RetrogeneDB ID: retro_mmus_3184

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 8:34111390..34111702(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000063412
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Erh
• Ensembl ID: ENSMUSG00000021131
• Aliases: None
• Description: enhancer of rudimentary homolog (Drosophila) [Source:MGI Symbol;Acc:MGI:108089]

Sequence

>retro_mmus_3184
ATGTCTCACACCATTTTGCTGGTACAGCCTACCAAGAGGCCAGAGGGCAGGACTTATGCTGACTATGAGTCTGTGAATGA
GTGCATGGAAGGTGTTTGTAAAATGTATGAAGAACATCTGAAGAGGATGAATCCCAACAGCCCTTCCATCACATACGATA
TCAGCCAGTTGTTTGATTTTATTGACGATCTGGCAGACCTCAGCTGTCTGGTTTACCGAGCTGATACACAGACATACCAG
CCGTATAACAAAGACTGGATCAAAGAGAAGATCTACGTGCTCCTCCGTCGGCAGGCCCAACAGGCTGGGAAG

Alignment

ORF - retro_mmus_3184 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 84.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSHTILLVQPTKRPEGRTYADYESVNECMEGVCKMYEEHLKRMNPNSPSITYDISQLFDFIDDLADLSCL
          MSHTILLVQPTKRPEGRTYADYESVNECMEGVCKMYEEHLKRMNPNSPSITYDISQLFDFIDDLADLSCL
Retrocopy MSHTILLVQPTKRPEGRTYADYESVNECMEGVCKMYEEHLKRMNPNSPSITYDISQLFDFIDDLADLSCL

Parental  VYRADTQTYQPYNKDWIKEKIYVLLRRQAQQAGK
          VYRADTQTYQPYNKDWIKEKIYVLLRRQAQQAGK
Retrocopy VYRADTQTYQPYNKDWIKEKIYVLLRRQAQQAGK

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	0.05 RPM	5.21 RPM
SRP007412_cerebellum	0.00 RPM	5.86 RPM
SRP007412_heart	0.12 RPM	7.81 RPM
SRP007412_kidney	0.06 RPM	5.99 RPM
SRP007412_liver	0.03 RPM	6.14 RPM
SRP007412_testis	0.09 RPM	19.26 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_3184 was not detected

EST

No EST(s) were mapped for retro_mmus_3184 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_141655	91 libraries	64 libraries	643 libraries	215 libraries	59 libraries

The graphical summary, for retro_mmus_3184 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_3184 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3184 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014940	2 retrocopies	retro_cjac_209, retro_cjac_846,
Equus caballus	ENSECAG00000019178	1 retrocopy	retro_ecab_45,
Myotis lucifugus	ENSMLUG00000011879	1 retrocopy	retro_mluc_142,
Mus musculus	ENSMUSG00000021131	4 retrocopies	retro_mmus_1576, retro_mmus_2599, retro_mmus_3184 , retro_mmus_39,
Oryctolagus cuniculus	ENSOCUG00000004636	1 retrocopy	retro_ocun_42,