RetrogeneDB ID: retro_mmus_44

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:94724674..94727296(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000073062
• Aliases: Zxdb, Zxda
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Zxdc
• Ensembl ID: ENSMUSG00000034430
• Aliases: Zxdc, A930012H20, B930086F11Rik, BC003332
• Description: ZXD family zinc finger C [Source:MGI Symbol;Acc:MGI:1933108]

Sequence

>retro_mmus_44
ATGGAAATCCCGAGGCTGCTCCCGGCTCGCGGGACACCGCAGGGCGCCGGTGGCGGCGGCTGCCCGGCGGGTGGCGGCGG
GGTGCACCGAGCCCCGGCCTCTCTGGCTTGTCAGGCCCCCACGCGCCGCCTCCTACTGCTCCGGGGGGCCCAAGATGGCG
GGCCGGGGCCGCGGAGCGCAGAGGCCCAGAGGGCCTCCCGGGGCCTGGGCCCGAGCCTGAACCGGTTGGCGCCGAGGCCC
GATCACCGGAGCAGCGGCGGCGGCAGAGGCGGCGGCGCTGGCGGAGGAGGAGGAGGCAGCGGCGGCGGCGGTGGCGGCGG
CGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCAGCAGAGGCGGCAGCGACGACTTCTTCCTGTTGCTGCTTGACCCGG
TGGGTGGCGATGTAGAAACCGTGGGCACGGAGCAGGCCGGAGCGCCCGTGCGGAGGGAGGAGGCCGGGGCAGGCCCGAGG
CCCGAGCGGCGCCAGAGCGCCGGGCCCCCAGCGGGCCGTCCCGAGCCGGGTCCCCGCTGTCTGTCTGCGGTCCCGGCCGC
GTCCCCGCTTCCCGCGGCCGGCCCGGGCCCAGCGGCGGCGGCGGCGGCGGCGGCGGCGGCGGCCTTCGCGGGCACCATCA
CCATCCACAACCAGGACTTGCTGCTGCGCTTCGAGAACGGCGTCCTCACCCTGACCACGCCCCCGCTGCCCGCCTGGGAG
CCGGGGGTCGCGCCGTTCCCGCAGCCTCAGCCGCCGCCGCAGCCGGGGGCGCTGATCGCCCCGCAGGCCGCCGCCGCCGG
GTTTCCGCCCGCCGCTGCCGCCGCCGCCGCCGCCGCCGCCGCCGGGGCGCAGCTGGGCGACTGCCCCGAGCTGCCGCCGG
ACCTCCTGCTGGCGGAGCCGGCGGAACCCGCGGCCTGCCCGGCGCCCCCGGAGGAGGAGGCCGAGGCCCCGGCCGCCGCC
GCCGCGCAGAGCCCCCGCGGGCCCGCGGGCCCGGGCCCGGGCCCGGGCGTGGTGCTGTACCTGTGCCCGGAGGCGCAGTG
CGGCCAGACCTTCGCCAAGAAGCACCAGCTGAAGGTGCACCTGCTGACGCACAGCAGCAGCCAGGGCCAGCGGCCCTTCA
AGTGCCCGCTCAGCGGCTGCGGCTGGACCTTCACCACCTCCTACAAGCTCAAGCGGCACCTGCAGTCGCACGACAAGCTG
CGGCCATTCGGCTGCCCGGTGCAGGGCTGCGGCAAGAGCTTCACCACCGTCTACAACCTCAAGGCGCACATGAAGGGGCA
CGAGCAGGAGAACTCCTTCAAATGCGAGGTGTGCGAGGAGAGCTTCCCCACGCAGGCCAAGCTCAGCACCCACCAGCGCA
GCCACTTCGAGCCCGAGAGGCCCTACCAGTGCGCGTTTTCGGGCTGCAAGAAGACCTTCATCACGGTGAGCGCCCTGTTC
TCGCACAACCGCGCCCATTTCAGGGAACAGGAACTCTTCGCCTGCTCCTTCCCTGGCTGCAGCAAGCAGTACGACAAGGC
CTGCAGGCTCAAGATCCACCTGCGCAGCCACACCGGGGAGAGACCCTTCCTGTGTGACTTCGACGGCTGCGGCTGGAACT
TCACCAGCATGTCCAAGCTCTTAAGGCACAAGCGGAAGCACGAGGACGACCGCAGGTTCACCTGTCCCGTCGAGGGCTGC
GGCAAGTCCTTCACCAGGGCCGAGCACCTGAAAGGCCACAGCATAACCCACCTGGGCACCAAGCCCTTCGTGTGCCCCGT
GGAGGGCTGCTGTGCCCGCTTCTCGGCTCGCAGCAGCCTCTACATCCACTCCAAGAAGCACTTGCAGGACGTGGGTGCGT
GGAAGAGCCGCTGCCCGGTCCCCACCTGTAACAAGCTCTTCACGTCCAAGCACAGCATGAAGACCCACATGACCAAAAGG
CACAACCTCAGCCAGGACCTCCTGGCCCAGCTAGAAGCTGCCAACTCTCTCACGCCCAGCAGTGAGCTCACCAGCCCGGG
GCAGAGCGATCTCAGTGGGGCCGAGCTCGTGTCTCTGTTCTCGGATGTGCCTGGCCACGGTTCCGCCGCGGTGCTGGACA
CGGCCTTGGTCAACTCTGGCATCTTGACTATTGATGTGGCCTCTGTGAACTCGAGCCTCGCGGGAAGTCTCCCTGCGGAT
AATAACAGCAACAACCATTCCTTGGGGCAAGCGGCCGAGCCTCGGGCCTTGAGGGGGGCCCCCAGTGACCTCCCCCAGAG
TCTGGATACCTCTCTCTTCTTCGGAACCTCGGTGGCTGGCTACCAGCACAGCCCCTTGGACATGGACGATGTCTCCGCCG
GGAACGTGGGGCTCTTTGGCTCCTTGGCCCTGAAAAACTCAAGCCTGGAGCCGCAGGCTTTGACACCCAGCAATAAGTTG
ACTGTGGACACGGAAGCTCTGACCCCCTCCAGCACCCTCTGTGAAAACAGTGTCTCCGAGCTACTGACCCCAGCCAAAGC
CGAGTGGAACGTGCACCCCGAATCTGACTTCTTTGGACACGAGGAAGAAACCCAGTTCGGATTCTCCCACCCAACAGGAA
GCCATGGGTCTCAGAAAGACACAGATCTTATCACGGTGACTGGCACCCCGTTTTTGGTATGA

