RetrogeneDB ID: retro_mmus_3081

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:119301254..119301673(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Gm20390
• Ensembl ID: ENSMUSG00000091228
• Aliases: None
• Description: predicted gene 20390 [Source:MGI Symbol;Acc:MGI:5141855]

Sequence

>retro_mmus_3081
CCAGATGGTGTGCAGTGCAGACTGGTGGGTGGTATCATCAAGCGCCTTGAGTAGGAGGGATTCCTCCTGGTGGCCATGAA
GTTCCTTCAGACATCTGAAGAATACCTGAAGCATCGCTACATTGATCTGAAAGGTTGTTCTTTCTTCCCAGGGCTAGTGA
AGTACATGAACTCAGCTCCTGTGATGGCCATGGTCTGTGAGAGGCTTAATGTAGTAAAGACAGGCTGGATGGTGTTGGGA
GGATCAAGTCCAGCTGATTCTAAGTCAGGCATCATCTGAGGGGATTTCTGCATCCAAGTGGGCAGGAACAATATTCATGG
CAGTGATTCGGTGGGAAGTATTGAGAAGTAGTCAGTCTATGCTTTAAGCCTGAAGAACTGATCGACTATAAGTCCTGTGC
CCATGGCTGGATCTATAAA

Alignment

ORF - retro_mmus_3081 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.34 %
• Parental protein coverage: 52.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PDGVQRGLVGEIIKRFEQKGFRLVAMKFLRASEEHLKQHYIDLKDRPFFPGLVKYMNSGPVVAMVWEGLN
          PDGVQ..LVG.IIKR.E..GF.LVAMKFL..SEE.LK..YIDLK...FFPGLVKYMNS.PV.AMV.E.LN
Retrocopy PDGVQCRLVGGIIKRLE*EGFLLVAMKFLQTSEEYLKHRYIDLKGCSFFPGLVKYMNSAPVMAMVCERLN

Parental  VVKTGRVMLGETNPADSKPGTIRGDFCIQVGRNIIHGSDSVESAEK-EIHLWFKPEELIDYKSCAHDWVY
          VVKTG...LG...PADSK.G.I.GDFCIQVGRN.IHGSDSV.S.EK....L.FKPEELIDYKSCAH.W.Y
Retrocopy VVKTGWMVLGGSSPADSKSGII*GDFCIQVGRNNIHGSDSVGSIEK<VVSLCFKPEELIDYKSCAHGWIY

Parental  E
          .
Retrocopy K

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	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.00 RPM
SRP007412_heart	0.00 RPM	0.00 RPM
SRP007412_kidney	0.00 RPM	0.00 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.00 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3081 was not detected

EST

No EST(s) were mapped for retro_mmus_3081 retrocopy.

TSS

No TSS is located nearby retro_mmus_3081 retrocopy 5' end.

Lab

retro_mmus_3081 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3081 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004651	1 retrocopy	retro_btau_1707,
Canis familiaris	ENSCAFG00000023628	7 retrocopies	retro_cfam_117, retro_cfam_1645, retro_cfam_37, retro_cfam_676, retro_cfam_69, retro_cfam_832, retro_cfam_96,
Cavia porcellus	ENSCPOG00000008413	1 retrocopy	retro_cpor_599,
Echinops telfairi	ENSETEG00000005563	4 retrocopies	retro_etel_242, retro_etel_547, retro_etel_71, retro_etel_803,
Gorilla gorilla	ENSGGOG00000016526	1 retrocopy	retro_ggor_71,
Monodelphis domestica	ENSMODG00000028492	1 retrocopy	retro_mdom_503,
Mustela putorius furo	ENSMPUG00000015559	5 retrocopies	retro_mputfur_1093, retro_mputfur_1357, retro_mputfur_442, retro_mputfur_667, retro_mputfur_997,
Mus musculus	ENSMUSG00000020857	1 retrocopy	retro_mmus_221,
Mus musculus	ENSMUSG00000024177	1 retrocopy	retro_mmus_309,
Mus musculus	ENSMUSG00000032478	1 retrocopy	retro_mmus_2376,
Mus musculus	ENSMUSG00000091228	3 retrocopies	retro_mmus_2712, retro_mmus_3081 , retro_mmus_581,
Nomascus leucogenys	ENSNLEG00000007919	2 retrocopies	retro_nleu_1029, retro_nleu_1030,
Oryctolagus cuniculus	ENSOCUG00000022135	1 retrocopy	retro_ocun_1728,
Pan troglodytes	ENSPTRG00000009415	1 retrocopy	retro_ptro_91,
Rattus norvegicus	ENSRNOG00000002693	3 retrocopies	retro_rnor_1198, retro_rnor_1600, retro_rnor_704,