RetrogeneDB ID: retro_mmus_1577

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 17:53734510..53734857(+)
• Located in intron of: None

Retrocopy information

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

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_1577
ATAATCCTGCACTAGCCCCTGTTGCAAGGTCCACCAAATCAGGACCACAGGCCACAACTGTGGTGATTTGTGGCCTGGAC
ATCAGGGAATATTTTCAAAGGAATTTCAAGATTGAGGAGTACATAACCACCCATTTATCCTGACTCAGCCTACATAATGA
CCACCCCTACTGCAGCCCACCCTGCTACTTTTCCCAAAGCCATGCCACCACTTAGGAGCCCTTGCCCAGAGCTGCATCTC
TGGTACTCTCCTGGAAGCCTGATTCCTGATGCCCTCCGGTTGCTGAGGCTGGGGGATACCCCCAGTCCCTATGACTCTGC
ATCTCCAACTGGGATATCATGGAGCTC

Alignment

ORF - retro_mmus_1577 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.23 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MILQQPLERGPPSRD-PRATTGVTRGLNAREPLHKQFLSEENMATHFSRLSLHNDHPYCSPP-VTFPEAL
          .IL..PL..GPP..D.P.ATT.V..GL..RE.....F..EE...TH.S.LSLHNDHPYCSPP..TFP.A.
Retrocopy IILH*PLLQGPPNQD<PQATTVVICGLDIREYFQRNFKIEEYITTHLS*LSLHNDHPYCSPP>ATFPKAM

Parental  PPLRSPCPELLLWRYPGSLIPEALRLLRLGDTPSPYYPASPAG-DIVEL
          PPLRSPCPEL.LW..PGSLIP.ALRLLRLGDTPSPY..ASP.G.DI.EL
Retrocopy PPLRSPCPELHLWYSPGSLIPDALRLLRLGDTPSPYDSASPTG<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	0.00 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 activity near the 5' end of retro_mmus_1577 was not detected

EST

No EST(s) were mapped for retro_mmus_1577 retrocopy.

TSS

No TSS is located nearby retro_mmus_1577 retrocopy 5' end.

Lab

retro_mmus_1577 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1577 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,