RetrogeneDB ID: retro_mmus_3549

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:153908554..153908830(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Polr2h
• Ensembl ID: ENSMUSG00000021018
• Aliases: None
• Description: polymerase (RNA) II (DNA directed) polypeptide H [Source:MGI Symbol;Acc:MGI:2384309]

Sequence

>retro_mmus_3549
CTATCTCAGCTTGGCTATGAGAGTGAATTTTTAAAGACAGAACTTATCTTAGATGTAAGCATTCAGATTTACCTTGTGAC
TTAGGTGAGAAGTTCTGATTGGTCAAAACTAGTACCTTGGATGAAGATGTGACCTTTGTTGACAGTGAATACAACCTCAC
AGATGATAGACCTTCCAGGGCAGCCTGGCTTGAATATATAATGTATGGGGAGGTATACAGGGTTGGGAGGGAACAATATC
GCTATTGAAGCAGCAACATGCCTTTCTATGTATGTA

Alignment

ORF - retro_mmus_3549 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.7 %
• Parental protein coverage: 61.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VSRLHCESESFKMDLILDVNIQIY-PVDLGDKFRLVIASTLYEDGTLDDGEYNPTDDRPSRADQFEYVMY
          .S.L..ESE..K..LILDV.IQIY.P.DLG.KF.LV..STL.ED.T..D.EYN.TDDRPSRA...EY.MY
Retrocopy LSQLGYESEFLKTELILDVSIQIY<PCDLGEKF*LVKTSTLDEDVTFVDSEYNLTDDRPSRAAWLEYIMY

Parental  GKVYRI-EGDETSTEAATRLSAYV
          G.VYR...G.....EAAT.LS.YV
Retrocopy GEVYRV>GGNNIAIEAATCLSMYV

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	11.17 RPM
SRP007412_cerebellum	0.00 RPM	7.56 RPM
SRP007412_heart	0.00 RPM	5.70 RPM
SRP007412_kidney	0.00 RPM	7.80 RPM
SRP007412_liver	0.00 RPM	9.12 RPM
SRP007412_testis	0.00 RPM	4.44 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3549 was not detected

EST

No EST(s) were mapped for retro_mmus_3549 retrocopy.

TSS

No TSS is located nearby retro_mmus_3549 retrocopy 5' end.

Lab

retro_mmus_3549 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3549 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000005751	1 retrocopy	retro_dnov_709,
Microcebus murinus	ENSMICG00000011294	1 retrocopy	retro_mmur_537,
Myotis lucifugus	ENSMLUG00000022295	2 retrocopies	retro_mluc_2322, retro_mluc_552,
Monodelphis domestica	ENSMODG00000002570	2 retrocopies	retro_mdom_1394, retro_mdom_1450,
Mus musculus	ENSMUSG00000021018	2 retrocopies	retro_mmus_3549 , retro_mmus_936,
Otolemur garnettii	ENSOGAG00000001599	1 retrocopy	retro_ogar_3073,
Rattus norvegicus	ENSRNOG00000001748	2 retrocopies	retro_rnor_1377, retro_rnor_773,