RetrogeneDB ID: retro_mmus_473

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 1:101753813..101754543(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Uqcrc1
• Ensembl ID: ENSMUSG00000025651
• Aliases: Uqcrc1, 1110032G10Rik
• Description: ubiquinol-cytochrome c reductase core protein 1 [Source:MGI Symbol;Acc:MGI:107876]

Sequence

>retro_mmus_473
CTAGACCAGGTTGTAGAGGTGCCCAGTGAGAACATCAGGAGGCTGACCCGTACAGACTTGACTGACTACCTCTACAGGCA
TTACAAAGATCACTGAATGGTGCTGACTGCAGCTGGAGGTGTGGAACGACAGATGCTGCTGGACCTTGCCCAGAAACACT
TCAGTAGTGTCTCCCAAGTGTATTAAGAAGGCGCCATACCTGGTGTACCTCTAAGTTGCTTTACTAGCAGTGAGATTTGC
CATTGTGATGATGCCCTGCATTTGGCCCACGTGGCCATTGCAGTAGAAGGACCTGGCTGGGTTAACCCAGACAAAGTAGC
CCTCCAAGCCAATGCCATCACAGGCCACTATGACTGCAATGTTTAGTGGTGGAGTGCACCTTCCCAGCCTGCTGGCTTCT
ATTGCTGCAGCTAACAAGCTCTGCCAGAGATTCTAGACCTTCAATATCACCTACCCTGAGACAGGGCTGCTGAGCACACA
CTTTGGCTGTGATACTGTGAGCATCAATGACATGGTCTTCTCCTTGCAAGGCCAGTAGATGCACATTTGCACCAGTGCTA
GAGAGTGAAGTGACTTGGGGAAAAAAAAATCTTAGGAAGGGGCCATGGTATCTCATTTGGATGGCACCACCCCTGTGTGT
GAAGACATTGGTCGCAGCCTCCTGACTTATGGTTGCCACATCCTTCTGTTTGAGTGGGAGAGATATATTCAGGTGGATGC
CCAGATGCTG

Alignment

ORF - retro_mmus_473 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.51 %
• Parental protein coverage: 51.04 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LAQAVEGPSENVRRLSRTDLTDYLNRHYKAPRMVLAAAGGVEHQQLLDLAQKHLSSVSRVYEEDAVPGLT
          L.Q.VE.PSEN.RRL.RTDLTDYL.RHYK...MVL.AAGGVE.Q.LLDLAQKH.SSVS.VY.E.A.PG..
Retrocopy LDQVVEVPSENIRRLTRTDLTDYLYRHYKDH*MVLTAAGGVERQMLLDLAQKHFSSVSQVY*EGAIPGVP

Parental  PCRFTGSEIRHRDDALPLAHVAIAVEGPGWANPDNVTLQVANAIIGHYDCT-YGGGVHLSSPLASVAVAN
          ...FT.SEI.H.DDAL.LAHVAIAVEGPGW.NPD.V.LQ.ANAI.GHYDC....GGVHL.S.LAS.A.AN
Retrocopy LSCFTSSEICHCDDALHLAHVAIAVEGPGWVNPDKVALQ-ANAITGHYDCN>FSGGVHLPSLLASIAAAN

Parental  KLCQSFQTFNISYSDTGLLGAHFVCDAMSIDDMVFFLQGQWMRLCTSATESEVTRGKNILRNALVSHLDG
          KLCQ.F.TFNI.Y..TGLL..HF.CD..SI.DMVF.LQGQ.M..CTSA.E............A.VSHLDG
Retrocopy KLCQRF*TFNITYPETGLLSTHFGCDTVSINDMVFSLQGQ*MHICTSARE*SDLGXXXS*EGAMVSHLDG

Parental  TTPVCEDIGRSLLTYGRRIPLAEWESRIQEVDAQML
          TTPVCEDIGRSLLTYG..I.L.EWE..IQ.VDAQML
Retrocopy TTPVCEDIGRSLLTYGCHILLFEWERYIQ-VDAQML

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	0.02 RPM	171.69 RPM
SRP007412_cerebellum	0.00 RPM	171.56 RPM
SRP007412_heart	0.06 RPM	920.55 RPM
SRP007412_kidney	0.04 RPM	448.27 RPM
SRP007412_liver	0.00 RPM	182.15 RPM
SRP007412_testis	0.05 RPM	197.18 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_473 was not detected

EST

No EST(s) were mapped for retro_mmus_473 retrocopy.

TSS

No TSS is located nearby retro_mmus_473 retrocopy 5' end.

Lab

retro_mmus_473 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_473 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003132	1 retrocopy	retro_cjac_2204,
Mus musculus	ENSMUSG00000025651	1 retrocopy	retro_mmus_473 ,