RetrogeneDB ID: retro_cfam_1740

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 5:50569935..50570652(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDCL3
• Ensembl ID: ENSCAFG00000002226
• Aliases: None
• Description: phosducin-like 3 [Source:HGNC Symbol;Acc:28860]

Sequence

>retro_cfam_1740
ATGCAGGACCCTAATGCAGACACTGAGTGGAATGACATCTTACGTAAAAAGGGCATCTTGCCCTCAAAGGAAAATTTGAA
AGATTTGAAAAAGGAGGCAGAAGAAGAACAGTGAGTCCTTCAGCAGTCAGTTGTGAAAACATATGAAGATATGACTTTGG
AAGAGCTGGAGGATAATGAAGACAAATTTAATGAGGAAGATGAACGTGCTATTGAAATGTACAGGCAGCCAAGGCTGGCT
GAGTGGAAAACAACTCAACTGAAGAATAAATTTGGAGAAGTTTAGGAGATCTCAGGAAAGGATTATGTTCAAGAAGTTAC
CAAAGCTGGTGAGGGCTTGTGGGTAATCTTGCACCTTTACAAATAAGGGATTCCCCTCTGTGCCCTCATAAATCAGCACT
TCAGTGGAATTGCCAGGAAGTTTTCTGATGTCAAATTTATCAAAGCCATTTCAACAACTTGCATACCCAATTATCCTGAT
AGGAATCTGCCTACAATATTTGTTTACCTTGAAGGTGATATCAAGGCTCAATTTATTGGACCTCTGGTGTTCAGTGGCAT
GAATCTGACAATAGATGAGTTGGAGTGGAAACTGTCAGAGTCTGAAGCAATCAAGACAGACTTGGATGAAAACCCTAAGA
AACCAATTGAAGACACTTTGCTATCCTCAGTGCAATGCTCCATTCCCACAAGAAGGGACAGCGATTTTGAGGATGAC

Alignment

ORF - retro_cfam_1740 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.33 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQDPNADTEWNDILRKKGILPSKESLKDLEKEAEEEEQRVLQQSVVKTYEDMTLEELEDNEDEFNEEDER
          MQDPNADTEWNDILRKKGILPSKE.LKDL.KEAEEE.Q.VLQQSVVKTYEDMTLEELEDNED.FNEEDER
Retrocopy MQDPNADTEWNDILRKKGILPSKENLKDLKKEAEEE-Q*VLQQSVVKTYEDMTLEELEDNEDKFNEEDER

Parental  AIEMYRQQRLAEWKATQLKNKFGEVLEISGKDYVQEVTKAGEGLWVILHLYKQGIPLCALINQHFSGLAR
          AIEMYRQ.RLAEWK.TQLKNKFGEV.EISGKDYVQEVTKAGEGLWVILHLYK.GIPLCALINQHFSG.AR
Retrocopy AIEMYRQPRLAEWKTTQLKNKFGEV*EISGKDYVQEVTKAGEGLWVILHLYK*GIPLCALINQHFSGIAR

Parental  KFPDVKFIKAISTTCIPNYPDRNLPTIFVYLEGDIKAQFIGPLVFGGMNLTIDELEWKLSESGAIKTDLE
          KF.DVKFIKAISTTCIPNYPDRNLPTIFVYLEGDIKAQFIGPLVF.GMNLTIDELEWKLSES.AIKTDL.
Retrocopy KFSDVKFIKAISTTCIPNYPDRNLPTIFVYLEGDIKAQFIGPLVFSGMNLTIDELEWKLSESEAIKTDLD

Parental  ENPKKPIEDTLLSSVRCSIPTRRDSDSEDD
          ENPKKPIEDTLLSSV.CSIPTRRDSD.EDD
Retrocopy ENPKKPIEDTLLSSVQCSIPTRRDSDFEDD

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	16.42 RPM
SRP017611_brain	0.00 RPM	11.51 RPM
SRP017611_kidney	0.00 RPM	32.69 RPM
SRP017611_liver	0.00 RPM	6.82 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_1740 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_1740 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_1740 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002226	1 retrocopy	retro_cfam_1740 ,
Callithrix jacchus	ENSCJAG00000010160	3 retrocopies	retro_cjac_1486, retro_cjac_1599, retro_cjac_2055,
Dipodomys ordii	ENSDORG00000012397	1 retrocopy	retro_dord_702,
Erinaceus europaeus	ENSEEUG00000000224	1 retrocopy	retro_eeur_506,
Homo sapiens	ENSG00000115539	7 retrocopies	retro_hsap_1132, retro_hsap_151, retro_hsap_2684, retro_hsap_2757, retro_hsap_3535, retro_hsap_3961, retro_hsap_4102,
Microcebus murinus	ENSMICG00000000657	1 retrocopy	retro_mmur_899,
Myotis lucifugus	ENSMLUG00000016446	1 retrocopy	retro_mluc_1443,
Monodelphis domestica	ENSMODG00000001489	1 retrocopy	retro_mdom_734,
Mus musculus	ENSMUSG00000026078	1 retrocopy	retro_mmus_2284,
Nomascus leucogenys	ENSNLEG00000014393	8 retrocopies	retro_nleu_1499, retro_nleu_1575, retro_nleu_2741, retro_nleu_2891, retro_nleu_538, retro_nleu_571, retro_nleu_778, retro_nleu_926,
Oryctolagus cuniculus	ENSOCUG00000001469	2 retrocopies	retro_ocun_1035, retro_ocun_920,
Otolemur garnettii	ENSOGAG00000015138	2 retrocopies	retro_ogar_1147, retro_ogar_2959,
Ochotona princeps	ENSOPRG00000011600	2 retrocopies	retro_opri_1070, retro_opri_289,
Tursiops truncatus	ENSTTRG00000006242	1 retrocopy	retro_ttru_1184,