLKKGGKDKNGMPMEPKSEPEKHRESLTLWLCPSRNELTEQAKAPKAMA

Parental  PARIADSFHVIKNSSLSEWLMGPTCKGGPKDVPNTEERAGKEMLQSSMATSWCPFNTADWVLPGKKVGSL
          PARIADSFHVIKNSSLSEWL.GPTCKGGPKDVPNTEERAGKEMLQSSMATSWCPFNTADWVLPGKKVGSL
Retrocopy PARIADSFHVIKNSSLSEWLIGPTCKGGPKDVPNTEERAGKEMLQSSMATSWCPFNTADWVLPGKKVGSL

Parental  SQFPSGEDKWLLRKKAQEAFLNSPLQEERNFRPDCYGLPAVCDLFACMQLKVDKEKWLYRTPLQM
          SQFPSGEDKWLLRKKAQEAFLNSPLQEERNFRPDCYGLPAVCDLFACMQLKVDKEKWLYRTPLQM
Retrocopy SQFPSGEDKWLLRKKAQEAFLNSPLQEERNFRPDCYGLPAVCDLFACMQLKVDKEKWLYRTPLQM

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.35 RPM	15.70 RPM
SRP007412_cerebellum	1.35 RPM	11.68 RPM
SRP007412_heart	0.31 RPM	14.41 RPM
SRP007412_kidney	4.20 RPM	24.27 RPM
SRP007412_liver	3.36 RPM	29.52 RPM
SRP007412_testis	5.17 RPM	46.93 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_14 was not detected

EST

82 EST(s) were mapped to retro_mmus_14 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA871762	119260944	119261595	100	651	0	651
AI788032	119260933	119261520	98.2	573	10	561
AI791039	119260933	119261562	99.6	624	3	621
AI931301	119260933	119261460	99.7	525	2	523
AI119109	119260933	119261464	100	529	0	529
AV483501	119260962	119261442	100	480	0	480
AV489667	119260955	119261455	99.4	494	2	490
AW681837	119261638	119262051	99.8	409	1	408
AW761850	119260979	119261556	99.7	574	2	572
AW822645	119260962	119261541	99.4	575	4	571
BG060958	119261271	119261660	99.8	388	1	387
BG173428	119261143	119261867	98.2	690	6	668
BM963299	119261305	119262049	99.9	734	1	725
BQ179847	119261399	119262091	99.3	684	4	678
BQ443829	119261587	119262279	99.9	690	1	689
BY044839	119260932	119261309	99.8	376	1	375
BY046307	119260935	119261310	99.8	374	1	373
BY047079	119260935	119261328	99.8	392	1	391
BY047296	119260932	119261318	100	385	0	385
BY048150	119260935	119261339	98.8	398	5	393
BY051809	119260932	119261304	100	372	0	372
BY058824	119260935	119261329	100	394	0	394
BY064014	119260931	119261310	99.8	378	1	377
BY072446	119260936	119261313	99.8	376	1	375
BY081426	119261119	119261470	99.2	346	3	343
BY089934	119261117	119261490	100	371	0	371
BY106212	119261071	119261411	100	340	0	340
BY226295	119260935	119261352	100	417	0	417
BY226675	119260935	119261348	100	413	0	413
BY713890	119260931	119261931	98.5	943	8	914
BY738478	119260932	119261589	100	656	0	656
BY740613	119260931	119261560	99.1	616	6	610
CA530233	119261271	119261874	100	600	0	599
CA532563	119261788	119262361	99.9	572	1	571
CA538207	119261057	119261417	100	360	0	360
CA558474	119261464	119261976	99.9	511	1	510
CD547859	119260960	119261500	100	540	0	540
CD553975	119260962	119261491	100	529	0	529
CD565398	119261081	119261508	100	427	0	427
CF163860	119260944	119261556	99.9	611	1	610
CF166272	119260956	119261424	99.6	466	2	464
CF173561	119261464	119262120	100	656	0	656
CF173948	119261309	119261938	100	629	0	629
CF174176	119260972	119261658	99.9	685	1	684
CF736162	119261191	119261863	99.9	669	1	668
CF739905	119261302	119262050	100	744	0	741
CF897386	119261209	119261827	99.9	617	1	616
CF910282	119261001	119261598	100	597	0	597
CJ093868	119260935	119261614	99.8	675	2	672
CJ164328	119260931	119261375	100	444	0	444
CK389649	119260950	119261308	100	358	0	358
CK790719	119260962	119261614	100	645	0	638
CN459674	119260944	119261720	100	774	0	773
CN527720	119260962	119261690	100	725	0	724
CN530256	119261019	119261828	100	800	0	794
CN538994	119260962	119261777	100	812	0	811
CN664047	119260958	119261589	100	631	0	631
CN664751	119260944	119261540	100	596	0	596
CN666978	119260944	119261500	100	556	0	556
CN669808	119261351	119261938	100	587	0	587
CN673558	119261373	119261904	99.9	530	1	529
CN675041	119260988	119261540	100	552	0	552
CN678529	119260949	119261508	100	559	0	559
CN679714	119261202	119261747	100	545	0	545
CN680754	119260976	119261446	99.8	469	1	468
CN686961	119260941	119261500	100	559	0	559
CN691660	119261017	119261595	100	578	0	578
CN691798	119260962	119261352	100	390	0	390
CN692685	119261132	119261483	99.8	350	1	349
CN695594	119260944	119261366	100	422	0	422
CN695978	119261410	119261903	100	493	0	493
CN700241	119260980	119261542	99.9	561	1	560
CN702075	119260950	119261519	100	569	0	569
CN704921	119260980	119261402	99.8	421	1	420
CN704992	119261318	119261747	100	429	0	429
CR758207	119261076	119261636	99	554	6	548
CV562600	119261156	119261921	99.8	761	1	757
CV783866	119261202	119261994	100	788	0	787
CX240505	119260962	119261743	100	781	0	781
CX563420	119261292	119262154	99.9	857	1	855
DT908197	119261078	119261633	99.5	552	3	549
DT930084	119261085	119261633	100	545	0	542

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_22166	140 libraries	167 libraries	212 libraries	125 libraries	428 libraries

The graphical summary, for retro_mmus_14 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_14 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_14 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019565	1 retrocopy	retro_btau_1761,
Choloepus hoffmanni	ENSCHOG00000004343	1 retrocopy	retro_chof_2540,
Callithrix jacchus	ENSCJAG00000013352	1 retrocopy	retro_cjac_916,
Myotis lucifugus	ENSMLUG00000000619	1 retrocopy	retro_mluc_2161,
Mus musculus	ENSMUSG00000056234	1 retrocopy	retro_mmus_14 ,