RetrogeneDB ID: retro_cpor_1538

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_95:4783728..4784042(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C9ORF85
• Ensembl ID: ENSCPOG00000025848
• Aliases: None
• Description: None

Sequence

>retro_cpor_1538
GTTGATGCAGAAGTTCATGATGGAGCAGGTGAGCGTGGTCAAGAAGTTCTAGAGGGATGGGTTAGACGGAGCAAATATAA
ACCACTATCAAAAACTAAAAATGCGTTAAATGTTGATAGAGACCAGAAAGAGTCCTCACCACATGATGTGTAGACCACGT
GGTTCTGAACTTGAAGTCTGCACAAAATGTAGGAAAGAAGGAGGCATTGTTACTGTTTCACAAAGAACCAGAAAAGACAG
AAAATATTGAAAATAATCAAAGATCCAGTCACAGAAGAAGCTACAAAAGGAATGAGGAAAGTGATGATAACTTA

Alignment

ORF - retro_cpor_1538 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.22 %
• Parental protein coverage: 68.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  INAKLHDGVCQRCKEVLEWRVKYSKYKPLSKPK-KCVKC-LQKTVKDSYHIMCRPCAYELEVCAKC-GKK
          ..A..HDG...R..EVLE..V..SKYKPLSK.K.KCVKC.L..T.K...H.MCRP...ELEVC.KC.GKK
Retrocopy VDAEVHDGAGERGQEVLEGWVRRSKYKPLSKTK<KCVKC<LIETRKSPHHMMCRPRGSELEVCTKC>GKK

Parental  EDIVIPFNKEPEKTENSENNQRANHRRSCKRNEESDDDL
          E.....F.KEPEKTEN.ENNQR..HRRS.KRNEESDD.L
Retrocopy EALLL-FHKEPEKTENIENNQRSSHRRSYKRNEESDDNL

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
SRP017611_brain	0.06 RPM	4.20 RPM
SRP017611_kidney	0.10 RPM	4.82 RPM
SRP017611_liver	0.00 RPM	8.62 RPM
SRP040447_lung	0.13 RPM	2.67 RPM
SRP040447_skeletal_muscle	0.03 RPM	2.60 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1538 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1538 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,