RetrogeneDB ID: retro_cfam_1258

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 28:5190965..5191355(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFS8
• Ensembl ID: ENSCAFG00000011083
• Aliases: None
• Description: None

Sequence

>retro_cfam_1258
CAGACCCTGCTGTGGTCTGAGCTCATCTGAAGCCTGGACATAACCCTGAGCTACCTGTTCCAGGAGCCTGTCACCATTGA
CTACCTATTCAGGAAGGGCCCACTGAGCTCATACTTTGGGTGAAGGGGAGCATGCACGGCACCACTATCCATCTGGAGAG
GAATGCTGAGTTGCCTGTAAGCTTTGTAAGGTTGTCTGCACCATCCAGGCCATCACCACTAAGGCTAAACCTACTGCCAA
TGGCAGCTGCCAGACCACCCACTATGACATCAACATGACCAAGTACACCTACTGTAGCTTCTACCAGGTGGCCTGCCCCA
TGGACACCATCACCAAGGGCCCCAACTTTTAGTTCTCCATGGAGACACACAGGAGCTACTGTACAACAGG

Alignment

ORF - retro_cfam_1258 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.09 %
• Parental protein coverage: 61.43 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QTLLWTELIRGLGMTLSYLFREPATINYPFEKGPLSPRFRGEHA-LRRYPSGEERC-IACKLCEAVCPAQ
          QTLLW.ELI..L..TLSYLF.EP.TI.Y.F.KGPLS..F....A..R......E.C..ACKLC..VC..Q
Retrocopy QTLLWSELI*SLDITLSYLFQEPVTIDYLFRKGPLSSYFG*RGA>ARHHYPSGEEC*VACKLCKVVCTIQ

Parental  AITIEAEPRADGSRRTTRYDIDMTKCIYCGFCQEACPVDAIVEGPNFEFSTETH-EELLYNK
          AIT..A.P.A.GS..TT.YDI.MTK..YC.F.Q.ACP.D.I..GPNF.FS.ETH..ELLYN.
Retrocopy AITTKAKPTANGSCQTTHYDINMTKYTYCSFYQVACPMDTITKGPNF*FSMETH<QELLYNR

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	0.00 RPM	49.22 RPM
SRP017611_brain	0.00 RPM	32.00 RPM
SRP017611_kidney	0.00 RPM	161.46 RPM
SRP017611_liver	0.00 RPM	42.93 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1258 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1258 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1258 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001217	2 retrocopies	retro_amel_366, retro_amel_613,
Canis familiaris	ENSCAFG00000011083	2 retrocopies	retro_cfam_1258 , retro_cfam_129,
Callithrix jacchus	ENSCJAG00000015686	4 retrocopies	retro_cjac_1088, retro_cjac_1652, retro_cjac_2237, retro_cjac_3810,
Macropus eugenii	ENSMEUG00000015013	2 retrocopies	retro_meug_1148, retro_meug_926,
Myotis lucifugus	ENSMLUG00000017611	1 retrocopy	retro_mluc_1771,
Mustela putorius furo	ENSMPUG00000004193	1 retrocopy	retro_mputfur_592,
Otolemur garnettii	ENSOGAG00000013220	1 retrocopy	retro_ogar_2669,
Xenopus tropicalis	ENSXETG00000020882	1 retrocopy	retro_xtro_50,