RetrogeneDB ID: retro_cpor_783

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_28:22909559..22909930(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VAPA
• Ensembl ID: ENSCPOG00000006042
• Aliases: None
• Description: None

Sequence

>retro_cpor_783
GTTATTACAGATCTAAAATTGTGAAATTCATCAGCTAGAAAAGTGTGTTTCAAAGTGAAAAGTACAGCATCTCACCAGTA
CTGGTAAAGCCCAATTGTGAAATTACTGACTCAGGGTCAGCTGTGACAGTAATGGAATGGCCCTTTTAACTATGAACCAA
GTAAGAAGAGTAAACACAATAAGTTCATGGCATGGTACAACTTGTGATCCGCCAAACATTTCAGAAAAGGAAGCTGTATG
GAAAGATGCAGCCCTGGTGAAATAATGGGTTTTAAACTGAGATGTATATTTGAAATCTCAAATGAAAAAGATAAATGAAT
GATAGGGGACCTAGGAAAGCTATTTCACTTAATATATCTAAACAAGATGGA

Alignment

ORF - retro_cpor_783 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.02 %
• Parental protein coverage: 55.07 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  VTTNLKLRNPSDRKVCFKVKTTAPRRY-CVRPNSGIIDPGSTVTVSVMLQPF-DYDPNEKSKH-KFMV-Q
          V.T.LKL.N.S.RKVCFKVK.TA...Y..V.PN..I.D.GS.VT..VM..PF..Y.P..KSKH.KFM...
Retrocopy VITDLKL*NSSARKVCFKVKSTASHQY<LVKPNCEITDSGSAVT--VMEWPF>NYEPSKKSKHNKFMA>G

Parental  TIFAPPNTSDMEAVWKEA-KPDELMDSKLRCVFEMPNENDK-LNDMEPSKAVPLNASKQDG
          T...PPN.S..EAVWK.A..P.E.M..KLRC.FE..NE.DK..ND..P.KA..LN.SKQDG
Retrocopy TTCDPPNISEKEAVWKDA<SPGEIMGFKLRCIFEISNEKDK<MNDRGPRKAISLNISKQDG

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	55.50 RPM
SRP017611_kidney	0.00 RPM	55.38 RPM
SRP017611_liver	0.00 RPM	60.89 RPM
SRP040447_lung	0.00 RPM	48.70 RPM
SRP040447_skeletal_muscle	0.00 RPM	61.12 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_783 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_783 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000006042	2 retrocopies	retro_cpor_783 , retro_cpor_931,
Myotis lucifugus	ENSMLUG00000008965	1 retrocopy	retro_mluc_542,
Monodelphis domestica	ENSMODG00000021442	1 retrocopy	retro_mdom_57,
Mus musculus	ENSMUSG00000024091	1 retrocopy	retro_mmus_1774,
Rattus norvegicus	ENSRNOG00000014765	1 retrocopy	retro_rnor_266,