RetrogeneDB ID: retro_rnor_2933

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: X:64997283..64998855(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000022607
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Zxdc
• Ensembl ID: ENSRNOG00000025818
• Aliases: Zxdc, RGD1561296
• Description: Protein Zxdc [Source:UniProtKB/TrEMBL;Acc:D3ZYP0]

Sequence

>retro_rnor_2933
GCCCAGAGCCCCCGCGGGCCTGTGGTCCCGGGCCCGGGCGTGGTGCTGTACCTGTGCCCCGAGGCGCAGTGCGGACAGAC
CTTCGCCAAGAAGCACCAGCTGAAGGTGCACCTGCTGACGCACAGCAGTAGCCAGGGCCAGCGGCCCTTCAAGTGCCCCC
TGAGCGGCTGCGGCTGGACCTTCACCACGTCTTACAAGCTCAAGAGACACCTGCAGTCGCACGACAAACTGCGGCCATTT
GGCTGCCCGGTGGAGGGCTGTGGCAAGAGCTTCACCACCGTGTACAACCTCAAGGCGCACATGAAGGGGCACGAGCAGGA
GAACTCCTTCAAATGCGAGGTGTGTGAGGAGAGCTTCCCCACGCAGGCCAAGCTCAGCACCCACCAGCGCAGCCACTTCG
AGCCCGAGAGGCCTTACCAGTGTGCGTTTTCTGGCTGCAAGAAGACGTTCATTACTGTGAGTGCCCTGTTTTCTCACAAC
CGCGCCCATTTCAGGGAGCAGGAACTCTTTGCCTGCTCTTTCCCGGGCTGCAGCAAGCAGTATGACAAGGCTTGCAGGCT
CAAGATCCACCTGCGGAGCCACACTGGGGAGAGGCCTTTCCTCTGCGACTTTGATGGCTGTGGCTGGAACTTCACCAGCA
TGTCCAAACTCTTAAGGCACAAGAGGAAGCACGAAGACGACCGCAGGTTCACCTGTCCCGTGGAGGGCTGTGGGAAGTCC
TTCACCAGGGCCGAGCACCTGAAAGGCCACAGCATAACCCACCTGGGCACGAAGCCTTTCGTGTGCCCCGTGGAAGGCTG
CTGTGCCAGGTTCTCTGCTCGCAGCAGCCTCTACATCCACTCCAAGAAGCACTTGCAGGACGTGGGTGCTTGGAAAAGCC
GCTGCCCGGTGCCCACCTGTAACAAGCTCTTCACGTCCAAGCACAGCATGAAGACCCACATGACCAAAAGGCACAACCTC
AGCCAGGACCTCTTGGCCCAGCTAGAAGCTGCCAACTCTCTCACCCCCAGCAGTGAACTCACCAGCCAGGGGCCGAACGA
TCTCAGTGGTGCCGAGCTAGTGTCTCTGTTCTCCGATGTGCCTGGCCACAGCTCTGCTGCGGTGCTGGACACGGCCCTGG
TCAACTCTGGCATCTTGACCATTGATGTGGCCTCTGTGAACTCGACCCTCGCAGGAGGTCTCCCTGCCGAAAATAGCAAC
AGCAACCATTCCTTGGGGCAAGCGGTGGACCCTCGGGCCTTGAGGGGGCCCCCCAGTGACCTTCCCCAGAGTCTGGATAC
CTCTCTCTTCTTCGGAACCACCTCCTCCTCGGTGGCTGGCTATCAGCACAGCCCCTTGGACATGGACGATGTCTCTGCTG
GGAATGTGGGGCTCTTTGGCTCCTTGGCTCTGAAAAACTCAAGCCTGGAGCCCCAGGCTTTGACACCCAGCAATAAGTTG
ACCGTGGACACGGAAGCTCTGACTCCCTCCAGCACCCTCTGTGAAAACAGTGTCTCCGAGCTACTGACCCCAGCCAAAGC
CGATTGGAGCATGCACCCCGAATCTGACTTCTTTGGGCACGAGGAAGAAACC

