RetrogeneDB ID: retro_ecab_141

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:120956445..120957041(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFAF6
• Ensembl ID: ENSECAG00000019146
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) complex I, assembly factor 6 [Source:HGNC Symbol;Acc:28625]

Sequence

>retro_ecab_141
TGGAAAGCTGCTGTCAAGAAACATAATTTGACTAAAAGATGGCTTATGAGAGTCATTGATGAAGGAGAAAAAAATTGGAT
GACAAAGCATATTGCAATATCCAGGAACTGGAAAATTATGCTGAAAACACACAGAACTCTCTTCTTTATTTGACACCAGA
AATATTGGGTATAATGACCTTCATGAAGATCATGTCACAAGCCACACTGGAAAAGCACAAGGTATTGTCACATGCTTGAG
AGCAACGTCCTATAGTGGTAGCAGAAGAAGGGTGTGCCCTCCCTTGAATATTTATATCTTTGACCAATACAACACATGGG
GTTTCACAAGAGGATGTTCTATGAAGAACCGAGGTAAAAATGTGAGAGATGCAATATATGTCATTTCTAGCCAGGCCTAC
TTGCACTGACAGCAGGCTAGGTCCTTACATACAAAGTGTTCTTGTGAAAGCATTTCCTATTTTTCTTCTGGTTCCTCTGG
AGGACTATTTAGAGAAAATTCAACAAGTGGATTTTAATATATTCCACCCATCTTTACAGGAGAAGAATACATTGCTTCCA
TTATCTTTGTATGTTCAGTCATAGAAAAAAAGATAT

Alignment

ORF - retro_ecab_141 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.95 %
• Parental protein coverage: 72.76 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  WKA-VKKHNLTKRWLMKIVDEREKN-LDDKAYRNIQELESYAENTQSSLLYLTLEILGI-KDLHADHAAS
          WKA.VKKHNLTKRWLM...DE.EKN.LDDKAY.NIQELE.YAENTQ.SLLYLT.EILGI..DLH.DH..S
Retrocopy WKAAVKKHNLTKRWLMRVIDEGEKN<LDDKAYCNIQELENYAENTQNSLLYLTPEILGI<NDLHEDHVTS

Parental  HIGKAQGIVTCLRAMPYHGSRRRVFLPMDICMLHGVSQEDFLR----KNRDKNVRDVIYDIASQAHLHLK
          H.GKAQGIVTCLRA..Y.GSRRRV..P..I..........F.R....KNR.KNVRD.IY.I.SQA.LH..
Retrocopy HTGKAQGIVTCLRATSYSGSRRRVCPPLNIYIFDQYNTWGFTRGCSMKNRGKNVRDAIYVISSQAYLH*Q

Parental  HARSFH-KSVPVKAFPAFLQTVALEDYLKKIQQVDFDIFHPSLQQKNTLLPLSLYIRSWRKRY
          .ARS.H..SV.VKAFP.FL..V.LEDYL.KIQQVDF.IFHPSLQ.KNTLLPLSLY..S..KRY
Retrocopy QARSLH>QSVLVKAFPIFL-LVPLEDYLEKIQQVDFNIFHPSLQEKNTLLPLSLYVQS*KKRY

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
SRP021940_articular_cartilage	0.00 RPM	0.47 RPM
SRP021940_cerebellum	0.00 RPM	2.54 RPM
SRP021940_embryo	0.00 RPM	3.27 RPM
SRP021940_placental_villous	0.00 RPM	3.70 RPM
SRP021940_synovial_membrane	0.00 RPM	2.11 RPM
SRP021940_testis	0.00 RPM	1.02 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_141 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_141 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_141 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Canis familiaris	retro_cfam_1423

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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,