RetrogeneDB ID: retro_cfam_1423

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 30:35873706..35874233(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFAF6
• Ensembl ID: ENSCAFG00000009419
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) complex I, assembly factor 6 [Source:HGNC Symbol;Acc:28625]

Sequence

>retro_cfam_1423
GCTATCAAAAGATATACTCTGATCAAAATATGGCTTATGAAAACCATTGGTAGAAGAGACAAAATTCGGATGACAAAGCA
TATCATAACATCCAAGAACTGAAAAATTATGCTGAAAATGCACAAAACTCTCTCTTCATTTAACACTGGAAGTATGGGGT
AAAAAGGAACTTCATACAGACCATGCCCAAGTCACACTGGAAAAGCACAGGGCATTGTCACATGCTTGAGAACAACGCCC
TATCATGGTAGCAGAAGAAGGGTGTTCCTTCCCTTGGATATTTGCATGTTTGACAAACACAATACATGGTGTTTCTCTTG
GAAGAACCAAGATATAAATCTGAGAGATGAAATATTTATGTCCTTGCTGGCCCAGCATGCTGGGCACTTAAAGCATGCTA
GACCTTTCGACAAAAGTGTTCTCATGAAAACATTTCCTGCTTTTCTTTGAATTGCTCTGGAGGACTGCTTAAAGAAAGTT
CAACAAAGAATTTTTATATATTCCACCCATCTTCACAGCAGAAGAAT

Alignment

ORF - retro_cfam_1423 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.19 %
• Parental protein coverage: 52.99 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  AVKRHNLTKRWLMKIIDEREK-NLDDKAYRNIQELENYAENTQSSL-LYLTLEILGVKDLHADHAA-SHI
          A.KR..L.K.WLMK.I..R.K.N.DDKAY.NIQEL.NYAEN.Q.SL.L.LTLE..G.K.LH.DHA..SH.
Retrocopy AIKRYTLIKIWLMKTIGRRDK<NSDDKAYHNIQELKNYAENAQNSL<LHLTLEVWGKKELHTDHAQ<SHT

Parental  GKAQGIVTCLRATPYHGSRRRVFLPMDICMLHGVSQEDFLRKNQDKNVRDVIY-DIASQAHLHLKHARSF
          GKAQGIVTCLR.TPYHGSRRRVFLP.DICM........F..KNQD.N.RD.I......Q...HLKHAR.F
Retrocopy GKAQGIVTCLRTTPYHGSRRRVFLPLDICMFDKHNTWCFSWKNQDINLRDEIFMSLLAQHAGHLKHARPF

Parental  HKSVPVKAFPAFLQTVALENYLKRIQQ-VDFDIFHPSLQQKD
          .KSV..K.FPAFL...ALE..LK..QQ...F.IFHPS.QQK.
Retrocopy DKSVLMKTFPAFL-*IALEDCLKKVQQ<KNFYIFHPSSQQKN

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	14.83 RPM
SRP017611_brain	0.00 RPM	18.50 RPM
SRP017611_kidney	0.00 RPM	17.04 RPM
SRP017611_liver	0.00 RPM	3.99 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1423 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1423 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1423 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Equus caballus	retro_ecab_141

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007570	1 retrocopy	retro_btau_868,
Canis familiaris	ENSCAFG00000009419	1 retrocopy	retro_cfam_1423 ,
Equus caballus	ENSECAG00000019146	1 retrocopy	retro_ecab_141,
Oryctolagus cuniculus	ENSOCUG00000006635	1 retrocopy	retro_ocun_1066,