RetrogeneDB ID: retro_cpor_712

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_25:1280759..1281244(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C9ORF78
• Ensembl ID: ENSCPOG00000009285
• Aliases: None
• Description: None

Sequence

>retro_cpor_712
CTGAAGAGGAGGAAGAGGATCATAGAACATGAGAAGCAGAAGCTGAAACTCAAGAAAGAAGACAACTGTCTGCATGAACT
CCCTGAGGACATCTGCATGTCCTCAGCCAAGTAAATGCTGTCTAACCAGAAGCTGAGTGGCATCCCTGAGGTGGATCTGG
CCATCTACACTAAAATCAAAAACATCATCTCCATGGAAGATGCCAAGGCCCACCTACTGGCAGAGAAGCAGCAACAGCAG
AAACAATAAGATGTCTCCTCTGTGCCCACTACCACAGATAATGCAGCAGCAGACCGATTTTATCACAAGGAGCTAAATGT
GCCACCGTGAGGAACAAAGAGCCCAAGGTCCTGCCCTTATGGAGTGGGCAACATGGAGAAGCTGGAGCCAAAGTGGCCTA
GTCCCCACCTAACCACAAGCTTCCCACTGAGAAAGTCACTGGTGACCACCATCACAAGAAGTTCAAGAAGATGAACAGGC
AGTAC

Alignment

ORF - retro_cpor_712 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.25 %
• Parental protein coverage: 57.79 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LKKRKGIVEHEEQKVKPRNAEDCLYELPESIRVASAKKTEEMLSNQMLSGIPEVDLGIDAKIKNIISTED
          LK.RK.I.EHE.QK.K......CL.ELPE.I...SA.....MLSNQ.LSGIPEVDL.I..KIKNIIS.ED
Retrocopy LKRRKRIIEHEKQKLKLKKEDNCLHELPEDICMSSA---K*MLSNQKLSGIPEVDLAIYTKIKNIISMED

Parental  AKARLLAEQQNKKKDSETSFVPTNMAVNYVQHNRFYHEELNAPIRRNKEEPKARPLRVGDTEKPEPE-RS
          AKA.LLAE.Q...K....S.VPT..........RFYH.ELN.P....K..P...P..VG..EK.EP...S
Retrocopy AKAHLLAEKQQQQKQ*DVSSVPT--TTDNAAADRFYHKELNVPP*GTK-SPRSCPYGVGNMEKLEPKWPS

Parental  P-PNRKRPANEKATDDYHYEKFKKMNRRY
          P.P.......EK.T.D.H..KFKKMNR.Y
Retrocopy P<PPNHKLPTEKVTGDHHHKKFKKMNRQY

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	0.00 RPM	23.70 RPM
SRP017611_kidney	0.00 RPM	23.97 RPM
SRP017611_liver	0.00 RPM	17.67 RPM
SRP040447_lung	0.08 RPM	33.24 RPM
SRP040447_skeletal_muscle	0.00 RPM	22.46 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_712 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_712 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 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020307	1 retrocopy	retro_btau_1138,
Canis familiaris	ENSCAFG00000019979	1 retrocopy	retro_cfam_116,
Choloepus hoffmanni	ENSCHOG00000013895	3 retrocopies	retro_chof_1103, retro_chof_1747, retro_chof_978,
Cavia porcellus	ENSCPOG00000009285	1 retrocopy	retro_cpor_712 ,
Equus caballus	ENSECAG00000018958	1 retrocopy	retro_ecab_174,
Gorilla gorilla	ENSGGOG00000013358	1 retrocopy	retro_ggor_1990,
Macropus eugenii	ENSMEUG00000010524	3 retrocopies	retro_meug_1046, retro_meug_1241, retro_meug_508,
Microcebus murinus	ENSMICG00000009596	1 retrocopy	retro_mmur_1466,
Monodelphis domestica	ENSMODG00000006832	1 retrocopy	retro_mdom_518,
Mus musculus	ENSMUSG00000026851	1 retrocopy	retro_mmus_2978,
Otolemur garnettii	ENSOGAG00000009770	1 retrocopy	retro_ogar_1015,
Pongo abelii	ENSPPYG00000019685	1 retrocopy	retro_pabe_2426,
Sarcophilus harrisii	ENSSHAG00000012313	1 retrocopy	retro_shar_746,
Ictidomys tridecemlineatus	ENSSTOG00000020630	1 retrocopy	retro_itri_1783,
Tupaia belangeri	ENSTBEG00000013115	1 retrocopy	retro_tbel_514,