RetrogeneDB ID: retro_mmus_2963

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 7:107863038..107863497(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000066245
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Rbm3
• Ensembl ID: ENSMUSG00000031167
• Aliases: Rbm3, 2600016C11Rik
• Description: RNA binding motif protein 3 [Source:MGI Symbol;Acc:MGI:1099460]

Sequence

>retro_mmus_2963
ATGTCGTCTGAAGAAGGGAAACTCTTCGTAGGAGGGCTCAACTTCAACACCGATGAACAGGCACTTGAAGACCACTTCAG
CAGCTTTGGGCCTATCTCTGAGGTGGTTGTTGTCAAGGACCGGGAGACTCAAAGATCCCAGGGTTTTGACTTCATCACCT
TCACAAACCCAGAGCATGCCTCAGATGCGATGAGAGCCATGAATGGAGAGTCCCTGGATGGGCGCCAAATCCGAGTTGAT
CATGCAGGAAAGTTTGCCAGGGGATCCAGAGGGGGTGCCTTTGGTGGGCGTGGTCGCAGTTACTCTAGAGGTGGTGGAGA
CCAGGGATATGGAAGTGGAAGATATGACAGTCGTCCTGGAGGATATGGATATGGGTATGGGCGGTCTAGAGACTACAGTG
GCAGCCAGGGTGGCTATGACCGCTACTCAGGAGGAAATTACAGAGACAATTATGACAAC

Alignment

ORF - retro_mmus_2963 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.04 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSEEGKLFVGGLNFNTDEQALEDHFSSFGPISEVVVVKDRETQRSRGFGFITFTNPEHASDAMRAMNGE
          MSSEEGKLFVGGLNFNTDEQALEDHFSSFGPISEVVVVKDRETQRS.GF.FITFTNPEHASDAMRAMNGE
Retrocopy MSSEEGKLFVGGLNFNTDEQALEDHFSSFGPISEVVVVKDRETQRSQGFDFITFTNPEHASDAMRAMNGE

Parental  SLDGRQIRVDHAGKSARGSRGGAFGGRGRSYSRGGGDQGYGSGRYDSRPGGYGYGYGRSRDYSGSQGGYD
          SLDGRQIRVDHAGK.ARGSRGGAFGGRGRSYSRGGGDQGYGSGRYDSRPGGYGYGYGRSRDYSGSQGGYD
Retrocopy SLDGRQIRVDHAGKFARGSRGGAFGGRGRSYSRGGGDQGYGSGRYDSRPGGYGYGYGRSRDYSGSQGGYD

Parental  RYSGGNYRDNYDN
          RYSGGNYRDNYDN
Retrocopy RYSGGNYRDNYDN

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	32.10 RPM
SRP007412_cerebellum	0.00 RPM	46.16 RPM
SRP007412_heart	0.00 RPM	27.61 RPM
SRP007412_kidney	0.02 RPM	33.07 RPM
SRP007412_liver	0.00 RPM	21.33 RPM
SRP007412_testis	0.00 RPM	8.60 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2963 was not detected

EST

No EST(s) were mapped for retro_mmus_2963 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_127551	413 libraries	72 libraries	250 libraries	217 libraries	120 libraries

The graphical summary, for retro_mmus_2963 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_2963 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2963 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 38 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013718	1 retrocopy	retro_acar_197,
Ailuropoda melanoleuca	ENSAMEG00000012653	1 retrocopy	retro_amel_519,
Bos taurus	ENSBTAG00000025848	1 retrocopy	retro_btau_1144,
Canis familiaris	ENSCAFG00000015485	2 retrocopies	retro_cfam_1475, retro_cfam_259,
Dipodomys ordii	ENSDORG00000000182	1 retrocopy	retro_dord_547,
Equus caballus	ENSECAG00000024257	2 retrocopies	retro_ecab_130, retro_ecab_589,
Homo sapiens	ENSG00000102317	1 retrocopy	retro_hsap_265,
Gadus morhua	ENSGMOG00000012137	1 retrocopy	retro_gmor_4,
Loxodonta africana	ENSLAFG00000007003	1 retrocopy	retro_lafr_1091,
Myotis lucifugus	ENSMLUG00000003996	1 retrocopy	retro_mluc_1013,
Mus musculus	ENSMUSG00000022858	6 retrocopies	retro_mmus_1187, retro_mmus_2253, retro_mmus_2313, retro_mmus_3139, retro_mmus_3617, retro_mmus_756,
Mus musculus	ENSMUSG00000031134	2 retrocopies	retro_mmus_170, retro_mmus_187,
Mus musculus	ENSMUSG00000031167	4 retrocopies	retro_mmus_2044, retro_mmus_2963 , retro_mmus_3019, retro_mmus_501,
Nomascus leucogenys	ENSNLEG00000007841	2 retrocopies	retro_nleu_2591, retro_nleu_867,
Pongo abelii	ENSPPYG00000020314	1 retrocopy	retro_pabe_40,
Pan troglodytes	ENSPTRG00000021864	1 retrocopy	retro_ptro_222,
Pteropus vampyrus	ENSPVAG00000015630	1 retrocopy	retro_pvam_953,
Sus scrofa	ENSSSCG00000021591	1 retrocopy	retro_sscr_842,
Ictidomys tridecemlineatus	ENSSTOG00000027493	1 retrocopy	retro_itri_142,
Tarsius syrichta	ENSTSYG00000008670	4 retrocopies	retro_tsyr_1733, retro_tsyr_197, retro_tsyr_2002, retro_tsyr_679,
Tursiops truncatus	ENSTTRG00000008587	3 retrocopies	retro_ttru_1898, retro_ttru_928, retro_ttru_938,