RetrogeneDB ID: retro_btau_868

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 2:48559564..48560212(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFAF6
• Ensembl ID: ENSBTAG00000007570
• Aliases: NDUFAF6, C14H8orf38
• Description: NADH dehydrogenase (ubiquinone) complex I, assembly factor 6 [Source:UniProtKB/Swiss-Prot;Acc:A7YVD7]

Sequence

>retro_btau_868
GAAAAAACTGTGAATGATTTATATTGTGACAGTCCACCACATCAGCGTGTGGCCACTGAACTATGGAAGGCTGTCAGAAA
ACATAATCTGACTAAAAGATGGCCTGTGAAAATCACTGATGAAAGAGAAAAGAATTTGGATGACAAAGTATATCATAACA
TCCAGAAACTAGGAAATTATGCTAAAAACACTCAGAGCTCTCTTCTTTATCTAACACTAGAAATATTGGGTATAAAGGAT
CTTCATGCAAATCATGCCACAAATCACACTGGAAAAACGCAAGGCATTGTCACTTGCTTGAGAGCAACACCCTGTCATGG
TAGCAGAAGAAAGCTGTCCCTTCCCATGGGTATTTGTATGCCGCGTGGTGTTTCACAAGAGGATTTTCTACAAAAGAGCC
AAAATGAAAATGTGAGAGATGTGGTGTATGACACTGCCAGCCAGGCACACTTGCACCTAAAGCATGCTAGGTCCTTCCAC
GAAAGTGTTCTTGTGAAAGCGTTTCCTGCTTTTGCACAGACAGTTGCTCTGGAGGACTATTTAAAGAAAATCCGACAAGT
GGATTTTGATCTATTCCACCCATCTTTACAGCAGAAGAATAGTTTACTTCCATTATCTTTATATATTCAGTCGTGGAGAA
AAAGATAT

Alignment

ORF - retro_btau_868 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.94 %
• Parental protein coverage: 64.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKTVDDIYSDNPPHQPVAIELWKAVRRHNLTKRWLMKIIDEREKNLDDKAYRNIQELENYAENTQSSLLY
          .KTV.D.Y.D.PPHQ.VA.ELWKAVR.HNLTKRW..KI.DEREKNLDDK.Y.NIQ.L.NYA.NTQSSLLY
Retrocopy EKTVNDLYCDSPPHQRVATELWKAVRKHNLTKRWPVKITDEREKNLDDKVYHNIQKLGNYAKNTQSSLLY

Parental  LTLEILGIKDLHADHAASHIGKAQGIVTCLRATPYHGSRRRVFLPMDICMLHGVSQEDFLRKSQDRNVRD
          LTLEILGIKDLHA.HA..H.GK.QGIVTCLRATP.HGSRR...LPM.ICM..GVSQEDFL.KSQ..NVRD
Retrocopy LTLEILGIKDLHANHATNHTGKTQGIVTCLRATPCHGSRRKLSLPMGICMPRGVSQEDFLQKSQNENVRD

Parental  VVYDVASQAHLHLKHARSFHRSIPVKAFPAFLQTVALEDYLKKIQQVDFDLFHPSLQRKNTLLPLSLYIQ
          VVYD.ASQAHLHLKHARSFH.S..VKAFPAF.QTVALEDYLKKI.QVDFDLFHPSLQ.KN.LLPLSLYIQ
Retrocopy VVYDTASQAHLHLKHARSFHESVLVKAFPAFAQTVALEDYLKKIRQVDFDLFHPSLQQKNSLLPLSLYIQ

Parental  SWRKRY
          SWRKRY
Retrocopy SWRKRY

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
ERP005899_liver	0.00 RPM	7.43 RPM
ERP005899_muscle	0.00 RPM	6.39 RPM
SRP017611_brain	0.00 RPM	14.98 RPM
SRP017611_kidney	0.00 RPM	18.31 RPM
SRP017611_liver	0.00 RPM	5.89 RPM
SRP030211_testis	0.02 RPM	10.94 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_868 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_868 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_868 has 0 orthologous retrocopies within eutheria group .

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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,