RetrogeneDB ID: retro_cpor_184

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_1:67758774..67759201(+)
• Located in intron of: ENSCPOG00000015508

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000005330
• Aliases: None
• Description: None

Sequence

>retro_cpor_184
GCCTGTACGGTCACCATTATCTTCCTGCTGTCGTGTGACTCTTGGGCAGTGAACAATGCCACAGGCAGACTAATGGCTGG
CCTATGTTGGTGGAGCCATACTTATGAGGATAGAAAACAGCCAATGGGTGTTTGAGCCCAGGAAAGCAAGTTCTCAAGAG
AATAAAGTATTTCACAGGCTGAATCAAGAATATTTTGGTTATCAGTTATTGCCTGTCCAGGGCTGTGGGCGAGATTTGCC
CTAGAAGTGCTTCTTTCCCTTAGGAGTAAAGTGGCTGGTGGTGGTCATCACGGGTTTGACGCTACATGGTGCCACCCTGT
ATGGTTGCACCAGCTGTGAGGTGGGCAGCAGGACTCTAACCAGCATGGTCACTGCGTATCCTGGGACGCAGTTTTTAAGA
CAAAACACTGGAGAGGCTCAGACTTCT

Alignment

ORF - retro_cpor_184 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.75 %
• Parental protein coverage: 69.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ACMVTIILLLSCDFWTVKNVTGRLMVGLRWWNHIDEDGK-SHWVFESRKATSQESKSF-SEAESRIFWLG
          AC.VTII.LLSCD.W.V.N.TGRLM.GL.WW.H..ED.K.S.WVFE.RKA.SQE.K.F.S.AESRIFWL.
Retrocopy ACTVTIIFLLSCDSWAVNNATGRLMAGLCWWSHTYEDRK>SQWVFEPRKASSQENKVF<SQAESRIFWLS

Parental  LIACPVLWVIFAFSALFSFR-LKWLAVVIMGVVLQGANLYGYVKCKVGSRKNLTSMATSYLGKQFLRQNT
          .IACP.LW..FA...L.S.R..KWL.VVI.G..L.GA.LYG...C.VGSR..LTSM.T.Y.G.QFLRQNT
Retrocopy VIACPGLWARFALEVLLSLR>VKWLVVVITGLTLHGATLYGCTSCEVGSR-TLTSMVTAYPGTQFLRQNT

Parental  GDDQTS
          G..QTS
Retrocopy GEAQTS

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	5.75 RPM
SRP017611_kidney	0.00 RPM	16.85 RPM
SRP017611_liver	0.00 RPM	14.45 RPM
SRP040447_lung	0.00 RPM	12.51 RPM
SRP040447_skeletal_muscle	0.00 RPM	3.83 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_184 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_184 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.

---

Parental genes homology:

Parental genes homology involve 15 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005330	1 retrocopy	retro_cpor_184 ,
Dasypus novemcinctus	ENSDNOG00000007609	2 retrocopies	retro_dnov_1041, retro_dnov_1390,
Homo sapiens	ENSG00000171928	1 retrocopy	retro_hsap_2278,
Homo sapiens	ENSG00000175106	1 retrocopy	retro_hsap_1625,
Loxodonta africana	ENSLAFG00000003854	1 retrocopy	retro_lafr_465,
Myotis lucifugus	ENSMLUG00000002825	1 retrocopy	retro_mluc_1484,
Macaca mulatta	ENSMMUG00000019203	5 retrocopies	retro_mmul_1032, retro_mmul_2125, retro_mmul_278, retro_mmul_600, retro_mmul_748,
Nomascus leucogenys	ENSNLEG00000014658	2 retrocopies	retro_nleu_1961, retro_nleu_2008,
Oryctolagus cuniculus	ENSOCUG00000000498	1 retrocopy	retro_ocun_759,
Otolemur garnettii	ENSOGAG00000012225	1 retrocopy	retro_ogar_978,
Pan troglodytes	ENSPTRG00000007790	1 retrocopy	retro_ptro_20,
Pan troglodytes	ENSPTRG00000008796	1 retrocopy	retro_ptro_996,
Rattus norvegicus	ENSRNOG00000050649	1 retrocopy	retro_rnor_636,
Ictidomys tridecemlineatus	ENSSTOG00000000642	6 retrocopies	retro_itri_1415, retro_itri_1841, retro_itri_310, retro_itri_473, retro_itri_711, retro_itri_782,
Tarsius syrichta	ENSTSYG00000008082	2 retrocopies	retro_tsyr_2000, retro_tsyr_530,