RetrogeneDB ID: retro_mmus_3221

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:79680283..79680824(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000094594
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Tpd52
• Ensembl ID: ENSMUSG00000027506
• Aliases: Tpd52, AI043038, mD52
• Description: tumor protein D52 [Source:MGI Symbol;Acc:MGI:107749]

Sequence

>retro_mmus_3221
ATGGACCGCGGCGAGCAAGGTCTGCTGAAGACAGAGCCAGTGGCCGAGGAAGGAGAGGATGCTGTTACCATGCTCAGTGC
TCCAGAGACGCTGACGGAAGAGGAGCAAGAGGAGCTGGGGCGGGAGCTTACTAAAGTGGAAGAAGAAATCCAGACTCTGT
CCCAAGTATTGGCCGCAAAAGAGAAGCGTCTCGCTGAGCTCAAGCGGAAGCTTGGCATCTCCTCGCTTCAGGAGTTCAAG
CAGAACATTGCCAAAGGGTGGCAAAGACGTGACGGCAACCAATGCATACAAGAAGACATCTGAAACTCTATCGCAAGCTG
GACAGAAGGCCTCCGCTGCATTTTCATCGGTTGGCTCAGTTATCACCAAAAAGCTGGAAGACGTGAAAAACTCCCCAACT
TTCAAGTCATTTGAAGAAAAAGTTGAAAATTTAAAGTCTAAAGTAGGAGGAGCCAAGCCTGCTGGCGGCGATTTTGGAGA
AGTCCTGAATTCCACAGCCAACGCTACCAGTGCCATGACCACAAAGCCTCCTCCAGAACAG

Alignment

ORF - retro_mmus_3221 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.69 %
• Parental protein coverage: 97.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDRGEQGLLKTEPVAEEGEDAVTMLSAPEALTEEEQEELRRELTKVEEEIQTLSQVLAAKEKHLAELKRK
          MDRGEQGLLKTEPVAEEGEDAVTMLSAPE.LTEEEQEEL.RELTKVEEEIQTLSQVLAAKEK.LAELKRK
Retrocopy MDRGEQGLLKTEPVAEEGEDAVTMLSAPETLTEEEQEELGRELTKVEEEIQTLSQVLAAKEKRLAELKRK

Parental  LGISSLQEFKQNIAKGWQ-DVTATNAYKKTSETLSQAGQKASAAFSSVGSVITKKLEDVKNSPTFKSFEE
          LGISSLQEFKQNIAKGWQ.DVTATNAYKKTSETLSQAGQKASAAFSSVGSVITKKLEDVKNSPTFKSFEE
Retrocopy LGISSLQEFKQNIAKGWQ>DVTATNAYKKTSETLSQAGQKASAAFSSVGSVITKKLEDVKNSPTFKSFEE

Parental  KVENLKSKVGGAKPAGGDFGEVLNSTANATSTMTTEPPPEQ
          KVENLKSKVGGAKPAGGDFGEVLNSTANATS.MTT.PPPEQ
Retrocopy KVENLKSKVGGAKPAGGDFGEVLNSTANATSAMTTKPPPEQ

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	0.33 RPM	34.83 RPM
SRP007412_cerebellum	1.69 RPM	25.92 RPM
SRP007412_heart	0.03 RPM	14.10 RPM
SRP007412_kidney	1.91 RPM	55.15 RPM
SRP007412_liver	0.44 RPM	8.25 RPM
SRP007412_testis	0.41 RPM	4.39 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_mmus_3221 in 1 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YIJ	POLR2A	8:79680301..79683672

EST

No EST(s) were mapped for retro_mmus_3221 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_144125	293 libraries	242 libraries	336 libraries	140 libraries	61 libraries

The graphical summary, for retro_mmus_3221 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_3221 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3221 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001357	1 retrocopy	retro_chof_1370,
Dasypus novemcinctus	ENSDNOG00000017379	2 retrocopies	retro_dnov_1294, retro_dnov_1451,
Mus musculus	ENSMUSG00000027506	1 retrocopy	retro_mmus_3221 ,
Oryctolagus cuniculus	ENSOCUG00000008247	1 retrocopy	retro_ocun_325,
Otolemur garnettii	ENSOGAG00000016601	2 retrocopies	retro_ogar_1677, retro_ogar_348,
Tursiops truncatus	ENSTTRG00000000088	1 retrocopy	retro_ttru_1888,