RetrogeneDB ID: retro_cfam_1291

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 29:18587995..18588320(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB2
• Ensembl ID: ENSCAFG00000003543
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 2 [Source:HGNC Symbol;Acc:9539]

Sequence

>retro_cfam_1291
GACTGTCTTTGGAGTCAGACCCCATATCATGTCAATCTCCTCCTGTCCAGTTATGATGAGCATGAGGGTCCAGCACTCTA
CTACATGGGCTACCTGGCAGTATTGGCGAAGGATCCTTTGGAACCCATGGCTATTGTGCCTTCCTGACTCTCAGCATTCT
GGACCAATACTACGTACCAACTATCTCTTGTAAGAGGGCAGTGGAACTTCTTAGGAAATAGCTCCAGAAATGTTTTATCC
TGAATCTACCAACCTTCAATGTTCAAATCATAGACAAAAATGGCAACTAGGACCAGAACAACATTTCCTTCCTTACCAGG
GCTCC

Alignment

ORF - retro_cfam_1291 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.44 %
• Parental protein coverage: 55.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DCLRSRTPYHVNLLLAGYDEHEGPALYYMDYLAALAKAP-FAAHGYGAFLTLSILDRYYTPTISRERAVE
          DCL.S.TPYHVNLLL..YDEHEGPALYYM.YLA.LAK.P.F..HGY.AFLTLSILD.YY.PTIS..RAVE
Retrocopy DCLWSQTPYHVNLLLSSYDEHEGPALYYMGYLAVLAKDP<FGTHGYCAFLTLSILDQYYVPTISCKRAVE

Parental  LLRKCLEELQKRFILNLPTFSVRIIDKNGIHDLDNISF-PKQGS
          LLRK.L...QK.FILNLPTF.V.IIDKNG..D..NISF.P.QGS
Retrocopy LLRK*L---QKCFILNLPTFNVQIIDKNGN*DQNNISF<PYQGS

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	61.86 RPM
SRP017611_brain	0.00 RPM	27.47 RPM
SRP017611_kidney	0.00 RPM	54.94 RPM
SRP017611_liver	0.00 RPM	20.23 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1291 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1291 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1291 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 16 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000715	1 retrocopy	retro_amel_743,
Canis familiaris	ENSCAFG00000003543	1 retrocopy	retro_cfam_1291 ,
Callithrix jacchus	ENSCJAG00000001547	1 retrocopy	retro_cjac_2110,
Dasypus novemcinctus	ENSDNOG00000017663	1 retrocopy	retro_dnov_159,
Equus caballus	ENSECAG00000021615	1 retrocopy	retro_ecab_769,
Echinops telfairi	ENSETEG00000019511	1 retrocopy	retro_etel_1529,
Felis catus	ENSFCAG00000030845	1 retrocopy	retro_fcat_1803,
Macropus eugenii	ENSMEUG00000000421	1 retrocopy	retro_meug_1235,
Monodelphis domestica	ENSMODG00000017902	1 retrocopy	retro_mdom_79,
Mustela putorius furo	ENSMPUG00000014891	1 retrocopy	retro_mputfur_1550,
Ochotona princeps	ENSOPRG00000012259	2 retrocopies	retro_opri_76, retro_opri_762,
Pteropus vampyrus	ENSPVAG00000001871	1 retrocopy	retro_pvam_909,
Sorex araneus	ENSSARG00000000409	2 retrocopies	retro_sara_557, retro_sara_660,
Sarcophilus harrisii	ENSSHAG00000016996	1 retrocopy	retro_shar_794,
Tupaia belangeri	ENSTBEG00000005230	1 retrocopy	retro_tbel_4039,
Tarsius syrichta	ENSTSYG00000005648	2 retrocopies	retro_tsyr_403, retro_tsyr_912,