RetrogeneDB ID: retro_cpor_508

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_175:1280514..1280886(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FUNDC1
• Ensembl ID: ENSCPOG00000012962
• Aliases: None
• Description: None

Sequence

>retro_cpor_508
AGAAGATACCCCTGGTGGAATCGAGTGTTTAGTAACCAATCACACCTATGGTAGAAATATACTCAGCAGCTACCCAGATT
CTAACAGATGGCATGACTGGCTGCTGCGCAGAATTTTTGTTTCAGAAAGTTAGAAAACTTGCAGCAATGGTAGGTGGTGG
ATTTCTTCCCCTACAGACTGCCAGTCTCAGTAGCTATTTCTAGATCAAATGGGAGAGTTGAAAAAGATGTAAGCAAAGAA
AAAGGCAAGATTTAGAAACCAGCAAATAAAGCAGTAACTGAAATCAATAATGTAATAAAAAAATTAACAGAATTTATCAA
ACAGAACACTGTGCTAACCAGTGGATTTGTGGGAGGGTTTTGCCTAGCCTTG

Alignment

ORF - retro_cpor_508 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.28 %
• Parental protein coverage: 81.29 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RRHHWWNRVFGHRSG-PMVEKYSVATQIVMGGVTGWCAGFLFQKVGKLAATAVGGGFLLLQIASHSGYVQ
          RR..WWNRVF...S..PMVE.YS.ATQI...G.TG.CA.FLFQKV.KLAA..VGGGFL.LQ.AS.S.Y..
Retrocopy RRYPWWNRVFSNQSH<PMVEIYSAATQILTDGMTGCCAEFLFQKVRKLAA-MVGGGFLPLQTASLSSYF*

Parental  IDWKRVEKDVNKAKRQ-IKKRANKAAPEINNVIEEATEFIKQNIVISSGFVGGFLLGL
          I.W....K.....KRQ.I.K.ANKA..EINNVI...TEFIKQN.V..SGFVGGF.L.L
Retrocopy IKWES-*KRCKQRKRQ>I*KPANKAVTEINNVIKKLTEFIKQNTVLTSGFVGGFCLAL

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	8.28 RPM
SRP017611_kidney	0.00 RPM	7.96 RPM
SRP017611_liver	0.00 RPM	4.35 RPM
SRP040447_lung	0.05 RPM	6.08 RPM
SRP040447_skeletal_muscle	0.00 RPM	6.18 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_508 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_508 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 18 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010876	1 retrocopy	retro_cjac_896,
Cavia porcellus	ENSCPOG00000012962	2 retrocopies	retro_cpor_507, retro_cpor_508 ,
Echinops telfairi	ENSETEG00000012763	3 retrocopies	retro_etel_1614, retro_etel_697, retro_etel_852,
Homo sapiens	ENSG00000069509	1 retrocopy	retro_hsap_936,
Gorilla gorilla	ENSGGOG00000023311	1 retrocopy	retro_ggor_755,
Latimeria chalumnae	ENSLACG00000010215	1 retrocopy	retro_lcha_74,
Macropus eugenii	ENSMEUG00000006795	5 retrocopies	retro_meug_1597, retro_meug_2127, retro_meug_232, retro_meug_415, retro_meug_994,
Microcebus murinus	ENSMICG00000000450	2 retrocopies	retro_mmur_1189, retro_mmur_1461,
Macaca mulatta	ENSMMUG00000003505	1 retrocopy	retro_mmul_38,
Monodelphis domestica	ENSMODG00000021088	3 retrocopies	retro_mdom_1262, retro_mdom_769, retro_mdom_917,
Nomascus leucogenys	ENSNLEG00000002513	2 retrocopies	retro_nleu_2760, retro_nleu_294,
Oryctolagus cuniculus	ENSOCUG00000029753	5 retrocopies	retro_ocun_1008, retro_ocun_1376, retro_ocun_1567, retro_ocun_27, retro_ocun_314,
Pongo abelii	ENSPPYG00000020268	2 retrocopies	retro_pabe_806, retro_pabe_829,
Pelodiscus sinensis	ENSPSIG00000013793	1 retrocopy	retro_psin_30,
Pan troglodytes	ENSPTRG00000021821	1 retrocopy	retro_ptro_648,
Rattus norvegicus	ENSRNOG00000003470	1 retrocopy	retro_rnor_2644,
Sarcophilus harrisii	ENSSHAG00000000501	1 retrocopy	retro_shar_222,
Tarsius syrichta	ENSTSYG00000009139	1 retrocopy	retro_tsyr_1522,