RetrogeneDB ID: retro_cfam_469

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 11:56670778..56671336(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MARC2
• Ensembl ID: ENSCAFG00000011332
• Aliases: None
• Description: mitochondrial amidoxime reducing component 2 [Source:HGNC Symbol;Acc:26064]

Sequence

>retro_cfam_469
AGGCTATTGGGCATGGACATTAAGGGCAGGGACTGTGGCGATGAGGCAGCGCAGTGATTCACCAGCTTCTTGAAAACAGA
AGCTTTCAGGCTGGTTCAGTTTGAGAAGCACATGAAAGGAAGATGGTTGAAGGAAATTTTCTCTCCTGTGGTACTGAATT
ACCAGTTGGCCTACCCAGACTGCAGCCCCATCATGGTCCTCCCTGAAGCCTCCTTGGTGGCTCTGAGTACCAGGCTGGAG
AAGAAAGTGAAAATGGACCAGTTCAGATCCAATATCATGGTGACAGGCTGTGATGCTTCCGAGGAGGACACCTGGGATGA
ACTCCTCATTGGCAACGTAGAAATGATAAAAGTTTTGTCTTGCCCCAGGTGCATCTTGACCACCACAGACCCAGATACTG
GAATCATAGATAGGAAGGAGCCCCTGGAAACCCTGAAGAGCTACCCCCTGTGTGCTCCTTTGGAGAAACAAATATACAAG
TCATCCCCACTTTTCAGGTTCTATTATTCAGTGGAGAAAATTGGCAAGATGCAAGCTGGTGACCCAGTGTATCAGATG

Alignment

ORF - retro_cfam_469 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.56 %
• Parental protein coverage: 99.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RLFGMDIKGRDCGDEAAQWFTSFLKTEAFRLVQFEKHMKGRPSKEIFSPVVPNYQVAYPDCSPIMILSEA
          RL.GMDIKGRDCGDEAAQ.FTSFLKTEAFRLVQFEKHMKGR..KEIFSPVV.NYQ.AYPDCSPIM.L.EA
Retrocopy RLLGMDIKGRDCGDEAAQ*FTSFLKTEAFRLVQFEKHMKGRWLKEIFSPVVLNYQLAYPDCSPIMVLPEA

Parental  SLADLNTRLEKKVKMDQFRPNIVVTGCDAFEEDTWDELLIGNVEMKKVLSCPRCILTTVDPDTGIIDRKE
          SL..L.TRLEKKVKMDQFR.NI.VTGCDA.EEDTWDELLIGNVEM.KVLSCPRCILTT.DPDTGIIDRKE
Retrocopy SLVALSTRLEKKVKMDQFRSNIMVTGCDASEEDTWDELLIGNVEMIKVLSCPRCILTTTDPDTGIIDRKE

Parental  PLETLKSYRLCDPSEKQIYKSSPLFGIYYSVEKIGSLQVGDPVYRM
          PLETLKSY.LC.P.EKQIYKSSPLF..YYSVEKIG..Q.GDPVY.M
Retrocopy PLETLKSYPLCAPLEKQIYKSSPLFRFYYSVEKIGKMQAGDPVYQM

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
SRP012049_cerebellum	1.81 RPM	16.04 RPM
SRP017611_brain	1.67 RPM	17.70 RPM
SRP017611_kidney	55.60 RPM	536.02 RPM
SRP017611_liver	41.48 RPM	399.91 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_469 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_469 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_469 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011332	1 retrocopy	retro_cfam_469 ,
Oryctolagus cuniculus	ENSOCUG00000013162	1 retrocopy	retro_ocun_1466,
Rattus norvegicus	ENSRNOG00000037850	1 retrocopy	retro_rnor_162,
Ictidomys tridecemlineatus	ENSSTOG00000006676	1 retrocopy	retro_itri_1413,