RetrogeneDB ID: retro_cfam_2126

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: X:114891916..114892202(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C9orf85
• Ensembl ID: ENSCAFG00000001820
• Aliases: None
• Description: chromosome 9 open reading frame 85 [Source:HGNC Symbol;Acc:28784]

Sequence

>retro_cfam_2126
GTCAAAGGCAGCAAATATGAACCATTTTCAAAGCCTTAAAAATCTGTTAAGAGTCTACAAAAGTCAGTGAAGGATGCTTA
TCACATAGTTTGTAGACTACTGTGCCTGCGGATTTCAGGTTTGTACAAAACATGGAAAGAAAGAAGACATCGTTGCTCTA
TTTAATAAACAATCAGAAAAGGCAGAAAATACTGGAAGTAATCTACGTTCCAACCATAGAAGTTGCAGAAGAAATGAAGA
TAGTGATGATGATCTCGAATTTGATACTGATTAAGATGATACAAAG

Alignment

ORF - retro_cfam_2126 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.79 %
• Parental protein coverage: 61.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VKYSKYKPLSKPKKCVKCLQKSVKDSYHIICRP-CACELEVCAKCGKKEDIVVPFNKEPEKTENPEINLH
          VK.SKY.P.SKP.K.VK.LQKSVKD.YHI.CR..CAC...VC.K.GKKEDIV..FNK..EK.EN...NL.
Retrocopy VKGSKYEPFSKP*KSVKSLQKSVKDAYHIVCRL>CACGFQVCTKHGKKEDIVALFNKQSEKAENTGSNLR

Parental  SNHRSCRRNEESDDDLDFDIDLDDPK
          SNHRSCRRNE.SDDDL.FD.D.DD.K
Retrocopy SNHRSCRRNEDSDDDLEFDTD*DDTK

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	1.81 RPM
SRP017611_brain	0.00 RPM	1.83 RPM
SRP017611_kidney	0.00 RPM	4.16 RPM
SRP017611_liver	0.00 RPM	2.97 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_2126 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_2126 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_2126 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007254	1 retrocopy	retro_amel_730,
Bos taurus	ENSBTAG00000006831	1 retrocopy	retro_btau_39,
Canis familiaris	ENSCAFG00000001820	1 retrocopy	retro_cfam_2126 ,
Callithrix jacchus	ENSCJAG00000001441	2 retrocopies	retro_cjac_1283, retro_cjac_1374,
Cavia porcellus	ENSCPOG00000025848	2 retrocopies	retro_cpor_1538, retro_cpor_316,
Felis catus	ENSFCAG00000031942	1 retrocopy	retro_fcat_1955,
Homo sapiens	ENSG00000155621	2 retrocopies	retro_hsap_2104, retro_hsap_2895,
Myotis lucifugus	ENSMLUG00000024309	2 retrocopies	retro_mluc_2449, retro_mluc_2526,
Macaca mulatta	ENSMMUG00000018881	2 retrocopies	retro_mmul_670, retro_mmul_988,
Mustela putorius furo	ENSMPUG00000008971	1 retrocopy	retro_mputfur_1413,
Mus musculus	ENSMUSG00000035171	6 retrocopies	retro_mmus_1049, retro_mmus_2254, retro_mmus_2286, retro_mmus_2781, retro_mmus_2941, retro_mmus_3698,
Nomascus leucogenys	ENSNLEG00000001023	1 retrocopy	retro_nleu_1272,
Oryctolagus cuniculus	ENSOCUG00000024578	2 retrocopies	retro_ocun_703, retro_ocun_766,
Otolemur garnettii	ENSOGAG00000011302	1 retrocopy	retro_ogar_979,
Pongo abelii	ENSPPYG00000029745	2 retrocopies	retro_pabe_1996, retro_pabe_2397,
Pan troglodytes	ENSPTRG00000021018	2 retrocopies	retro_ptro_1543, retro_ptro_1958,
Rattus norvegicus	ENSRNOG00000027161	5 retrocopies	retro_rnor_1898, retro_rnor_2010, retro_rnor_2242, retro_rnor_2859, retro_rnor_2960,
Sorex araneus	ENSSARG00000004523	1 retrocopy	retro_sara_260,
Tupaia belangeri	ENSTBEG00000015556	6 retrocopies	retro_tbel_1998, retro_tbel_200, retro_tbel_2406, retro_tbel_2410, retro_tbel_3539, retro_tbel_940,