RetrogeneDB ID: retro_cfam_2108

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:85933961..85934341(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB1
• Ensembl ID: ENSCAFG00000004116
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 1 [Source:HGNC Symbol;Acc:9537]

Sequence

>retro_cfam_2108
TTGAGTGAAGGGTTTTAATTCACACTGGGGACAGCCCCAAGTGATACAAACTCACAGGCCAAACAGTCACTGGATACTGG
ATACAGTGTTTTTCATGGAGACTGTCTTACCCTGACAAAGATTATTGAAGCAAGACTAAAGATGTATAAGCATTCTAATA
ACCAGACCATGACTATGGGGGCGATTGCTGCAATGCTGTCTACAATCCTCTATTCAAGGCACTTTTTTTTCCATACTATG
TTTACATCACTGGGGGAATGGATGAAGAAGGGAAAGGAGGTATGGACAACTTTGACCCGGTTGGGTCCTACCGGAGAGAT
TCTTTCAAGGCTGGAGGCTCACCTAGTGCCATGCTACAGCCCCAGCTTGATCACCAAGTT

Alignment

ORF - retro_cfam_2108 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.19 %
• Parental protein coverage: 66.14 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LSEGF--SIHTRDSPKCYKLTDKTVIGCSGFHGDCLTLTKIIEARLKMYKHSNNKTMTTGAIAAMLSTIL
          LSEGF.....T..S............G.S.FHGDCLTLTKIIEARLKMYKHSNN.TMT.GAIAAMLSTIL
Retrocopy LSEGF*FTLGTAPSDTNSQAKQSLDTGYSVFHGDCLTLTKIIEARLKMYKHSNNQTMTMGAIAAMLSTIL

Parental  YSRRFFPY-YVYNIIGGLDEEGKGAVYSFDPVGSYQRDSFKAGGSASAMLQPLLDNQV
          YSR......Y...I.GG.DEEGKG....FDPVGSY.RDSFKAGGS.SAMLQP.LD.QV
Retrocopy YSRHXXXH<YYVYITGGMDEEGKGGMDNFDPVGSYRRDSFKAGGSPSAMLQPQLDHQV

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	63.59 RPM
SRP017611_brain	0.00 RPM	38.58 RPM
SRP017611_kidney	0.00 RPM	102.75 RPM
SRP017611_liver	0.00 RPM	34.95 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2108 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2108 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2108 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017047	1 retrocopy	retro_amel_1066,
Canis familiaris	ENSCAFG00000004116	1 retrocopy	retro_cfam_2108 ,
Callithrix jacchus	ENSCJAG00000020644	1 retrocopy	retro_cjac_632,
Dasypus novemcinctus	ENSDNOG00000019502	1 retrocopy	retro_dnov_2087,
Felis catus	ENSFCAG00000031269	1 retrocopy	retro_fcat_911,
Gorilla gorilla	ENSGGOG00000022128	1 retrocopy	retro_ggor_1661,
Microcebus murinus	ENSMICG00000007469	1 retrocopy	retro_mmur_173,
Macaca mulatta	ENSMMUG00000019919	1 retrocopy	retro_mmul_1135,
Mustela putorius furo	ENSMPUG00000007150	1 retrocopy	retro_mputfur_1196,
Mus musculus	ENSMUSG00000014769	2 retrocopies	retro_mmus_1784, retro_mmus_3664,
Oryctolagus cuniculus	ENSOCUG00000007973	2 retrocopies	retro_ocun_1029, retro_ocun_620,
Procavia capensis	ENSPCAG00000000344	1 retrocopy	retro_pcap_329,
Pongo abelii	ENSPPYG00000017191	1 retrocopy	retro_pabe_130,
Vicugna pacos	ENSVPAG00000006517	1 retrocopy	retro_vpac_521,