RetrogeneDB ID: retro_mmus_124

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 6:43210332..43210755(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000096158
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Pole3
• Ensembl ID: ENSMUSG00000028394
• Aliases: None
• Description: polymerase (DNA directed), epsilon 3 (p17 subunit) [Source:MGI Symbol;Acc:MGI:1933378]

Sequence

>retro_mmus_124
ATGGCAGAGAGGTCCAAGGACCTAAATATGCCCAAGGCCATCATTACCAGGATCATCAAGGAGGCACTCCAAGACAGGGT
CAAAATCTCCAAAGAGGACCTAAGCTCCATCTCCTTTGCCACCAGTATCTTCGTTCTTTATGCCACATCCTGTGCCAATA
ACTCTGCAATGAAAGGAAAGCACAAGACTCCGAATGTCAGCGGTGTGCTGTCAGCCATGGAAGAGATGGAGTTCCAGCGA
TTCATAACACCATTGAAAGAAGCTCTAGAAGCACACAGGGGGGAGCAGAAAGGCAAGAAGGAAGCTGGGGAACAAAAGAA
GAAGAGGGACAAAGACAAAAGAGATTCAGAAGAGCAAGACAAAAGCAGAGAGGAGGCAGATGGAGATGAGGAAAGACTGG
AAGAGGAGGAAGTAGACAACTGA

Alignment

ORF - retro_mmus_124 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.1 %
• Parental protein coverage: 93.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAERPEDLNLPNAVITRIIKEALPDGVNISKEARSAISRAASVFVLYATSCANNFAMKGKRKTLNASDVL
          MAER..DLN.P.A.ITRIIKEAL.D.V.ISKE..S.IS.A.S.FVLYATSCANN.AMKGK.KT.N.S.VL
Retrocopy MAERSKDLNMPKAIITRIIKEALQDRVKISKEDLSSISFATSIFVLYATSCANNSAMKGKHKTPNVSGVL

Parental  SAMEEMEFQRFITPLKEALEAYRREQKGKKEASEQKKK-DKDKKDSEEQDKSREEEEEDEERLDEDD
          SAMEEMEFQRFITPLKEALEA.R.EQKGKKEA.EQKKK.DKDK.DSEEQDKSREE...DEERL.E..
Retrocopy SAMEEMEFQRFITPLKEALEAHRGEQKGKKEAGEQKKKRDKDKRDSEEQDKSREEADGDEERLEEEE

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	19.51 RPM
SRP007412_cerebellum	0.00 RPM	29.70 RPM
SRP007412_heart	0.00 RPM	18.77 RPM
SRP007412_kidney	0.00 RPM	36.15 RPM
SRP007412_liver	0.00 RPM	21.38 RPM
SRP007412_testis	0.00 RPM	124.23 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_124 was not detected

EST

No EST(s) were mapped for retro_mmus_124 retrocopy.

TSS

No TSS is located nearby retro_mmus_124 retrocopy 5' end.

Lab

retro_mmus_124 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_124 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017917	1 retrocopy	retro_cjac_4121,
Cavia porcellus	ENSCPOG00000000313	1 retrocopy	retro_cpor_355,
Dipodomys ordii	ENSDORG00000003073	2 retrocopies	retro_dord_526, retro_dord_652,
Monodelphis domestica	ENSMODG00000004358	3 retrocopies	retro_mdom_1680, retro_mdom_1920, retro_mdom_647,
Mus musculus	ENSMUSG00000028394	2 retrocopies	retro_mmus_124 , retro_mmus_555,
Pteropus vampyrus	ENSPVAG00000004717	1 retrocopy	retro_pvam_302,
Rattus norvegicus	ENSRNOG00000015392	1 retrocopy	retro_rnor_55,
Ictidomys tridecemlineatus	ENSSTOG00000027365	1 retrocopy	retro_itri_866,
Tupaia belangeri	ENSTBEG00000005211	1 retrocopy	retro_tbel_4052,