RetrogeneDB ID: retro_mmus_767

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 11:21493610..21493955(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082040
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Hcfc1r1
• Ensembl ID: ENSMUSG00000023904
• Aliases: None
• Description: host cell factor C1 regulator 1 (XPO1-dependent) [Source:MGI Symbol;Acc:MGI:2663619]

Sequence

>retro_mmus_767
ATGATCCTGCAACAGCCCCTGTGGCAAGGTCTACCAAGTCAGGACCACAGGCCACCACTGGGGTGATTCGTGGCCTGGAC
ATCAGGGAATATTTCCACAAGCAGTTCCTGATTGAGGAGAACATGGCTACCCATTTCTCCTGACTCAGCCTACATAATGA
CCATCCCTACTGCAGCCCCCCTGTGACTTTTCCTGAAGCCCTGCCACCTCTTAGGAGCCCTTGCCCAGAGCTGCATCTCT
GGTACTATCCTGAAGCCTGATTCCTGATGCCCTCAGGTTGCTGAGGCTGGGGGATACCTCCAGCCCCTACTACTCTGCAT
CTCCAACTGGGATATCATGGAGCTC

Alignment

ORF - retro_mmus_767 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.67 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MILQQPLERGPPSRD-PRATTGVTRGLNAREPLHKQFLSEENMATHFSRLSLHNDHPYCSPPVTFPEALP
          MILQQPL..G.PS.D.P.ATTGV.RGL..RE..HKQFL.EENMATHFS.LSLHNDHPYCSPPVTFPEALP
Retrocopy MILQQPLWQGLPSQD<PQATTGVIRGLDIREYFHKQFLIEENMATHFS*LSLHNDHPYCSPPVTFPEALP

Parental  PLRSPCPELLLWRYPG-SLIPEALRLLRLGDTPSPYYPASPAG-DIVEL
          PLRSPCPEL.LW.YP..SLIP.ALRLLRLGDT.SPYY.ASP.G.DI.EL
Retrocopy PLRSPCPELHLWYYPE<SLIPDALRLLRLGDTSSPYYSASPTG<DIMEL

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	34.95 RPM
SRP007412_cerebellum	0.00 RPM	29.57 RPM
SRP007412_heart	0.00 RPM	49.59 RPM
SRP007412_kidney	0.02 RPM	30.18 RPM
SRP007412_liver	0.00 RPM	14.91 RPM
SRP007412_testis	0.00 RPM	7.91 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_767 was not detected

EST

No EST(s) were mapped for retro_mmus_767 retrocopy.

TSS

No TSS is located nearby retro_mmus_767 retrocopy 5' end.

Lab

retro_mmus_767 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_767 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005504	1 retrocopy	retro_amel_1251,
Callithrix jacchus	ENSCJAG00000015444	1 retrocopy	retro_cjac_1037,
Mus musculus	ENSMUSG00000023904	5 retrocopies	retro_mmus_1485, retro_mmus_1577, retro_mmus_1646, retro_mmus_2644, retro_mmus_767 ,