RetrogeneDB ID: retro_cfam_591

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 14:10615494..10616573(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD4
• Ensembl ID: ENSCAFG00000012565
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 4 [Source:HGNC Symbol;Acc:9561]

Sequence

>retro_cfam_591
ATGGTGTTGGAAAGCACTATGGTTTGTGTGGACAACAGTGAGTATATGGGGAATGGGGACTTCTTACCCACCTGGCTGCA
GGCCCAACAGATGCTGTCAACATCGTTTGTCACTCCTAAGACCCGCAGCAATCGTGAAAACAATGTGGGCCTCATCACAC
TGGCCAATGACTGTGAAATGCTGACCACACTCACCCCTGACACCGGCCACACTCTTTCCAAGCTCCACACTGTCCAACCC
AAGGGCAAGATCACCTTCTGCACTGGTATCCCCGCGGCTCATCTGGCTCTCGAAGCACCGGCAGGGCAAGAATCACAAGA
TGCGCATTTTTGCCTTGGTGGGAAGCCCCGTGGAGGACAACGAGAAGGATCTGGTGAAACTGGCTAAACGTTTCAAGAAG
GAAAAGGTATATGTTGACATTATAAGTCTTGGGAAAGAGGAGGTGAACACAGAAAAGCTGACAGCCTTTGTAAACACATT
GAAGGGCAACGATGGAACCGGTTCTCCTCTGGTGGCAGTGCCCCCTGGGCCCAGCTTGGCTGACGCGCTCATCAGTTCTC
CGGTTCTGGGCTGGCAAGGTGGTGCCATGCTGGGTCTTGGCGCTAGTGGCTTTGAGTTCGGGGTGGATCCCAGCGCTGAT
CCCCAGCTGGCCCTGGCGCTCCGGGTTCTATGGAAGAGCAGCGGCAGGCCCAGGCCGAGGAGGCCCGGGGGGCGGCTGCG
GCCCCCGCGGCTGGGGCGGGGATGGCTACGGCTGGGCCCAAGGCTAGTGACGCCCTGCTCAAGGTGACCATCGGCCCTCA
GGAGGTGGGCCGCAGCGGGCCCCCCGACCTGAGCAGATGACTGAGGAGGAGCAGATTGCCTGTGCCAGGCAGATGTCCCC
GCAGGGTGCAGAGTTCGGCCAGGCGGAATGCGCGGACATTGATGCCAGCTCAGCCACGGACACATCTGAGCCCGCCAAGG
AGGAGGATGCTCGTGATGCGCTGCGGGACCCCGAGTTCCTGCAGAGCGTCCCGGAGAGCCTTCCAGGCGAGGATCTCGAC
AACGAAGCTGTTTGAAATGTCATGGGCTCTCTGGCCTCA

Alignment

ORF - retro_cfam_591 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.51 %
• Parental protein coverage: 95.76 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MVLESTMVCVDNSEYMRNGDFLPTRLQAQQ-DAVNIVCHS-KTRSNPENNVGLITLANDCEVLTTLTPDT
          MVLESTMVCVDNSEYM.NGDFLPT.LQAQQ.DAVNIVCHS.KTRSN.ENNVGLITLANDCE.LTTLTPDT
Retrocopy MVLESTMVCVDNSEYMGNGDFLPTWLQAQQ<DAVNIVCHS>KTRSNRENNVGLITLANDCEMLTTLTPDT

Parental  GRILSKLHTVQPKGKITFCTGIRVAHLAL-KHRQGKNHKMRIIAFVGSPVEDNEKDLVKLAKRLKKEKVN
          G..LSKLHTVQPKGKITFCTGI..AHLAL.KHRQGKNHKMRI.A.VGSPVEDNEKDLVKLAKR.KKEKV.
Retrocopy GHTLSKLHTVQPKGKITFCTGIPAAHLAL>KHRQGKNHKMRIFALVGSPVEDNEKDLVKLAKRFKKEKVY

Parental  VDIINFGEEEVNTEKLTAFVNTLNGKDGTGSHLVTVPPGPSLADALISSPILAGEGGAMLGLGASDFEFG
          VDII..G.EEVNTEKLTAFVNTL.G.DGTGS.LV.VPPGPSLADALISSP.L...GGAMLGLGAS.FEFG
Retrocopy VDIISLGKEEVNTEKLTAFVNTLKGNDGTGSPLVAVPPGPSLADALISSPVLGWQGGAMLGLGASGFEFG

Parental  VDPSADPELALALRV-SMEEQRQRQEEEARRAAAASAAEAGIATAGAEDSDDALLKMTISQQEFGRSGLP
          VDPSADP.LALALRV.SMEEQRQ.Q.EEAR.AAAA.AA.AG.ATAG...S.DALLK.TI..QE.GRSG.P
Retrocopy VDPSADPQLALALRV<SMEEQRQAQAEEARGAAAAPAAGAGMATAGPKAS-DALLKVTIGPQEVGRSGPP

Parental  DLS-SMTEEEQIAYAMQMSLQGAEFGQAESADIDASSAMDTSEPAKEEDDYDVMQDPEFLQSVLENLPGV
          DLS..MTEEEQIA.A.QMS.QGAEFGQAE.ADIDASSA.DTSEPAKEED..D...DPEFLQSV.E.LPG.
Retrocopy DLS<QMTEEEQIACARQMSPQGAEFGQAECADIDASSATDTSEPAKEEDARDALRDPEFLQSVPESLPGE

Parental  DPNNEAIRNAMGSLAS
          D..NEA..N.MGSLAS
Retrocopy DLDNEAV*NVMGSLAS

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	70.31 RPM
SRP017611_brain	0.00 RPM	41.36 RPM
SRP017611_kidney	0.00 RPM	68.41 RPM
SRP017611_liver	0.00 RPM	27.85 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_591 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_591 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_591 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012565	1 retrocopy	retro_cfam_591 ,
Callithrix jacchus	ENSCJAG00000007357	1 retrocopy	retro_cjac_2808,
Dasypus novemcinctus	ENSDNOG00000007446	1 retrocopy	retro_dnov_1556,
Homo sapiens	ENSG00000159352	1 retrocopy	retro_hsap_2531,
Nomascus leucogenys	ENSNLEG00000010139	1 retrocopy	retro_nleu_1450,
Pongo abelii	ENSPPYG00000000871	1 retrocopy	retro_pabe_1862,
Pan troglodytes	ENSPTRG00000013893	1 retrocopy	retro_ptro_1474,
Sus scrofa	ENSSSCG00000006628	1 retrocopy	retro_sscr_981,
Tupaia belangeri	ENSTBEG00000016911	1 retrocopy	retro_tbel_238,
Tursiops truncatus	ENSTTRG00000007019	1 retrocopy	retro_ttru_903,