RetrogeneDB ID: retro_cfam_246

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 1:13812247..13812786(+)
• Located in intron of: ENSCAFG00000000068

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSME1
• Ensembl ID: ENSCAFG00000011924
• Aliases: None
• Description: proteasome (prosome, macropain) activator subunit 1 (PA28 alpha) [Source:HGNC Symbol;Acc:9568]

Sequence

>retro_cfam_246
AAGACAGAGGACCTACTCAGGAGCAATTTCCCCAAGAAGACTTCTGAGCTGGCAGCATTTTTTAAAGGATCCAGCTCTCA
GTGAAGCTCACCTGAGCAATCTGAAGGCCCCTATAGATGTTCTGGTGCCTGATCCTGTGAAGGGGAAAGAGAAGGAAGAG
CAGAAGAAACTGCAAGAGAAGGAAGAAATGGATTAAAAATGAAAGGGTTAACTGAAGGCCAAGGTTTTCTCAGTAGCCCA
GTGAATGGCAAGAAGATCATGATTCTTTTGCAGCACCTAACCCCCGGGACTGAGGATGTCACTGAGCCGTCAGCCTGATC
CTCACCTGGCTGCAGCTGCAAATACCTTGGATTGAGGATAGGGTCAGTTTTGGAGTGGCTGCCCAGCAGGAGGTCTGTGA
GCTGACGACCACCCTTTATACTGAGCTGGAAGCCTCCAACACTCCAGTCTCCAAGGATTCCTCTGAATGGGGCAATGTAG
CCAAGCAATCCCATGAGTGCAGTTATCCAGGGCTGGTGTGAGAGCTGGATGAAGCAGAG

Alignment

ORF - retro_cfam_246 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.04 %
• Parental protein coverage: 79.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KTENLLGSYFPKKISELDAF-LKEPALNEANLSNLKAPLDIPVPDPVKEKEKEERKKQQEKEEKD-EKKK
          KTE.LL.S.FPKK.SEL.AF.LK.PAL.EA.LSNLKAP.D..VPDPVK.KEKEE.KK.QEKEE.D..K.K
Retrocopy KTEDLLRSNFPKKTSELAAF>LKDPALSEAHLSNLKAPIDVLVPDPVKGKEKEEQKKLQEKEEMD<LKMK

Parental  GEDEDKGPPCGPVNCNEKIVVLLQRLKPEIKDVIE-QLNLVTTWLQLQIPRIEDGNNFGVAVQEKVFELM
          G..E..G....PVN...KI..LLQ.L.P...DV.E....L..TWLQLQIP.IED...FGVA.Q..V.EL.
Retrocopy GLTEGQGFLSSPVN-GKKIMILLQHLTPGTEDVTE<AVSLILTWLQLQIPWIEDRVSFGVAAQQEVCELT

Parental  TALHTKLEGFHTQISKYFSERGDAVTKAAKQPHVGDYRQLVHELDEAE
          T.L.T.LE...T..SK..SE.G......AKQ.H...Y..LV.ELDEAE
Retrocopy TTLYTELEASNTPVSKDSSEWGN----VAKQSHECSYPGLV*ELDEAE

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	0.13 RPM	65.27 RPM
SRP017611_brain	0.08 RPM	32.23 RPM
SRP017611_kidney	0.20 RPM	76.07 RPM
SRP017611_liver	1.09 RPM	40.24 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_246 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_246 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_246 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016433	1 retrocopy	retro_amel_637,
Bos taurus	ENSBTAG00000021395	1 retrocopy	retro_btau_1189,
Canis familiaris	ENSCAFG00000011924	1 retrocopy	retro_cfam_246 ,
Equus caballus	ENSECAG00000016855	1 retrocopy	retro_ecab_1001,
Felis catus	ENSFCAG00000005583	1 retrocopy	retro_fcat_1567,
Macropus eugenii	ENSMEUG00000014712	1 retrocopy	retro_meug_1052,
Mus musculus	ENSMUSG00000022216	1 retrocopy	retro_mmus_466,
Rattus norvegicus	ENSRNOG00000019041	1 retrocopy	retro_rnor_50,
Tursiops truncatus	ENSTTRG00000008620	1 retrocopy	retro_ttru_569,