Alignment

ORF - retro_mmus_44 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.51 %
• Parental protein coverage: 78.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LAAAPAPAAPSLHPATTPGLEPSSAAASRRGPVAASAGSPA--YRCPEPQCALSFAKKHQLKVHLLTHGS
          LA....PAA....P..........AA.S.RGP.....G.....Y.CPE.QC...FAKKHQLKVHLLTH.S
Retrocopy LAEPAEPAACPAPPEEEAEAPAAAAAQSPRGPAGPGPGPGVVLYLCPEAQCGQTFAKKHQLKVHLLTHSS

Parental  LQGRRPFKCPLDGCGWAFTTSYKLKRHLQSHDKLRPFSCPVGGCGKKFTTVYNLKAHMKGHEQESLFKCE
          .QG.RPFKCPL.GCGW.FTTSYKLKRHLQSHDKLRPF.CPV.GCGK.FTTVYNLKAHMKGHEQE..FKCE
Retrocopy SQGQRPFKCPLSGCGWTFTTSYKLKRHLQSHDKLRPFGCPVQGCGKSFTTVYNLKAHMKGHEQENSFKCE

Parental  VCAERFPTHAKLNSHQRSHFEPERPYKCDFPGCEKTFITVSALFSHNRAHFREQELFSCSFPGCNKQYDK
          VC.E.FPT.AKL..HQRSHFEPERPY.C.F.GC.KTFITVSALFSHNRAHFREQELF.CSFPGC.KQYDK
Retrocopy VCEESFPTQAKLSTHQRSHFEPERPYQCAFSGCKKTFITVSALFSHNRAHFREQELFACSFPGCSKQYDK

Parental  ACRLKIHLRSHTGERPFICDSDSCGWTFTSMSKLLRHKRKHDDDRRFTCPVEGCGKSFTRAEHLKGHSIT
          ACRLKIHLRSHTGERPF.CD.D.CGW.FTSMSKLLRHKRKH.DDRRFTCPVEGCGKSFTRAEHLKGHSIT
Retrocopy ACRLKIHLRSHTGERPFLCDFDGCGWNFTSMSKLLRHKRKHEDDRRFTCPVEGCGKSFTRAEHLKGHSIT