Alignment

ORF - retro_rnor_2933 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.68 %
• Parental protein coverage: 60.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AASRRGPVAASAGSPAYRCPEPQCALSFAKKHQLKVHLLTHGSLQGRRPFKCPLDGCGWAFTTSYKLKRH
          A.S.RGPV....G...Y.CPE.QC...FAKKHQLKVHLLTH.S.QG.RPFKCPL.GCGW.FTTSYKLKRH
Retrocopy AQSPRGPVVPGPGVVLYLCPEAQCGQTFAKKHQLKVHLLTHSSSQGQRPFKCPLSGCGWTFTTSYKLKRH

Parental  LQSHDKLRPFSCPVGGCGKKFTTVYNLKAHMKGHEQESLFKCEVCAERFPTHAKLNSHQRSHFEPERPYK
          LQSHDKLRPF.CPV.GCGK.FTTVYNLKAHMKGHEQE..FKCEVC.E.FPT.AKL..HQRSHFEPERPY.
Retrocopy LQSHDKLRPFGCPVEGCGKSFTTVYNLKAHMKGHEQENSFKCEVCEESFPTQAKLSTHQRSHFEPERPYQ

Parental  CDFPGCEKTFITVSALFSHNRAHFREQELFSCSFPGCNKQYDKACRLKIHLRSHTGERPFICDSDSCGWT
          C.F.GC.KTFITVSALFSHNRAHFREQELF.CSFPGC.KQYDKACRLKIHLRSHTGERPF.CD.D.CGW.
Retrocopy CAFSGCKKTFITVSALFSHNRAHFREQELFACSFPGCSKQYDKACRLKIHLRSHTGERPFLCDFDGCGWN

Parental  FTSMSKLLRHKRKHDDDRRFTCPVEGCGKSFTRAEHLKGHSITHLGTKPFECPVEGCCARFSARSSLYIH
          FTSMSKLLRHKRKH.DDRRFTCPVEGCGKSFTRAEHLKGHSITHLGTKPF.CPVEGCCARFSARSSLYIH
Retrocopy FTSMSKLLRHKRKHEDDRRFTCPVEGCGKSFTRAEHLKGHSITHLGTKPFVCPVEGCCARFSARSSLYIH

Parental  SKKHLQDVGTPKSRCPVSSCNRLFTSKHSMKAHMVRQHSRRQDLVPQLEAPSSLTPSSELSSPGQSELTN
          SKKHLQDVG..KSRCPV..CN.LFTSKHSMK.HM...H...QDL..QLEA..SLTPSSEL.S.G...L..
Retrocopy SKKHLQDVGAWKSRCPVPTCNKLFTSKHSMKTHMTKRHNLSQDLLAQLEAANSLTPSSELTSQGPNDLSG

Parental  IDLAALFSDTPANSSSSTAGSDEALNSGILTIDVTSVSSSLGGNLPT----NNNSLGP-MDPLVLVAH-S
          ..L..LFSD.P..SS..........NSGILTIDV.SV.S.L.G.LP......N.SLG...DP..L....S
Retrocopy AELVSLFSDVPGHSSAAVLDT-ALVNSGILTIDVASVNSTLAGGLPAENSNSNHSLGQAVDPRALRGPPS

Parental  DMPPSLDSPLVLGTPATVLQPGSFSADDSQAMSTGAVGCLVALPMRNLSQDSPALTPSNNLTALGTTPTS
          D.P.SLD..L..GT..........S..D....S.G.VG....L...N.S....ALTPSN.LT......T.
Retrocopy DLPQSLDTSLFFGTTSSSVAGYQHSPLDMDDVSAGNVGLFGSLALKNSSLEPQALTPSNKLTVDTEALTP

Parental  SDTTQETASVPDLLVPIKVEQDLSPVPDVVQGQKES
          S.T..E..SV..LL.P.K......P..D......E.
Retrocopy SSTLCEN-SVSELLTPAKADWSMHPESDFFGHEEET

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
SRP017611_brain	14.16 RPM	13.23 RPM
SRP017611_kidney	6.49 RPM	15.14 RPM
SRP017611_liver	2.56 RPM	7.60 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2933 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2933 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2933 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,