RetrogeneDB ID: retro_cfam_1639

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 4:3054346..3054755(+)
• Located in intron of: ENSCAFG00000010034

Retrocopy information

• Ensembl ID: ENSCAFG00000010041
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PFDN5
• Ensembl ID: ENSCAFG00000007016
• Aliases: None
• Description: Canis lupus familiaris prefoldin subunit 5 (PFDN5), mRNA. [Source:RefSeq mRNA;Acc:NM_001251949]

Sequence

>retro_cfam_1639
CAGTCAATTGGCATCGCTGAGTAGAACCTGCCACAGCTAGAAATGCTTATGAACCAGCCAGTCCAGGAAGTGGAGCTCTG
GTCCATGTCTGCTACCCAGCTCAGGGTGGTACAGACCAAGTATGTGGAAGACCAGGACAGCCTGCTCACACCAAACAAGA
GCAATGAGGGGAAACAATGACTCGTCCCACCAACGGGCTCGGTGTCCAGTCCCTGGGAAGCTGTATAATGTGGAACATGT
ACTCATCAATGTGGGAACTGGCTATTATGTAGAGAAGATAGCTGAGGATGCCAAGGGCCTTCTCAAGAAGGAGACAGACT
TCCTCCCCAAGCAAATGGAGAAAACCCAACCAGCCCTGCAGGAGAAGCACGCCATAAAGCAGGCTGTGACGGAGATGATG
ATGAGCAAG

Alignment

ORF - retro_cfam_1639 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.61 %
• Parental protein coverage: 88.31 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  QSVNITELNLPQLEMLKNQLDQEVEFLSTSIAQLKVVQTKYVEAKDCLHVLNKNNEGKELLVPLTSSMY-
          QS..I.E.NLPQLEML.NQ..QEVE..S.S..QL.VVQTKYVE..D.L...NK.NEGK..LVP.T.S...
Retrocopy QSIGIAE*NLPQLEMLMNQPVQEVELWSMSATQLRVVQTKYVEDQDSLLTPNKSNEGKQ*LVPPTGSVS>

Parental  VPGKLHDVEHVLIDVGTGYYVEKTAEDAKDFFKRKIDFLTKQMEKIQPALQEKHAMKQAVMEMMSQK
          VPGKL..VEHVLI.VGTGYYVEK.AEDAK...K...DFL.KQMEK.QPALQEKHA.KQAV.EMM..K
Retrocopy VPGKLYNVEHVLINVGTGYYVEKIAEDAKGLLKKETDFLPKQMEKTQPALQEKHAIKQAVTEMMMSK

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	63.38 RPM
SRP017611_brain	0.00 RPM	31.60 RPM
SRP017611_kidney	0.00 RPM	123.42 RPM
SRP017611_liver	0.00 RPM	45.10 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1639 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1639 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1639 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 20 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012402	2 retrocopies	retro_amel_322, retro_amel_99,
Canis familiaris	ENSCAFG00000007016	4 retrocopies	retro_cfam_1382, retro_cfam_1421, retro_cfam_1639 , retro_cfam_919,
Callithrix jacchus	ENSCJAG00000018477	6 retrocopies	retro_cjac_1590, retro_cjac_1614, retro_cjac_1707, retro_cjac_2274, retro_cjac_42, retro_cjac_993,
Dasypus novemcinctus	ENSDNOG00000013002	1 retrocopy	retro_dnov_1994,
Echinops telfairi	ENSETEG00000002111	3 retrocopies	retro_etel_1815, retro_etel_372, retro_etel_950,
Felis catus	ENSFCAG00000005871	4 retrocopies	retro_fcat_1215, retro_fcat_1468, retro_fcat_1566, retro_fcat_828,
Homo sapiens	ENSG00000123349	1 retrocopy	retro_hsap_515,
Gorilla gorilla	ENSGGOG00000026308	1 retrocopy	retro_ggor_475,
Macropus eugenii	ENSMEUG00000012110	1 retrocopy	retro_meug_1682,
Macaca mulatta	ENSMMUG00000022030	2 retrocopies	retro_mmul_1677, retro_mmul_428,
Mustela putorius furo	ENSMPUG00000006059	1 retrocopy	retro_mputfur_18,
Mus musculus	ENSMUSG00000001289	1 retrocopy	retro_mmus_3707,
Nomascus leucogenys	ENSNLEG00000017706	3 retrocopies	retro_nleu_1369, retro_nleu_1370, retro_nleu_1549,
Otolemur garnettii	ENSOGAG00000009463	2 retrocopies	retro_ogar_1820, retro_ogar_292,
Ochotona princeps	ENSOPRG00000015638	1 retrocopy	retro_opri_394,
Procavia capensis	ENSPCAG00000012413	2 retrocopies	retro_pcap_132, retro_pcap_167,
Pongo abelii	ENSPPYG00000004575	1 retrocopy	retro_pabe_229,
Pan troglodytes	ENSPTRG00000005010	1 retrocopy	retro_ptro_384,
Sorex araneus	ENSSARG00000006221	1 retrocopy	retro_sara_439,
Tupaia belangeri	ENSTBEG00000016436	4 retrocopies	retro_tbel_1068, retro_tbel_2415, retro_tbel_3132, retro_tbel_768,