Parental  HLGTKPFECPVEGCCARFSARSSLYIHSKKHLQDVGTPKSRCPVSSCNRLFTSKHSMKAHVVRQHSRRQD
          HLGTKPF.CPVEGCCARFSARSSLYIHSKKHLQDVG..KSRCPV..CN.LFTSKHSMK.H....H...QD
Retrocopy HLGTKPFVCPVEGCCARFSARSSLYIHSKKHLQDVGAWKSRCPVPTCNKLFTSKHSMKTHMTKRHNLSQD

Parental  LVPQLEAPSSLTPSSELSSPGQSELTNIDLAALFSDTPANSSSSTAGSDEALNSGILTIDVTSVSSSLGG
          L..QLEA..SLTPSSEL.SPGQS.L....L..LFSD.P...S..........NSGILTIDV.SV.SSL.G
Retrocopy LLAQLEAANSLTPSSELTSPGQSDLSGAELVSLFSDVPGHGSAAVLDT-ALVNSGILTIDVASVNSSLAG

Parental  NLP----TNNNSLGPM-DPLVLV-AHGDMPPSLDSPLVLGTSATVLQPGSFSADDSQAMSTGAVGCLVAL
          .LP.....NN.SLG....P..L..A..D.P.SLD..L..GTS....Q......DD....S.G.VG....L
Retrocopy SLPADNNSNNHSLGQAAEPRALRGAPSDLPQSLDTSLFFGTSVAGYQHSPLDMDD---VSAGNVGLFGSL

Parental  PVRNLNQDSPALTPSNNLTAPGTTPTSSDTTQETGSVPDLLVPIKVEQDLSPVPDVVQGQKESHGPSQSV
          ...N......ALTPSN.LT......T.S.T..E..SV..LL.P.K.E....P..D......E.....Q..
Retrocopy ALKNSSLEPQALTPSNKLTVDTEALTPSSTLCE-NSVSELLTPAKAEWNVHPESDFFGHEEE----TQFG

Parental  LSSSTERPGAQKDSELSAGTGSLYLV
          .S..T...G.QKD..L...TG...LV
Retrocopy FSHPTGSHGSQKDTDLITVTGTPFLV

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	0.00 RPM	24.37 RPM
SRP007412_cerebellum	0.00 RPM	23.40 RPM
SRP007412_heart	0.00 RPM	15.35 RPM
SRP007412_kidney	0.00 RPM	20.04 RPM
SRP007412_liver	0.00 RPM	14.09 RPM
SRP007412_testis	0.00 RPM	9.15 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_44 was not detected

EST

24 EST(s) were mapped to retro_mmus_44 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA277793	94726175	94726588	99.3	406	2	399
AA386833	94726221	94726600	99.5	373	2	368
AI414520	94725652	94726056	97.5	393	6	384
BB645531	94725511	94726155	98.8	620	7	607
BB647745	94725605	94726254	99.9	647	1	646
BQ831326	94726162	94726703	99.1	535	5	530
BU696266	94726659	94726967	99.7	291	0	286
BY716393	94725505	94726310	99.2	796	6	786
BY727690	94724938	94726121	99.3	645	4	638
BY727784	94725563	94726201	100	637	0	637
BY749128	94724620	94725995	100	667	0	665
CJ050369	94724808	94725936	99.6	472	1	469
CJ055580	94725028	94725434	100	404	0	403
CJ055673	94725500	94725856	98.1	350	4	345
CJ057052	94725829	94726579	97.8	399	8	388
CJ058390	94725075	94725274	98	194	4	190
CJ060865	94724691	94725284	97.7	298	6	290
CJ062481	94725606	94726066	100	460	0	460
CJ066686	94725733	94726154	98.9	416	5	411
CJ093422	94724614	94725908	98.9	436	3	430
CJ112083	94724631	94725665	99.5	502	1	498
CJ138942	94724614	94725596	99.2	448	4	443
CJ160548	94725650	94726099	100	449	0	449
DT917754	94725655	94726351	100	695	0	694

TSS

No TSS is located nearby retro_mmus_44 retrocopy 5' end.

Lab

retro_mmus_44 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_44 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006438	1 retrocopy	retro_amel_1830,
Equus caballus	ENSECAG00000026954	2 retrocopies	retro_ecab_1064, retro_ecab_1107,
Mus musculus	ENSMUSG00000034430	1 retrocopy	retro_mmus_44 ,
Rattus norvegicus	ENSRNOG00000025818	1 retrocopy	retro_rnor_2933,
Sus scrofa	ENSSSCG00000001824	1 retrocopy	retro_sscr_50,
Ictidomys tridecemlineatus	ENSSTOG00000007207	1 retrocopy	retro_itri_60,