RetrogeneDB ID: retro_cpor_1142

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_5:47983476..47983773(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C1ORF123
• Ensembl ID: ENSCPOG00000011509
• Aliases: None
• Description: None

Sequence

>retro_cpor_1142
AAAACCATGTTACAGCTCACGGTTGTACTGAAAAACACCACCAACTTCAGCCCCTGGGTGAGGACTTATGGTGGTTCCTA
AAGATGAAATGTGGCAACTGCGGTGAAATTTTAGGAGAAGTGGCAACACTGATGAGCTGACGGACAGTGTGGTGCTGACA
AGAGGCCATGACAGTGCCTCTGTGGCCCATAAGTACAAGCTGTGGCATGGGAAAATTTCACTGAGATTTTGAGTAGCACT
ATCAGATCTTGTACTGCTGAAGATGGTAAGAAGTTCAAGACAATTGTGAAGTTTAAG

Alignment

ORF - retro_cpor_1142 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.19 %
• Parental protein coverage: 61.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KIALQLKATLENITN-LRPLGEDFRWYLKMKCGNCGEIS-EKWQY-IRLMDSVALKGGRGSASMVQKCKL
          K..LQL...L.N.TN.L.PLGED..W.LKMKCGNCGEI..EKWQ....L.DSV.L..G..SAS...K.KL
Retrocopy KTMLQLTVVLKNTTN<LQPLGEDLWWFLKMKCGNCGEIL>EKWQH>DELTDSVVLTRGHDSASVAHKYKL

Parental  -CARENSIEILSSTIKPYNAEDNEKFKTIVEFE
          ..A.EN..EILSSTI....AED..KFKTIV.F.
Retrocopy <VAWENFTEILSSTIRSCTAEDGKKFKTIVKFK

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	38.82 RPM
SRP017611_kidney	0.00 RPM	19.68 RPM
SRP017611_liver	0.00 RPM	21.85 RPM
SRP040447_lung	0.00 RPM	22.82 RPM
SRP040447_skeletal_muscle	0.00 RPM	12.98 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1142 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1142 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 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004526	3 retrocopies	retro_cjac_2948, retro_cjac_3149, retro_cjac_3186,
Cavia porcellus	ENSCPOG00000011509	1 retrocopy	retro_cpor_1142 ,
Homo sapiens	ENSG00000162384	1 retrocopy	retro_hsap_192,
Gorilla gorilla	ENSGGOG00000004027	1 retrocopy	retro_ggor_271,
Microcebus murinus	ENSMICG00000006397	1 retrocopy	retro_mmur_1113,
Myotis lucifugus	ENSMLUG00000002439	1 retrocopy	retro_mluc_101,
Mus musculus	ENSMUSG00000028608	1 retrocopy	retro_mmus_975,
Nomascus leucogenys	ENSNLEG00000017988	1 retrocopy	retro_nleu_1001,
Oryctolagus cuniculus	ENSOCUG00000029317	1 retrocopy	retro_ocun_770,
Otolemur garnettii	ENSOGAG00000013324	1 retrocopy	retro_ogar_861,
Ochotona princeps	ENSOPRG00000009003	2 retrocopies	retro_opri_351, retro_opri_711,
Pongo abelii	ENSPPYG00000001336	1 retrocopy	retro_pabe_443,
Pan troglodytes	ENSPTRG00000000752	1 retrocopy	retro_ptro_99,
Rattus norvegicus	ENSRNOG00000012724	3 retrocopies	retro_rnor_1999, retro_rnor_2403, retro_rnor_2705,