RetrogeneDB ID: retro_mmus_2439

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:19993201..19993497(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Copz1
• Ensembl ID: ENSMUSG00000060992
• Aliases: Copz1, 5930435A22Rik, AA407760, D4Ertd360e
• Description: coatomer protein complex, subunit zeta 1 [Source:MGI Symbol;Acc:MGI:1929063]

Sequence

>retro_mmus_2439
TCCTTGTACACTGTCAAGGCCACCCTGATTTTGGACAATGATGGAGACACACTCTTTGCCAAGTACTATGACGACACCTA
CCCCAGAGTCAAAGAGCAAGGGCCTTTGGAATGAACATTTGCAACAAGACACATTGGATGGATAGTGAAATTACCCTTTT
GGAAGGGATGCCAGTGATCTATAAAAGTAGCATCAATCTCTATTTCTGTGCGATTGTCTGCTTCTATGAAAGTGAACTGA
TGCTTATGGCTGTTCTCAACTGCCTCTTCAACTCCCTGAGCCCGATGCTGAGGAAA

Alignment

ORF - retro_mmus_2439 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.0 %
• Parental protein coverage: 55.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SLYTVKAILILDNDGDRLFAKYYDDTYPSVKEQ-KAFEKNIFNKTHRTDSEIALLEGLTVVYKSSIDLYF
          SLYTVKA.LILDNDGD.LFAKYYDDTYP.VKEQ..AF..NI.NKTH..DSEI.LLEG..V.YKSSI.LYF
Retrocopy SLYTVKATLILDNDGDTLFAKYYDDTYPRVKEQ<RAFGMNICNKTHWMDSEITLLEGMPVIYKSSINLYF

Parental  YVIGSSYENELMLMAVLNCLFDSLSQMLRK
          ..I...YE.ELMLMAVLNCLF.SLS.MLRK
Retrocopy CAIVCFYESELMLMAVLNCLFNSLSPMLRK

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	60.51 RPM
SRP007412_cerebellum	0.00 RPM	44.33 RPM
SRP007412_heart	0.00 RPM	39.78 RPM
SRP007412_kidney	0.00 RPM	77.58 RPM
SRP007412_liver	0.05 RPM	115.27 RPM
SRP007412_testis	0.05 RPM	35.54 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2439 was not detected

EST

No EST(s) were mapped for retro_mmus_2439 retrocopy.

TSS

No TSS is located nearby retro_mmus_2439 retrocopy 5' end.

Lab

retro_mmus_2439 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2439 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_2209

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005384	1 retrocopy	retro_btau_1500,
Canis familiaris	ENSCAFG00000006536	1 retrocopy	retro_cfam_30,
Callithrix jacchus	ENSCJAG00000018887	2 retrocopies	retro_cjac_1771, retro_cjac_3951,
Echinops telfairi	ENSETEG00000013499	1 retrocopy	retro_etel_1782,
Microcebus murinus	ENSMICG00000008401	1 retrocopy	retro_mmur_757,
Mus musculus	ENSMUSG00000060992	1 retrocopy	retro_mmus_2439 ,
Rattus norvegicus	ENSRNOG00000036835	1 retrocopy	retro_rnor_2209,
Tupaia belangeri	ENSTBEG00000008730	1 retrocopy	retro_tbel_3749,
Tursiops truncatus	ENSTTRG00000001654	2 retrocopies	retro_ttru_114, retro_ttru_856,