RetrogeneDB ID: retro_cpor_549

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_19:35680593..35681127(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000024280
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: LYPLA1
• Ensembl ID: ENSCPOG00000022715
• Aliases: None
• Description: None

Sequence

>retro_cpor_549
GTGATTTTCCTTCATGGGCTGGGAGGCGCTGGGCATGGACGGGCAGAAGCCTCTGTAGGTATTAGAAGTGCGCACACCAA
ACATATCTGCCCACTGGGGCCTGTAGCATTAAACGTGGACGTGGCTGTGCCTTCTTGGTTTGATATCGTTGGGCTTTCAC
CAGCTTCTCATGAGGATGAACCTGGAATTAAACGAGCAGCAGAAAATGTAAAAGCTTTCATAGATGAGGAGCTGAGGAAT
GGCTTTCCTGCTAACAGAATTATTGGGGAGAATATTCTCAGGGAGGAACAAAGATCTTTATACACTGCTCTAAGCACACG
GCAGACTCTGGCGGGTGTCACTGCCCTGAGCTGCTGGCTTCCACTTCGGGCTGGCTTTCCGCGGGGGCCCATCAGTGGTG
TCAAAGGTATTTCTATTCTCCAGCGCCATGGAGATTGTGACCCTTTAGTTTCCCTAATGTTTGGTTCCCTCACTGCTGAA
AAACTAAAATCATTGGTAAATCTGCCCAGTGTAACCTTCAAAACCTACGAGGGC

Alignment

ORF - retro_cpor_549 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.46 %
• Parental protein coverage: 87.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VIFLHGLGDTGHGWAEAFAGIRSSHIKYICPHAPVMPVTLNMNMAMPSWFDIIGLSPDAHEDEPGIKRAA
          VIFLHGLG..GHG.AEA..GIRS.H.K.IC...P..PV.LN...A.PSWFDI.GLSP..HEDEPGIKRAA
Retrocopy VIFLHGLGGAGHGRAEASVGIRSAHTKHIC---PLGPVALNVDVAVPSWFDIVGLSPASHEDEPGIKRAA

Parental  ESVKALIDQEVKNGIPSNRII-LGGFSQGGAL-SLYTALTTQQKLAGVTALSCWLPLRASFPQGPISGVN
          E.VKA.ID.E..NG.P.NRII..G..SQGG...SLYTAL.T.Q.LAGVTALSCWLPLRA.FP.GPISGV.
Retrocopy ENVKAFIDEELRNGFPANRII<WGEYSQGGTK>SLYTALSTRQTLAGVTALSCWLPLRAGFPRGPISGV-

Parental  KDISILQCHGDCDPLVPLMFGSLTAEKLKSLVNPANVTFKTYEG
          K.ISILQ.HGDCDPLV.LMFGSLTAEKLKSLVN...VTFKTYEG
Retrocopy KGISILQRHGDCDPLVSLMFGSLTAEKLKSLVNLPSVTFKTYEG

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	0.23 RPM	6.67 RPM
SRP017611_kidney	0.00 RPM	50.77 RPM
SRP017611_liver	0.00 RPM	51.45 RPM
SRP040447_lung	0.13 RPM	19.39 RPM
SRP040447_skeletal_muscle	0.05 RPM	9.15 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_549 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_549 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 16 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006978	1 retrocopy	retro_cfam_523,
Callithrix jacchus	ENSCJAG00000011562	2 retrocopies	retro_cjac_1260, retro_cjac_3100,
Cavia porcellus	ENSCPOG00000022715	3 retrocopies	retro_cpor_142, retro_cpor_549 , retro_cpor_782,
Dipodomys ordii	ENSDORG00000001479	1 retrocopy	retro_dord_88,
Equus caballus	ENSECAG00000016530	1 retrocopy	retro_ecab_238,
Echinops telfairi	ENSETEG00000001727	2 retrocopies	retro_etel_612, retro_etel_791,
Homo sapiens	ENSG00000120992	3 retrocopies	retro_hsap_3078, retro_hsap_3485, retro_hsap_3897,
Myotis lucifugus	ENSMLUG00000008208	1 retrocopy	retro_mluc_1683,
Macaca mulatta	ENSMMUG00000013157	3 retrocopies	retro_mmul_1734, retro_mmul_2459, retro_mmul_2474,
Nomascus leucogenys	ENSNLEG00000001027	4 retrocopies	retro_nleu_1137, retro_nleu_2015, retro_nleu_2817, retro_nleu_2869,
Oryctolagus cuniculus	ENSOCUG00000006751	3 retrocopies	retro_ocun_1510, retro_ocun_1623, retro_ocun_1679,
Pongo abelii	ENSPPYG00000018590	3 retrocopies	retro_pabe_2550, retro_pabe_3177, retro_pabe_3565,
Pteropus vampyrus	ENSPVAG00000005246	2 retrocopies	retro_pvam_224, retro_pvam_838,
Rattus norvegicus	ENSRNOG00000008320	3 retrocopies	retro_rnor_1747, retro_rnor_2612, retro_rnor_406,
Tarsius syrichta	ENSTSYG00000012350	6 retrocopies	retro_tsyr_1287, retro_tsyr_1303, retro_tsyr_1465, retro_tsyr_1901, retro_tsyr_1996, retro_tsyr_2158,
Tursiops truncatus	ENSTTRG00000011836	3 retrocopies	retro_ttru_1643, retro_ttru_169, retro_ttru_291,