RetrogeneDB ID: retro_cfam_424

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 11:45443562..45443979(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMG2
• Ensembl ID: ENSCAFG00000018855
• Aliases: PSMG2, TNFSF5IP1
• Description: proteasome (prosome, macropain) assembly chaperone 2 [Source:HGNC Symbol;Acc:24929]

Sequence

>retro_cfam_424
ATATTTGTTCCCTGTAGAGAGTTGGTCCTGACCTCATGCGTTTTACCTTTCTAATGCCAGCAGTATCTGCTGGAAATGTT
GGCCAGCTTACAATAGATTTGATTATTTCTACACTGGATATGTGTACGATTGGTTACTTCTGACTTGTGTCAATGGTTGG
AAACAATCCATATGCAATTGCAGAAAAAAACTCAACAGAACTCAGTATAAGGCTGAAGTCTATTCATTGCCTTCAAAGAA
ACTAGTGGCTCTTCAGTTAAGATCCATTTTTATTAAGTATAAATCAAAACCATTCTATTAAATACTGCTTTACTGGGTGA
AAAGTAGTAACTGTGCTAAAGTTATGACCTTTCAAGCAGTCATTCACATTACCATAATGATCTATAGCTTCGCTGAACTC
CCTTCAGATACCTACTT

Alignment

ORF - retro_cfam_424 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.29 %
• Parental protein coverage: 54.17 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MFVPCGDSV-PDLAGHTLLMPAVSVGNVGQLAIDLIISTLNMRKIGYFYTDCLVPMVGNNPYATAEENST
          .FVPC...V.PDL...T.LMPAVS.GNVGQL.IDLIISTL.M..IGYF.....V...GNNPYA.AE.NST
Retrocopy IFVPCRELV<PDLMRFTFLMPAVSAGNVGQLTIDLIISTLDMCTIGYF*LVSMV---GNNPYAIAEKNST

Parental  ELCI-NAEVYSLPSKKLVALQLRSIFIKYKSKPFCEKLLSWVKSSNCAKVIV-LSSSHSYHRNDLQLRST
          EL.I..AEVYSLPSKKLVALQLRSIFIKYKSKPF...LL.WVKSSNCAKV...LSSSHS...NDL.LR.T
Retrocopy ELSI<KAEVYSLPSKKLVALQLRSIFIKYKSKPFY*ILLYWVKSSNCAKVMT<LSSSHSHYHNDL*LR*T

Parental  PFRYLL
          PFRYLL
Retrocopy PFRYLL

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	14.36 RPM
SRP017611_brain	0.00 RPM	14.69 RPM
SRP017611_kidney	0.00 RPM	44.64 RPM
SRP017611_liver	0.00 RPM	10.01 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_424 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_424 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_424 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018855	1 retrocopy	retro_cfam_424 ,
Choloepus hoffmanni	ENSCHOG00000010042	1 retrocopy	retro_chof_1738,
Myotis lucifugus	ENSMLUG00000017744	1 retrocopy	retro_mluc_2496,
Macaca mulatta	ENSMMUG00000021855	1 retrocopy	retro_mmul_198,
Nomascus leucogenys	ENSNLEG00000009063	1 retrocopy	retro_nleu_1753,
Oryctolagus cuniculus	ENSOCUG00000005086	1 retrocopy	retro_ocun_1448,
Sus scrofa	ENSSSCG00000021827	2 retrocopies	retro_sscr_1008, retro_sscr_763,